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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Mechanisms on Boron-Induced Alleviation of Aluminum-Toxicity in <italic>Citrus grandis</italic> Seedlings at a Transcriptional Level Revealed by cDNA-AFLP Analysis</title><author><name sortKey="Zhou, Xin Xing" sort="Zhou, Xin Xing" uniqKey="Zhou X" first="Xin-Xing" last="Zhou">Xin-Xing Zhou</name><affiliation><nlm:aff id="aff001"><addr-line>College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff002"><addr-line>Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation></author><author><name sortKey="Yang, Lin Tong" sort="Yang, Lin Tong" uniqKey="Yang L" first="Lin-Tong" last="Yang">Lin-Tong Yang</name><affiliation><nlm:aff id="aff001"><addr-line>College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff002"><addr-line>Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation></author><author><name sortKey="Qi, Yi Ping" sort="Qi, Yi Ping" uniqKey="Qi Y" first="Yi-Ping" last="Qi">Yi-Ping Qi</name><affiliation><nlm:aff id="aff003"><addr-line>Institute of Materia Medica, Fujian Academy of Medical Sciences, Fuzhou 350001, China</addr-line></nlm:aff></affiliation></author><author><name sortKey="Guo, Peng" sort="Guo, Peng" uniqKey="Guo P" first="Peng" last="Guo">Peng Guo</name><affiliation><nlm:aff id="aff001"><addr-line>College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff002"><addr-line>Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation></author><author><name sortKey="Chen, Li Song" sort="Chen, Li Song" uniqKey="Chen L" first="Li-Song" last="Chen">Li-Song Chen</name><affiliation><nlm:aff id="aff001"><addr-line>College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff002"><addr-line>Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff004"><addr-line>The Higher Educational Key Laboratory of Fujian Province for Soil Ecosystem Health and Regulation, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff005"><addr-line>Fujian Key Laboratory for Plant Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25747450</idno><idno type="pmc">4352013</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4352013</idno><idno type="RBID">PMC:4352013</idno><idno type="doi">10.1371/journal.pone.0115485</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000127</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Mechanisms on Boron-Induced Alleviation of Aluminum-Toxicity in <italic>Citrus grandis</italic> Seedlings at a Transcriptional Level Revealed by cDNA-AFLP Analysis</title><author><name sortKey="Zhou, Xin Xing" sort="Zhou, Xin Xing" uniqKey="Zhou X" first="Xin-Xing" last="Zhou">Xin-Xing Zhou</name><affiliation><nlm:aff id="aff001"><addr-line>College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff002"><addr-line>Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation></author><author><name sortKey="Yang, Lin Tong" sort="Yang, Lin Tong" uniqKey="Yang L" first="Lin-Tong" last="Yang">Lin-Tong Yang</name><affiliation><nlm:aff id="aff001"><addr-line>College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff002"><addr-line>Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation></author><author><name sortKey="Qi, Yi Ping" sort="Qi, Yi Ping" uniqKey="Qi Y" first="Yi-Ping" last="Qi">Yi-Ping Qi</name><affiliation><nlm:aff id="aff003"><addr-line>Institute of Materia Medica, Fujian Academy of Medical Sciences, Fuzhou 350001, China</addr-line></nlm:aff></affiliation></author><author><name sortKey="Guo, Peng" sort="Guo, Peng" uniqKey="Guo P" first="Peng" last="Guo">Peng Guo</name><affiliation><nlm:aff id="aff001"><addr-line>College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff002"><addr-line>Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation></author><author><name sortKey="Chen, Li Song" sort="Chen, Li Song" uniqKey="Chen L" first="Li-Song" last="Chen">Li-Song Chen</name><affiliation><nlm:aff id="aff001"><addr-line>College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff002"><addr-line>Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff004"><addr-line>The Higher Educational Key Laboratory of Fujian Province for Soil Ecosystem Health and Regulation, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation><affiliation><nlm:aff id="aff005"><addr-line>Fujian Key Laboratory for Plant Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The physiological and biochemical mechanisms on boron (B)-induced alleviation of aluminum (B)-toxicity in plants have been examined in some details, but our understanding of the molecular mechanisms underlying these processes is very limited. In this study, we first used the cDNA-AFLP to investigate the gene expression patterns in <italic>Citrus grandis</italic> roots responsive to B and Al interactions, and isolated 100 differentially expressed genes. Results showed that genes related to detoxification of reactive oxygen species (ROS) and aldehydes (i.e., <italic>glutathione S-transferase zeta class-like isoform X1</italic>, <italic>thioredoxin M-type 4</italic>, and <italic>2-alkenal reductase (NADP<sup>+</sup>-dependent)-like</italic>), metabolism (i.e., <italic>carboxylesterases and lecithin-cholesterol acyltransferase-like 4-like</italic>, <italic>nicotianamine aminotransferase A-like isoform X3</italic>, <italic>thiosulfate sulfurtransferase 18-like isoform X1</italic>, and <italic>FNR</italic>, <italic>root isozyme 2</italic>), cell transport (i.e., <italic>non-specific lipid-transfer protein-like protein At2g13820-like</italic> and <italic>major facilitator superfamily protein</italic>), Ca signal and hormone (i.e., <italic>calcium-binding protein CML19-like</italic> and <italic>IAA-amino acid hydrolase ILR1-like 4-like</italic>), gene regulation (i.e., <italic>Gag-pol polyprotein</italic>) and cell wall modification (i.e., <italic>glycosyl hydrolase family 10 protein</italic>) might play a role in B-induced alleviation of Al-toxicity. Our results are useful not only for our understanding of molecular processes associated with B-induced alleviation of Al-toxicity, but also for obtaining key molecular genes to enhance Al-tolerance of plants in the future.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Foy, Cd" uniqKey="Foy C">CD Foy</name></author><author><name sortKey="Chaney, Rl" uniqKey="Chaney R">RL Chaney</name></author><author><name sortKey="White, Mc" uniqKey="White M">MC White</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kochian, Lv" uniqKey="Kochian L">LV Kochian</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rezaee, F" uniqKey="Rezaee F">F Rezaee</name></author><author><name sortKey="Ghanati, F" uniqKey="Ghanati F">F Ghanati</name></author><author><name sortKey="Behmanesh, M" uniqKey="Behmanesh M">M 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, CA USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25747450</article-id><article-id pub-id-type="pmc">4352013</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0115485</article-id><article-id pub-id-type="publisher-id">PONE-D-14-42360</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Mechanisms on Boron-Induced Alleviation of Aluminum-Toxicity in <italic>Citrus grandis</italic> Seedlings at a Transcriptional Level Revealed by cDNA-AFLP Analysis</article-title><alt-title alt-title-type="running-head">B-Induced Alleviation of Citrus Al-Toxicity Revealed by cDNA-AFLP</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Zhou</surname><given-names>Xin-Xing</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Yang</surname><given-names>Lin-Tong</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Qi</surname><given-names>Yi-Ping</given-names></name><xref ref-type="aff" rid="aff003"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Guo</surname><given-names>Peng</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Li-Song</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff002"><sup>2</sup></xref><xref ref-type="aff" rid="aff004"><sup>4</sup></xref><xref ref-type="aff" rid="aff005"><sup>5</sup></xref><xref rid="cor001" ref-type="corresp">*</xref></contrib></contrib-group><aff id="aff001"><label>1</label><addr-line>College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></aff><aff id="aff002"><label>2</label><addr-line>Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></aff><aff id="aff003"><label>3</label><addr-line>Institute of Materia Medica, Fujian Academy of Medical Sciences, Fuzhou 350001, China</addr-line></aff><aff id="aff004"><label>4</label><addr-line>The Higher Educational Key Laboratory of Fujian Province for Soil Ecosystem Health and Regulation, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></aff><aff id="aff005"><label>5</label><addr-line>Fujian Key Laboratory for Plant Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Fang</surname><given-names>David D</given-names></name><role>Academic Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>USDA-ARS-SRRC, UNITED STATES</addr-line></aff><author-notes><fn fn-type="conflict" id="coi001"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con" id="contrib001"><p>Conceived and designed the experiments: XXZ LTY YPQ LSC. Performed the experiments: XXZ. Analyzed the data: XXZ PG. Wrote the paper: LSC XXZ.</p></fn><corresp id="cor001">* E-mail: <email>lisongchen2002@hotmail.com</email></corresp></author-notes><pub-date pub-type="epub"><day>6</day><month>3</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>10</volume><issue>3</issue><elocation-id>e0115485</elocation-id><history><date date-type="received"><day>23</day><month>9</month><year>2014</year></date><date date-type="accepted"><day>24</day><month>11</month><year>2014</year></date></history><permissions><copyright-year>2015</copyright-year><copyright-holder>Zhou et al</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited</license-p></license></permissions><self-uri content-type="pdf" xlink:type="simple" xlink:href="pone.0115485.pdf"></self-uri><abstract><p>The physiological and biochemical mechanisms on boron (B)-induced alleviation of aluminum (B)-toxicity in plants have been examined in some details, but our understanding of the molecular mechanisms underlying these processes is very limited. In this study, we first used the cDNA-AFLP to investigate the gene expression patterns in <italic>Citrus grandis</italic> roots responsive to B and Al interactions, and isolated 100 differentially expressed genes. Results showed that genes related to detoxification of reactive oxygen species (ROS) and aldehydes (i.e., <italic>glutathione S-transferase zeta class-like isoform X1</italic>, <italic>thioredoxin M-type 4</italic>, and <italic>2-alkenal reductase (NADP<sup>+</sup>-dependent)-like</italic>), metabolism (i.e., <italic>carboxylesterases and lecithin-cholesterol acyltransferase-like 4-like</italic>, <italic>nicotianamine aminotransferase A-like isoform X3</italic>, <italic>thiosulfate sulfurtransferase 18-like isoform X1</italic>, and <italic>FNR</italic>, <italic>root isozyme 2</italic>), cell transport (i.e., <italic>non-specific lipid-transfer protein-like protein At2g13820-like</italic> and <italic>major facilitator superfamily protein</italic>), Ca signal and hormone (i.e., <italic>calcium-binding protein CML19-like</italic> and <italic>IAA-amino acid hydrolase ILR1-like 4-like</italic>), gene regulation (i.e., <italic>Gag-pol polyprotein</italic>) and cell wall modification (i.e., <italic>glycosyl hydrolase family 10 protein</italic>) might play a role in B-induced alleviation of Al-toxicity. Our results are useful not only for our understanding of molecular processes associated with B-induced alleviation of Al-toxicity, but also for obtaining key molecular genes to enhance Al-tolerance of plants in the future.</p></abstract><funding-group><funding-statement>This study was financially supported by the earmarked fund for China Agriculture Research System and the National Natural Science Foundation of China (No. 30771487).</funding-statement></funding-group><counts><fig-count count="3"></fig-count><table-count count="2"></table-count><page-count count="27"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>All relevant data are within the paper and its Supporting Information files.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>All relevant data are within the paper and its Supporting Information files.</p></notes></front><body><sec sec-type="intro" id="sec001"><title>Introduction</title><p>Aluminum (Al) is the most abundant metal and the third abundant element in earth’s crust after oxygen and silicon [<xref rid="pone.0115485.ref001" ref-type="bibr">1</xref>]. Al-toxicity is a major limiting factor for crop production in many acidic soils throughout the tropics and subtropics. Al-toxicity can inhibit the root growth which is the primary symptom of Al injury [<xref rid="pone.0115485.ref002" ref-type="bibr">2</xref>] through inhibiting root cell expansion and elongation.</p><p>Boron (B), as an essential element required for normal growth and development of higher plants, is absorbed from soil solution by plant roots mainly in the form of boron acid. B can alleviate Al-toxicity in many plants including lisianthus (<italic>Eustoma grandiflorum</italic>) [<xref rid="pone.0115485.ref003" ref-type="bibr">3</xref>], squash (<italic>Cucurbita pepo</italic>) [<xref rid="pone.0115485.ref004" ref-type="bibr">4</xref>], alfalfa (<italic>Medicago sativa</italic>) [<xref rid="pone.0115485.ref005" ref-type="bibr">5</xref>], <italic>Citrus grandis</italic> [<xref rid="pone.0115485.ref006" ref-type="bibr">6</xref>], flax (<italic>Linum usitatissimum</italic>) [<xref rid="pone.0115485.ref007" ref-type="bibr">7</xref>], pea (<italic>Pisum sativum</italic> [<xref rid="pone.0115485.ref008" ref-type="bibr">8</xref>], common bean (<italic>Phaseolus vulgari</italic>s) [<xref rid="pone.0115485.ref009" ref-type="bibr">9</xref>], sunflower (<italic>Helianthus annuus</italic>) [<xref rid="pone.0115485.ref010" ref-type="bibr">10</xref>], soybean (<italic>Glycine max</italic>) [<xref rid="pone.0115485.ref011" ref-type="bibr">11</xref>], apple (<italic>Malus</italic> sp.) rootstocks [<xref rid="pone.0115485.ref012" ref-type="bibr">12</xref>], cucumber (<italic>Cucumis sativus</italic>), maize (<italic>Zea mays</italic>) [<xref rid="pone.0115485.ref013" ref-type="bibr">13</xref>] and wheat (<italic>Triticum aestivum</italic>) [<xref rid="pone.0115485.ref014" ref-type="bibr">14</xref>].</p><p>B-deficiency is a widespread problem in many agricultural crops, including citrus [<xref rid="pone.0115485.ref015" ref-type="bibr">15</xref>]. Like Al-toxicity, B-deficiency also primarily inhibits root growth through limiting cell elongation rather than cell division [<xref rid="pone.0115485.ref016" ref-type="bibr">16</xref>]. In addition, Al is likely to be present as Al(OH)<sub>3</sub>, which is structurally similar to B(OH)<sub>3</sub> [<xref rid="pone.0115485.ref002" ref-type="bibr">2</xref>]. Previous study showed that B-deficiency- or Al-toxicity-induced inhibition of root growth in squash plants could be a consequence of an impaired ascorbate (ASA) metabolism [<xref rid="pone.0115485.ref017" ref-type="bibr">17</xref>]. Based on the similarities of the molecules and of the symptom characteristic for Al-toxic and B-deficient plants, Blevins and Lukaszewski [<xref rid="pone.0115485.ref018" ref-type="bibr">18</xref>] proposed that Al-toxicity might exert its toxic effect by inducing B-deficiency. However, our studies with <italic>C</italic>. <italic>grandis</italic> seedlings showed that Al-toxicity increased or did not affect B concentration of roots, stems and leaves, demonstrating that the Al-induced growth inhibition was not caused by Al-induced B-deficiency [<xref rid="pone.0115485.ref006" ref-type="bibr">6</xref>]. It has been known that the primary function of B is related to the formation of primary cell walls, where it cross-links with the pectic polypectic polysaccharide rhamnogalacturonan II (RG-II). A higher degree of cross-linked RGII may contribute to a more stable network of cell walls with reduced pore sizes [<xref rid="pone.0115485.ref019" ref-type="bibr">19</xref>], thus preventing Al from getting into contact with sensitive targets at the plasma membrane and/or symplasm [<xref rid="pone.0115485.ref013" ref-type="bibr">13</xref>]. In addition, it has been suggested that B reduces the binding sites for Al in cell walls, thus ameliorating Al-toxicity [<xref rid="pone.0115485.ref008" ref-type="bibr">8</xref>,<xref rid="pone.0115485.ref009" ref-type="bibr">9</xref>]. Jiang et al. [<xref rid="pone.0115485.ref006" ref-type="bibr">6</xref>] showed that the antagonistic actions of B against inhibitory effects of Al-toxicity on <italic>C</italic>. <italic>grandis</italic> root growth was probably due to Al-induced alteration in Al speciation and/or sub-cellular compartmentation, and that B-induced alleviation of shoot and photosynthesis could be due to less accumulation in shoots. Corrales et al. [<xref rid="pone.0115485.ref013" ref-type="bibr">13</xref>] observed that B mitigated Al-induced damage of cell integrity in root tips, possibly through stimulating antioxidant responses in Al-stressed roots. Ruiz et al. [<xref rid="pone.0115485.ref010" ref-type="bibr">10</xref>] suggested that glutathione metabolism was one of the key processes for Al detoxification in sunflower. Recent study with flax showed that B decreased root activities of enzymes (i.e., phenylalanine ammonia-lyase, polyphenol oxidase and peroxidase) involved in phenolic compounds, and root concentrations of lignin and wall-bound phenols under Al-stress, thereby ameliorating Al-toxicity [<xref rid="pone.0115485.ref007" ref-type="bibr">7</xref>]. To conclude, the physiological and biochemical mechanisms on B-induced alleviation of Al-toxicity in plants have been examined in some details, our understanding of the molecular mechanisms underlying these processes is very limited.</p><p>Gene expression analyses offer us the opportunity to understand the molecular mechanisms involved in B-induced alleviation of plant Al-toxicity. Extensive research has shown that Al-toxicity affects the transcript levels of root genes associated with organic acid (OA) metabolism, OA transport and secretion, glycolytic pathways, carbohydrate and energy metabolism, cell wall modification, oxidative stress, protein metabolism, immobilization of Al by phosphate, signaling and hormones, gene regulation, cell death and senescence, and stress response [<xref rid="pone.0115485.ref020" ref-type="bibr">20</xref>–<xref rid="pone.0115485.ref029" ref-type="bibr">29</xref>]. Also, the effects of B-deficiency on root gene expression have been investigated by some workers [<xref rid="pone.0115485.ref030" ref-type="bibr">30</xref>–<xref rid="pone.0115485.ref032" ref-type="bibr">32</xref>]. However, very limited data are available on the differential expression of genes in response to B and Al interactions in plants.</p><p>Citrus belong to evergreen subtropical fruit trees cultivated in humid and subhumid tropical, subtropical and temperate regions of the world mainly on acidic soils. In China, high Al and low B are common in citrus plantations [<xref rid="pone.0115485.ref006" ref-type="bibr">6</xref>,<xref rid="pone.0115485.ref033" ref-type="bibr">33</xref>]. Although we investigated the effects of B and Al on citrus growth, the concentrations of B and Al in roots, stems and leaves, root and leaf OA metabolism, leaf photosynthesis and photosystem II photochemistry [<xref rid="pone.0115485.ref006" ref-type="bibr">6</xref>,<xref rid="pone.0115485.ref034" ref-type="bibr">34</xref>], there is hardly any information on the changes in gene expression of citrus roots in response to B and Al interactions. In this study, we investigated the effects of B and Al interactions on <italic>C</italic>. <italic>grandis</italic> growth, B and Al concentration in roots, and expression of root genes revealed by cDNA-amplified fragment length polymorphism (cDNA-AFLP). The objectives of this study were to understand the molecular mechanisms on B-induced alleviation of Al-toxicity in plants and to identify differentially expressed genes, which might contribute to B-induced alleviation of Al-toxicity.</p></sec><sec sec-type="materials|methods" id="sec002"><title>Materials and Methods</title><sec id="sec003"><title>Plant culture, B and Al treatments and sampling</title><p>This study was conducted from February to December, 2012 at Fujian Agriculture and Forestry University (FAFU), Fuzhou, China. Plant culture, treatments and sampling were performed according to Jiang et al. [<xref rid="pone.0115485.ref006" ref-type="bibr">6</xref>]. Briefly, 5-week-old seedlings of ‘Sour pummelo’ [<italic>Citrus grandis</italic> (L.) Osbeck] were transplanted to a 6 L pots (two plants per pot) containing fine river sand and grown in a greenhouse under natural photoperiod at FAFU. Six weeks after transplanting, seedlings were supplied with nutrient solution containing two B (i.e., 2.5 and 20 μM H<sub>3</sub>BO<sub>3</sub>) × two Al [i.e., 0 (-Al) and 1.2 mM AlCl<sub>3</sub>·6 H<sub>2</sub>O (+Al)] levels. The nutrient solution was formulated with macronutrients (in mM): KNO<sub>3</sub>, 1; Ca(NO<sub>3</sub>)<sub>2</sub>,1; KH<sub>2</sub>PO<sub>4</sub>, 0.1; and MgSO<sub>4</sub>, 0.5; and micronutrients (in μM): MnCl<sub>2</sub>, 2; ZnSO<sub>4</sub>, 2; CuSO<sub>4</sub>, 0.5; (NH<sub>4</sub>)<sub>6</sub>Mo<sub>7</sub>O<sub>24</sub>, 0.065; and Fe-EDTA, 20. The pH of the nutrient solution was adjusted to 4.1–4.2 using HCl or NaOH solution. There were 20 pots per treatment in a completely randomized design. Eighteen weeks after the beginning of B and Al treatments, approx. 5-mm-long root apices from new white roots were excised, immediately frozen in liquid N<sub>2</sub> and stored at −80°C until extraction. The remaining seedlings that were not sampled were used to measure dry weight (DW), B and Al concentrations in roots.</p></sec><sec id="sec004"><title>Plant DW, B and Al concentrations in roots</title><p>Ten plants per treatment from different replications were harvested and divided into their parts (shoots and roots). The plant parts were dried at 70°C for 48 h and DW were measured.</p><p>For the determination of B and Al, fibrous roots were collected and dried. B was assayed by the modified curcumin method [<xref rid="pone.0115485.ref035" ref-type="bibr">35</xref>] after samples were ashed at 500°C for 5 h, and dissolved in 0.1 M HCl. Al was assayed by the aluminon method [<xref rid="pone.0115485.ref036" ref-type="bibr">36</xref>] after samples were digested in a mixture of HNO<sub>3</sub>: HClO<sub>4</sub> (5:1 v/v).</p></sec><sec id="sec005"><title>Collection of root exudates and determination of malate and citrate in exudates</title><p>Root exudates were collected according to Yang et al. [<xref rid="pone.0115485.ref037" ref-type="bibr">37</xref>]. Briefly, 18 weeks after the beginning of B and Al treatments, ten to twelve approx. 5-mm-long root apices from new white roots were excised, then collected in Petri dishes containing 5 mL control solution (0.5 mM CaCl<sub>2</sub>, pH 4.1–4.2). After three rinses with 5 mL control solution (each for 20 min), the root apices were transferred to 2 mL centrifuge tubes containing 1 mL control solution in the absence or presence of 0.5 mM AlCl<sub>3</sub>·6H<sub>2</sub>O (pH 4.1–4.2). The tubes were placed vertically on a shaker (200 rpm) at dark. The treatment times for malate and citrate collection were 12 and 24 h, respectively. Malate and citrate in exudates were assayed by enzymatic method [<xref rid="pone.0115485.ref037" ref-type="bibr">37</xref>].</p></sec><sec id="sec006"><title>RNA extraction, cDNA synthesis and cDNA-AFLP analysis</title><p>Root tips of six plants from different pots were mixed as a biological replicate. Equal amounts of root tips were collected from each plant. There were three biological replicates for each treatment (total of 18 plants from 18 pots). Total RNA were independently extracted three times from four B and Al combinations using Recalcirtant Plant Total RNA Extraction Kit (Centrifugal column type, Bioteke Corporation, China) according to manufacturer’s instructions. cDNA synthesis and cDNA-AFLP analysis were performed according to Zhou et al. [<xref rid="pone.0115485.ref038" ref-type="bibr">38</xref>].</p></sec><sec id="sec007"><title>Quantitative RT-PCR (qRT-PCR) analysis</title><p>Total RNA extracted as described above was used for qRT-PCR analysis, which was performed according to Zhou et al. [<xref rid="pone.0115485.ref038" ref-type="bibr">38</xref>]. The primers of candidate TDFs were listed in <xref rid="pone.0115485.s003" ref-type="supplementary-material">S1 Table</xref>.</p></sec><sec id="sec008"><title>Experimental design and statistical analysis</title><p>There were 20 pots (40 seedlings) per treatment in a completely randomized design. Experiments were performed with 3–10 replicates. Results represented the means ± SE. Differences among four treatments were analyzed by two × two ANOVA. Means were separated by the Duncan's new multiple range test at <italic>P</italic> < 0.05 level.</p></sec></sec><sec sec-type="results" id="sec009"><title>Results</title><sec id="sec010"><title>Effects of B and Al interactions on seedling growth, Al and B concentrations in roots</title><p>In non-Al-treated (-Al) seedlings, root DW, shoot DW and root DW/shoot DW ratio did not significantly change in response to B supply. In Al-treated (+Al) seedlings, both root DW and shoot DW were higher under 20 μM B than under 2.5μM B, while root DW/shoot DW ratio was lower under 20 μM B. Al decreased root DW and shoot DW except for a similar root DW between Al treatments under 20 μM B, and increased root DW/shoot DW ratio (<xref rid="pone.0115485.g001" ref-type="fig">Fig. 1A-C</xref>).</p><fig id="pone.0115485.g001" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0115485.g001</object-id><label>Fig 1</label><caption><title>Effects of B-Al interactions on root DW (A), shoot DW (B), root DW/shoot DW ratio (C), root Al (D) and B (E) concentrations in <italic>C</italic>. <italic>grandis</italic> seedlings.</title><p>Data are means ± SE (<italic>n</italic> = 10 except for 5 for root Al and B concentrations DW). Differences among four treatments were analyzed by 2 (B levels) × 2 (Al levels) ANOVA. Different letters indicate a significant difference at <italic>P</italic> < 0.05.</p></caption><graphic xlink:href="pone.0115485.g001"></graphic></fig><p>Al increased root Al concentration, whereas B did not significantly affect root Al concentration (<xref rid="pone.0115485.g001" ref-type="fig">Fig. 1D</xref>). B supply increased root B concentration. B concentration was higher in +Al roots than in −Al roots under 2.5 μM B, while B concentration in 20 μM B-treated roots did not differ between the two Al treatments (<xref rid="pone.0115485.g001" ref-type="fig">Fig. 1E</xref>).</p></sec><sec id="sec011"><title>Effects of B and Al interactions on Al-induced secretion of malate and citrate from roots</title><p>B supply did not significantly affect Al-induced secretion of malate and citrate from +Al excised or −Al excised roots. Al-induced secretion of malate and citrate from +Al excised roots was higher than from −Al excised roots (<xref rid="pone.0115485.g002" ref-type="fig">Fig. 2</xref>).</p><fig id="pone.0115485.g002" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0115485.g002</object-id><label>Fig 2</label><caption><title>Al-induced-secretion of malate (A and C) and citrate (B and D) by excised from <italic>C</italic>. <italic>grandis</italic> seedlings treated with different B and Al levels.</title><p>Malate and citrate secretion from excised roots were measured after 12 or 24 h treatment, respectively in 0.5 mM CaCl<sub>2</sub> + 0.5 mM AlCl<sub>3</sub>·6H<sub>2</sub>O (A and B) or 0.5 mM CaCl<sub>2</sub> solution (C and D), pH 4.1–4.2. Bars represent means ± SE (<italic>n</italic> = 4). Differences among four treatments were analyzed by 2 (B levels) × 2 (Al levels) ANOVA. Different letters indicate a significant difference at <italic>P</italic> < 0.05.</p></caption><graphic xlink:href="pone.0115485.g002"></graphic></fig></sec><sec id="sec012"><title>Identification of root differentially expressed genes and their expression patterns under B-Al interactions</title><p>We used a total of 256 selective primer combinations for cDNA-AFLP analysis in order to isolate the differentially expressed transcript-derived fragments (TDFs) responsive to B and Al interactions. In this study, approx. 5970 clear and unambiguous TDFs were amplified, with an average of 29.5 (7–52) TDFs for each primer combination. A total of 169 differentially expressed and reproducible TDFs were obtained. All these TDFs were reamplified, cloned and sequenced, and 142 cDNA fragments produced useable sequence data. Homology analyses were conducted using BLAST from GenBank. Among these TDFs, 89 TDFs showed significant homology to genes encoding known or putative proteins; 11 TDFs were homologus to genes encoding uncharacterized and hypothetical proteins; and the remaining 42 TDFs did not show homologus to any nucleotide or amino sequence in the public databases. These TDFs were associated with metabolism (21), stress response (10), autophagy and senescence (15), signal transduction and hormone (12), gene regulation (15), cell transport (12), cell wall modification (4) and others (11). Further analysis showed that in 2.5 (20) μM B-treated roots, 25 (35) TDFs were upregulated by Al-toxicity, and 36 (29) TDFs were downregulated by Al-toxicity; and in −Al (+Al) roots, the expression levels of 22 (30) TDFs increased and 36 (22) TDFs decreased as B supply increased from 2.5 to 20 μM. Obviously, B-Al interaction affected root gene expression (Tables <xref rid="pone.0115485.t001" ref-type="table">1</xref> and <xref rid="pone.0115485.t002" ref-type="table">2</xref>).</p><table-wrap id="pone.0115485.t001" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0115485.t001</object-id><label>Table 1</label><caption><title>Homology of differentially expressed cDNA-AFLP fragments with known gene sequences in database using BLASTN algorithm along their expression patterns in roots from <italic>Citrus grandis</italic> seedlings treated with two B × Al levels.</title></caption><alternatives><graphic id="pone.0115485.t001g" xlink:href="pone.0115485.t001"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col></colgroup><thead><tr><th align="left" rowspan="1" colspan="1">TDF#</th><th align="left" rowspan="1" colspan="1">Genebank ID</th><th align="left" rowspan="1" colspan="1">E value</th><th align="left" rowspan="1" colspan="1">Max score</th><th align="left" rowspan="1" colspan="1">Organism origin</th><th align="left" rowspan="1" colspan="1">Size (bp)</th><th align="left" rowspan="1" colspan="1">Description</th><th align="left" rowspan="1" colspan="1">Identity</th><th colspan="4" align="left" rowspan="1">Fold change</th></tr><tr><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1">2.5 B -Al</th><th align="left" rowspan="1" colspan="1">2.5 B + Al</th><th align="left" rowspan="1" colspan="1">20 B - Al</th><th align="left" rowspan="1" colspan="1">20 B + Al</th></tr></thead><tbody><tr><td colspan="4" align="left" rowspan="1"><bold><italic>Metabolism</italic></bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">157-6</td><td align="left" rowspan="1" colspan="1">XP_006479398</td><td align="left" rowspan="1" colspan="1">2.E-30</td><td align="left" rowspan="1" colspan="1">118</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">185</td><td align="left" rowspan="1" colspan="1">Flavonol synthase/flavanone 3-hydroxylase-like</td><td align="left" rowspan="1" colspan="1">100%</td><td align="left" rowspan="1" colspan="1">0 b</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0 b</td><td align="left" rowspan="1" colspan="1">1.03 a</td></tr><tr><td align="left" rowspan="1" colspan="1">134-14</td><td align="left" rowspan="1" colspan="1">NP_197540</td><td align="left" rowspan="1" colspan="1">5.E-15</td><td align="left" rowspan="1" colspan="1">76.3</td><td align="left" rowspan="1" colspan="1"><italic>Arabidopsis thaliana</italic></td><td align="left" rowspan="1" colspan="1">171</td><td align="left" rowspan="1" colspan="1">Flavanone 3 hydroxylase-like protein</td><td align="left" rowspan="1" colspan="1">65%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">2.80 a</td><td align="left" rowspan="1" colspan="1">0.07 c</td><td align="left" rowspan="1" colspan="1">0.21 c</td></tr><tr><td align="left" rowspan="1" colspan="1">149-2</td><td align="left" rowspan="1" colspan="1">XP_006487080</td><td align="left" rowspan="1" colspan="1">7.E-29</td><td align="left" rowspan="1" colspan="1">115</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">255</td><td align="left" rowspan="1" colspan="1">Probable carboxylesterase 12-like</td><td align="left" rowspan="1" colspan="1">81%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">1.08 ab</td><td align="left" rowspan="1" colspan="1">0.12 c</td><td align="left" rowspan="1" colspan="1">1.22 a</td></tr><tr><td align="left" rowspan="1" colspan="1">216-2</td><td align="left" rowspan="1" colspan="1">XP_006490283</td><td align="left" rowspan="1" colspan="1">3.E-41</td><td align="left" rowspan="1" colspan="1">147</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">236</td><td align="left" rowspan="1" colspan="1">Carboxylesterase 1-like</td><td align="left" rowspan="1" colspan="1">95%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">0.16 c</td><td align="left" rowspan="1" colspan="1">0.16 c</td><td align="left" rowspan="1" colspan="1">1.47 a</td></tr><tr><td align="left" rowspan="1" colspan="1">250-3</td><td align="left" rowspan="1" colspan="1">XP_006468458</td><td align="left" rowspan="1" colspan="1">4.E-51</td><td align="left" rowspan="1" colspan="1">179</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">297</td><td align="left" rowspan="1" colspan="1">Lecithin-cholesterol acyltransferase-like 4-like</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.45 b</td><td align="left" rowspan="1" colspan="1">1.10 a</td><td align="left" rowspan="1" colspan="1">1.01 a</td></tr><tr><td align="left" rowspan="1" colspan="1">51-12</td><td align="left" rowspan="1" colspan="1">YP_740484</td><td align="left" rowspan="1" colspan="1">9.E-24</td><td align="left" rowspan="1" colspan="1">101</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">162</td><td align="left" rowspan="1" colspan="1">Acetyl-CoA carboxylase carboxyltransferase beta subunit</td><td align="left" rowspan="1" colspan="1">98%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.05 b</td><td align="left" rowspan="1" colspan="1">0.05 b</td><td align="left" rowspan="1" colspan="1">0.05 b</td></tr><tr><td align="left" rowspan="1" colspan="1">136-3</td><td align="left" rowspan="1" colspan="1">XP_006492541</td><td align="left" rowspan="1" colspan="1">2.E-39</td><td align="left" rowspan="1" colspan="1">145</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">239</td><td align="left" rowspan="1" colspan="1">Adenosylhomocysteinase-like</td><td align="left" rowspan="1" colspan="1">91%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">1.06 b</td><td align="left" rowspan="1" colspan="1">0.10 c</td><td align="left" rowspan="1" colspan="1">5.97 a</td></tr><tr><td align="left" rowspan="1" colspan="1">141-5</td><td align="left" rowspan="1" colspan="1">XP_006471128</td><td align="left" rowspan="1" colspan="1">6.E-50</td><td align="left" rowspan="1" colspan="1">172</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">279</td><td align="left" rowspan="1" colspan="1">Probable S-adenosylmethionine-dependent methyltransferase At5g37990-like</td><td align="left" rowspan="1" colspan="1">95%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.08 b</td><td align="left" rowspan="1" colspan="1">0.09 b</td><td align="left" rowspan="1" colspan="1">0.08 b</td></tr><tr><td align="left" rowspan="1" colspan="1">87-2</td><td align="left" rowspan="1" colspan="1">NP_180524</td><td align="left" rowspan="1" colspan="1">8.E-33</td><td align="left" rowspan="1" colspan="1">129</td><td align="left" rowspan="1" colspan="1"><italic>Arabidopsis thaliana</italic></td><td align="left" rowspan="1" colspan="1">279</td><td align="left" rowspan="1" colspan="1">Phosphomethylpyrimidine synthase</td><td align="left" rowspan="1" colspan="1">76%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.10 b</td><td align="left" rowspan="1" colspan="1">0.11 b</td><td align="left" rowspan="1" colspan="1">0.10 b</td></tr><tr><td align="left" rowspan="1" colspan="1">138-5</td><td align="left" rowspan="1" colspan="1">XP_006469907</td><td align="left" rowspan="1" colspan="1">5.E-20</td><td align="left" rowspan="1" colspan="1">90.9</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">256</td><td align="left" rowspan="1" colspan="1">Nicotianamine aminotransferase A-like isoform X3</td><td align="left" rowspan="1" colspan="1">75%</td><td align="left" rowspan="1" colspan="1">0 b</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0 b</td><td align="left" rowspan="1" colspan="1">1.02 a</td></tr><tr><td align="left" rowspan="1" colspan="1">138-3</td><td align="left" rowspan="1" colspan="1">NP_567934</td><td align="left" rowspan="1" colspan="1">4.E-44</td><td align="left" rowspan="1" colspan="1">158</td><td align="left" rowspan="1" colspan="1"><italic>Arabidopsis thaliana</italic></td><td align="left" rowspan="1" colspan="1">276</td><td align="left" rowspan="1" colspan="1">LL-diaminopimelate aminotransferase</td><td align="left" rowspan="1" colspan="1">83%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">1.05 a</td><td align="left" rowspan="1" colspan="1">1.06 a</td><td align="left" rowspan="1" colspan="1">0.13 b</td></tr><tr><td align="left" rowspan="1" colspan="1">134-12</td><td align="left" rowspan="1" colspan="1">XP_007043658</td><td align="left" rowspan="1" colspan="1">2.E-24</td><td align="left" rowspan="1" colspan="1">103</td><td align="left" rowspan="1" colspan="1"><italic>Theobroma cacao</italic></td><td align="left" rowspan="1" colspan="1">256</td><td align="left" rowspan="1" colspan="1">Tyrosine transaminase family protein</td><td align="left" rowspan="1" colspan="1">80%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">1.08 a</td><td align="left" rowspan="1" colspan="1">1.10 a</td><td align="left" rowspan="1" colspan="1">0.06 b</td></tr><tr><td align="left" rowspan="1" colspan="1">18-2</td><td align="left" rowspan="1" colspan="1">XP_006466965</td><td align="left" rowspan="1" colspan="1">1.E-41</td><td align="left" rowspan="1" colspan="1">143</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">225</td><td align="left" rowspan="1" colspan="1">Thiosulfate sulfurtransferase 18-like isoform X1</td><td align="left" rowspan="1" colspan="1">92%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.16 b</td><td align="left" rowspan="1" colspan="1">0.17 b</td><td align="left" rowspan="1" colspan="1">1.07 a</td></tr><tr><td align="left" rowspan="1" colspan="1">178-4</td><td align="left" rowspan="1" colspan="1">XP_006466965</td><td align="left" rowspan="1" colspan="1">9.E-41</td><td align="left" rowspan="1" colspan="1">141</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">225</td><td align="left" rowspan="1" colspan="1">Thiosulfate sulfurtransferase 18-like isoform X1</td><td align="left" rowspan="1" colspan="1">92%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.22 b</td><td align="left" rowspan="1" colspan="1">0.18 b</td><td align="left" rowspan="1" colspan="1">1.03 a</td></tr><tr><td align="left" rowspan="1" colspan="1">54-2</td><td align="left" rowspan="1" colspan="1">XP_002308954</td><td align="left" rowspan="1" colspan="1">2.E-24</td><td align="left" rowspan="1" colspan="1">101</td><td align="left" rowspan="1" colspan="1"><italic>Populus trichocarpa</italic></td><td align="left" rowspan="1" colspan="1">189</td><td align="left" rowspan="1" colspan="1">40S ribosomal protein S2</td><td align="left" rowspan="1" colspan="1">84%</td><td align="left" rowspan="1" colspan="1">1.00 c</td><td align="left" rowspan="1" colspan="1">15.58 a</td><td align="left" rowspan="1" colspan="1">4.60 b</td><td align="left" rowspan="1" colspan="1">15.11 a</td></tr><tr><td align="left" rowspan="1" colspan="1">80-2</td><td align="left" rowspan="1" colspan="1">XP_003523292</td><td align="left" rowspan="1" colspan="1">2.E-56</td><td align="left" rowspan="1" colspan="1">184</td><td align="left" rowspan="1" colspan="1"><italic>Glycine max</italic></td><td align="left" rowspan="1" colspan="1">313</td><td align="left" rowspan="1" colspan="1">60S ribosomal protein L10</td><td align="left" rowspan="1" colspan="1">95%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">1.03 b</td><td align="left" rowspan="1" colspan="1">6.49 a</td><td align="left" rowspan="1" colspan="1">1.09 b</td></tr><tr><td align="left" rowspan="1" colspan="1">201-1</td><td align="left" rowspan="1" colspan="1">NP_564355</td><td align="left" rowspan="1" colspan="1">1.E-30</td><td align="left" rowspan="1" colspan="1">119</td><td align="left" rowspan="1" colspan="1"><italic>Arabidopsis thaliana</italic></td><td align="left" rowspan="1" colspan="1">201</td><td align="left" rowspan="1" colspan="1">Ferredoxin-NADP reductase, root isozyme 2</td><td align="left" rowspan="1" colspan="1">90%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">1.03 a</td><td align="left" rowspan="1" colspan="1">0.16 b</td><td align="left" rowspan="1" colspan="1">1.09 a</td></tr><tr><td align="left" rowspan="1" colspan="1">25-4</td><td align="left" rowspan="1" colspan="1">ACG28186</td><td align="left" rowspan="1" colspan="1">3.E-32</td><td align="left" rowspan="1" colspan="1">121</td><td align="left" rowspan="1" colspan="1"><italic>Zea mays</italic></td><td align="left" rowspan="1" colspan="1">212</td><td align="left" rowspan="1" colspan="1">Cytochrome b6-f complex iron-sulfur subunit</td><td align="left" rowspan="1" colspan="1">85%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.18 b</td><td align="left" rowspan="1" colspan="1">0.08 b</td><td align="left" rowspan="1" colspan="1">0.09 b</td></tr><tr><td align="left" rowspan="1" colspan="1">29-2</td><td align="left" rowspan="1" colspan="1">ACG28186</td><td align="left" rowspan="1" colspan="1">5.E-31</td><td align="left" rowspan="1" colspan="1">118</td><td align="left" rowspan="1" colspan="1"><italic>Zea mays</italic></td><td align="left" rowspan="1" colspan="1">212</td><td align="left" rowspan="1" colspan="1">Cytochrome b6-f complex iron-sulfur subunit</td><td align="left" rowspan="1" colspan="1">84%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.27 b</td><td align="left" rowspan="1" colspan="1">0.24 b</td><td align="left" rowspan="1" colspan="1">0.21 b</td></tr><tr><td align="left" rowspan="1" colspan="1">134-9</td><td align="left" rowspan="1" colspan="1">XP_002518810</td><td align="left" rowspan="1" colspan="1">3.E-18</td><td align="left" rowspan="1" colspan="1">87.8</td><td align="left" rowspan="1" colspan="1"><italic>Ricinus communis</italic></td><td align="left" rowspan="1" colspan="1">232</td><td align="left" rowspan="1" colspan="1">Electron transporter, putative</td><td align="left" rowspan="1" colspan="1">75%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">1.02 b</td><td align="left" rowspan="1" colspan="1">1.13 b</td><td align="left" rowspan="1" colspan="1">21.82 a</td></tr><tr><td align="left" rowspan="1" colspan="1">51-9</td><td align="left" rowspan="1" colspan="1">XP_002531030</td><td align="left" rowspan="1" colspan="1">2.E-16</td><td align="left" rowspan="1" colspan="1">76.3</td><td align="left" rowspan="1" colspan="1"><italic>Ricinus communis</italic></td><td align="left" rowspan="1" colspan="1">175</td><td align="left" rowspan="1" colspan="1">Ribulose-bisphosphate carboxylase, putative</td><td align="left" rowspan="1" colspan="1">94%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.30 b</td><td align="left" rowspan="1" colspan="1">0.32 b</td><td align="left" rowspan="1" colspan="1">0.04 c</td></tr><tr><td colspan="2" align="center" rowspan="1"><bold><italic>Stress response</italic></bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">78-4</td><td align="left" rowspan="1" colspan="1">XP_006470782</td><td align="left" rowspan="1" colspan="1">8.E-12</td><td align="left" rowspan="1" colspan="1">67</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">250</td><td align="left" rowspan="1" colspan="1">Glutathione S-transferase zeta class-like isoform X1</td><td align="left" rowspan="1" colspan="1">100%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.26 b</td><td align="left" rowspan="1" colspan="1">0.24 b</td><td align="left" rowspan="1" colspan="1">0.97 a</td></tr><tr><td align="left" rowspan="1" colspan="1">164-1</td><td align="left" rowspan="1" colspan="1">XP_006493708</td><td align="left" rowspan="1" colspan="1">3.E-04</td><td align="left" rowspan="1" colspan="1">47.8</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">299</td><td align="left" rowspan="1" colspan="1">Glutathione reductase, cytosolic-like</td><td align="left" rowspan="1" colspan="1">88%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">1.03 a</td><td align="left" rowspan="1" colspan="1">0.14 b</td><td align="left" rowspan="1" colspan="1">1.02 a</td></tr><tr><td align="left" rowspan="1" colspan="1">217-2</td><td align="left" rowspan="1" colspan="1">NP_192897</td><td align="left" rowspan="1" colspan="1">9.E-14</td><td align="left" rowspan="1" colspan="1">72.4</td><td align="left" rowspan="1" colspan="1"><italic>Arabidopsis thaliana</italic></td><td align="left" rowspan="1" colspan="1">227</td><td align="left" rowspan="1" colspan="1">Glutathione peroxidase 6</td><td align="left" rowspan="1" colspan="1">63%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">1.23 b</td><td align="left" rowspan="1" colspan="1">9.45 a</td><td align="left" rowspan="1" colspan="1">1.20 b</td></tr><tr><td align="left" rowspan="1" colspan="1">60-1</td><td align="left" rowspan="1" colspan="1">XP_007021413</td><td align="left" rowspan="1" colspan="1">4.E-10</td><td align="left" rowspan="1" colspan="1">62.4</td><td align="left" rowspan="1" colspan="1"><italic>Theobroma cacao</italic></td><td align="left" rowspan="1" colspan="1">300</td><td align="left" rowspan="1" colspan="1">Thioredoxin M-type 4</td><td align="left" rowspan="1" colspan="1">71%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">1.07 b</td><td align="left" rowspan="1" colspan="1">1.15 b</td><td align="left" rowspan="1" colspan="1">10.70 a</td></tr><tr><td align="left" rowspan="1" colspan="1">243-1</td><td align="left" rowspan="1" colspan="1">XP_006475833</td><td align="left" rowspan="1" colspan="1">1.E-38</td><td align="left" rowspan="1" colspan="1">141</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">242</td><td align="left" rowspan="1" colspan="1">2-alkenal reductase (NADP<sup>+</sup>- dependent) -like</td><td align="left" rowspan="1" colspan="1">97%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">6.00 a</td><td align="left" rowspan="1" colspan="1">1.06 b</td><td align="left" rowspan="1" colspan="1">6.15 a</td></tr><tr><td align="left" rowspan="1" colspan="1">178-1</td><td align="left" rowspan="1" colspan="1">XP_007017815</td><td align="left" rowspan="1" colspan="1">5.E-05</td><td align="left" rowspan="1" colspan="1">48.1</td><td align="left" rowspan="1" colspan="1"><italic>Theobroma cacao</italic></td><td align="left" rowspan="1" colspan="1">304</td><td align="left" rowspan="1" colspan="1">Chaperone DnaJ-domain superfamily protein, putative</td><td align="left" rowspan="1" colspan="1">70%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.14 c</td><td align="left" rowspan="1" colspan="1">0.39 b</td><td align="left" rowspan="1" colspan="1">0.39 b</td></tr><tr><td align="left" rowspan="1" colspan="1">83-5</td><td align="left" rowspan="1" colspan="1">BAJ11779</td><td align="left" rowspan="1" colspan="1">5.E+00</td><td align="left" rowspan="1" colspan="1">30.8</td><td align="left" rowspan="1" colspan="1"><italic>Corchorus tridens</italic></td><td align="left" rowspan="1" colspan="1">125</td><td align="left" rowspan="1" colspan="1">Dehydration responsive protein</td><td align="left" rowspan="1" colspan="1">78%</td><td align="left" rowspan="1" colspan="1">1.00 c</td><td align="left" rowspan="1" colspan="1">9.62 ab</td><td align="left" rowspan="1" colspan="1">1.34 bc</td><td align="left" rowspan="1" colspan="1">9.92 a</td></tr><tr><td align="left" rowspan="1" colspan="1">219-3</td><td align="left" rowspan="1" colspan="1">XP_007035783</td><td align="left" rowspan="1" colspan="1">1.E+00</td><td align="left" rowspan="1" colspan="1">35.4</td><td align="left" rowspan="1" colspan="1"><italic>Theobroma cacao</italic></td><td align="left" rowspan="1" colspan="1">212</td><td align="left" rowspan="1" colspan="1">Adenine nucleotide alpha hydrolases-like superfamily protein</td><td align="left" rowspan="1" colspan="1">84%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">7.91 a</td><td align="left" rowspan="1" colspan="1">1.02 b</td><td align="left" rowspan="1" colspan="1">5.71 a</td></tr><tr><td align="left" rowspan="1" colspan="1">59-1</td><td align="left" rowspan="1" colspan="1">XP_002310744</td><td align="left" rowspan="1" colspan="1">1.E-13</td><td align="left" rowspan="1" colspan="1">75.9</td><td align="left" rowspan="1" colspan="1"><italic>Populus trichocarpa</italic></td><td align="left" rowspan="1" colspan="1">282</td><td align="left" rowspan="1" colspan="1">Disease resistance family protein</td><td align="left" rowspan="1" colspan="1">41%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.08 b</td><td align="left" rowspan="1" colspan="1">0.25 b</td><td align="left" rowspan="1" colspan="1">0.09 b</td></tr><tr><td align="left" rowspan="1" colspan="1">176-1</td><td align="left" rowspan="1" colspan="1">XP_006494011</td><td align="left" rowspan="1" colspan="1">2.E-21</td><td align="left" rowspan="1" colspan="1">98.2</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">286</td><td align="left" rowspan="1" colspan="1">Putative disease resistance protein At3g14460-like</td><td align="left" rowspan="1" colspan="1">66%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">1.09 a</td><td align="left" rowspan="1" colspan="1">0.23 b</td><td align="left" rowspan="1" colspan="1">1.02 a</td></tr><tr><td colspan="3" align="left" rowspan="1"><bold><italic>Autophagy and senescence</italic></bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">158-1</td><td align="left" rowspan="1" colspan="1">NP_564664</td><td align="left" rowspan="1" colspan="1">4.E-11</td><td align="left" rowspan="1" colspan="1">67.8</td><td align="left" rowspan="1" colspan="1"><italic>Arabidopsis thaliana</italic></td><td align="left" rowspan="1" colspan="1">236</td><td align="left" rowspan="1" colspan="1">Autophagy 18H-like protein</td><td align="left" rowspan="1" colspan="1">53%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">0.23 c</td><td align="left" rowspan="1" colspan="1">2.69 a</td><td align="left" rowspan="1" colspan="1">0.23 c</td></tr><tr><td align="left" rowspan="1" colspan="1">2-1</td><td align="left" rowspan="1" colspan="1">BAB33421</td><td align="left" rowspan="1" colspan="1">8.E-39</td><td align="left" rowspan="1" colspan="1">140</td><td align="left" rowspan="1" colspan="1"><italic>Pisum sativum</italic></td><td align="left" rowspan="1" colspan="1">244</td><td align="left" rowspan="1" colspan="1">Putative senescence-associated protein</td><td align="left" rowspan="1" colspan="1">86%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">1.04 a</td><td align="left" rowspan="1" colspan="1">1.06 a</td><td align="left" rowspan="1" colspan="1">0.12 b</td></tr><tr><td align="left" rowspan="1" colspan="1">5-3</td><td align="left" rowspan="1" colspan="1">BAB33421</td><td align="left" rowspan="1" colspan="1">1.E-25</td><td align="left" rowspan="1" colspan="1">104</td><td align="left" rowspan="1" colspan="1"><italic>Pisum sativum</italic></td><td align="left" rowspan="1" colspan="1">191</td><td align="left" rowspan="1" colspan="1">Putative senescence-associated protein</td><td align="left" rowspan="1" colspan="1">89%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.96 a</td><td align="left" rowspan="1" colspan="1">1.02 a</td><td align="left" rowspan="1" colspan="1">0.15 b</td></tr><tr><td align="left" rowspan="1" colspan="1">139-8</td><td align="left" rowspan="1" colspan="1">BAB33421</td><td align="left" rowspan="1" colspan="1">2.E-35</td><td align="left" rowspan="1" colspan="1">131</td><td align="left" rowspan="1" colspan="1"><italic>Pisum sativum</italic></td><td align="left" rowspan="1" colspan="1">236</td><td align="left" rowspan="1" colspan="1">Putative senescence-associated protein</td><td align="left" rowspan="1" colspan="1">89%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">0 c</td><td align="left" rowspan="1" colspan="1">0 c</td><td align="left" rowspan="1" colspan="1">3.62 a</td></tr><tr><td align="left" rowspan="1" colspan="1">156-3</td><td align="left" rowspan="1" colspan="1">BAB33421</td><td align="left" rowspan="1" colspan="1">3.E-08</td><td align="left" rowspan="1" colspan="1">58.2</td><td align="left" rowspan="1" colspan="1"><italic>Pisum sativum</italic></td><td align="left" rowspan="1" colspan="1">274</td><td align="left" rowspan="1" colspan="1">Putative senescence-associated protein</td><td align="left" rowspan="1" colspan="1">69%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.17 b</td><td align="left" rowspan="1" colspan="1">1.06 a</td><td align="left" rowspan="1" colspan="1">1.06 a</td></tr><tr><td align="left" rowspan="1" colspan="1">141-7</td><td align="left" rowspan="1" colspan="1">AAR25995</td><td align="left" rowspan="1" colspan="1">3.E-31</td><td align="left" rowspan="1" colspan="1">115</td><td align="left" rowspan="1" colspan="1"><italic>Pyrus communis</italic></td><td align="left" rowspan="1" colspan="1">259</td><td align="left" rowspan="1" colspan="1">Putative senescence-associated protein</td><td align="left" rowspan="1" colspan="1">96%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">1.01 b</td><td align="left" rowspan="1" colspan="1">1.04 b</td><td align="left" rowspan="1" colspan="1">7.99 a</td></tr><tr><td align="left" rowspan="1" colspan="1">209-1</td><td align="left" rowspan="1" colspan="1">AAR25995</td><td align="left" rowspan="1" colspan="1">1.E-56</td><td align="left" rowspan="1" colspan="1">181</td><td align="left" rowspan="1" colspan="1"><italic>Pyrus communis</italic></td><td align="left" rowspan="1" colspan="1">296</td><td align="left" rowspan="1" colspan="1">Putative senescence-associated protein</td><td align="left" rowspan="1" colspan="1">98%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">8.39 a</td><td align="left" rowspan="1" colspan="1">1.18 b</td><td align="left" rowspan="1" colspan="1">0.95 b</td></tr><tr><td align="left" rowspan="1" colspan="1">217-1</td><td align="left" rowspan="1" colspan="1">AAR25995</td><td align="left" rowspan="1" colspan="1">2.E-51</td><td align="left" rowspan="1" colspan="1">167</td><td align="left" rowspan="1" colspan="1"><italic>Pyrus communis</italic></td><td align="left" rowspan="1" colspan="1">309</td><td align="left" rowspan="1" colspan="1">Putative senescence-associated protein</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">3.31 a</td><td align="left" rowspan="1" colspan="1">2.86 ab</td><td align="left" rowspan="1" colspan="1">1.14 b</td></tr><tr><td align="left" rowspan="1" colspan="1">219-2</td><td align="left" rowspan="1" colspan="1">AAR25995</td><td align="left" rowspan="1" colspan="1">2.E-50</td><td align="left" rowspan="1" colspan="1">165</td><td align="left" rowspan="1" colspan="1"><italic>Pyrus communis</italic></td><td align="left" rowspan="1" colspan="1">296</td><td align="left" rowspan="1" colspan="1">Putative senescence-associated protein</td><td align="left" rowspan="1" colspan="1">97%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">1.14 b</td><td align="left" rowspan="1" colspan="1">10.80 a</td><td align="left" rowspan="1" colspan="1">1.11 b</td></tr><tr><td align="left" rowspan="1" colspan="1">223-1</td><td align="left" rowspan="1" colspan="1">AAR25995</td><td align="left" rowspan="1" colspan="1">2.E-49</td><td align="left" rowspan="1" colspan="1">162</td><td align="left" rowspan="1" colspan="1"><italic>Pyrus communis</italic></td><td align="left" rowspan="1" colspan="1">314</td><td align="left" rowspan="1" colspan="1">Putative senescence-associated protein</td><td align="left" rowspan="1" colspan="1">97%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.16 b</td><td align="left" rowspan="1" colspan="1">1.09 a</td><td align="left" rowspan="1" colspan="1">0.99 a</td></tr><tr><td align="left" rowspan="1" colspan="1">179-6</td><td align="left" rowspan="1" colspan="1">XP_006473584</td><td align="left" rowspan="1" colspan="1">1.E-37</td><td align="left" rowspan="1" colspan="1">138</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">215</td><td align="left" rowspan="1" colspan="1">Cysteine proteinase 15A-like</td><td align="left" rowspan="1" colspan="1">98%</td><td align="left" rowspan="1" colspan="1">0 c</td><td align="left" rowspan="1" colspan="1">0 c</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.54 b</td></tr><tr><td align="left" rowspan="1" colspan="1">246-9</td><td align="left" rowspan="1" colspan="1">XP_006467009</td><td align="left" rowspan="1" colspan="1">2.E-21</td><td align="left" rowspan="1" colspan="1">94.7</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">154</td><td align="left" rowspan="1" colspan="1">Aspartic proteinase-like protein 1-like</td><td align="left" rowspan="1" colspan="1">94%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">1.06 b</td><td align="left" rowspan="1" colspan="1">5.68 a</td><td align="left" rowspan="1" colspan="1">1.13 b</td></tr><tr><td align="left" rowspan="1" colspan="1">87-3</td><td align="left" rowspan="1" colspan="1">XP_002882118</td><td align="left" rowspan="1" colspan="1">7.E-34</td><td align="left" rowspan="1" colspan="1">133</td><td align="left" rowspan="1" colspan="1"><italic>Arabidopsis lyrata subsp</italic>. <italic>lyrata</italic></td><td align="left" rowspan="1" colspan="1">272</td><td align="left" rowspan="1" colspan="1">Serine-type peptidase</td><td align="left" rowspan="1" colspan="1">71%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">1.16 b</td><td align="left" rowspan="1" colspan="1">4.32 a</td><td align="left" rowspan="1" colspan="1">1.25 b</td></tr><tr><td align="left" rowspan="1" colspan="1">179-4</td><td align="left" rowspan="1" colspan="1">XP_003633155</td><td align="left" rowspan="1" colspan="1">3.E-19</td><td align="left" rowspan="1" colspan="1">90.5</td><td align="left" rowspan="1" colspan="1"><italic>Vitis vinifera</italic></td><td align="left" rowspan="1" colspan="1">238</td><td align="left" rowspan="1" colspan="1">Ubiquitin carboxyl-terminal hydrolase 22-like</td><td align="left" rowspan="1" colspan="1">93%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.05 c</td><td align="left" rowspan="1" colspan="1">0.06 c</td><td align="left" rowspan="1" colspan="1">0.48 b</td></tr><tr><td align="left" rowspan="1" colspan="1">78-2</td><td align="left" rowspan="1" colspan="1">XP_006484457</td><td align="left" rowspan="1" colspan="1">1.E-29</td><td align="left" rowspan="1" colspan="1">117</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">208</td><td align="left" rowspan="1" colspan="1">Ubiquitin receptor RAD23c-like</td><td align="left" rowspan="1" colspan="1">98%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">1.16 b</td><td align="left" rowspan="1" colspan="1">5.76 a</td><td align="left" rowspan="1" colspan="1">1.07 b</td></tr><tr><td colspan="4" align="left" rowspan="1"><bold><italic>Signal transduction and hormone</italic></bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">19-4</td><td align="left" rowspan="1" colspan="1">XP_003549848</td><td align="left" rowspan="1" colspan="1">2.E-25</td><td align="left" rowspan="1" colspan="1">102</td><td align="left" rowspan="1" colspan="1"><italic>Glycine max</italic></td><td align="left" rowspan="1" colspan="1">274</td><td align="left" rowspan="1" colspan="1">Putative calcium-binding protein CML19-like</td><td align="left" rowspan="1" colspan="1">63%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">0.99 b</td><td align="left" rowspan="1" colspan="1">3.68 ab</td><td align="left" rowspan="1" colspan="1">4.15 a</td></tr><tr><td align="left" rowspan="1" colspan="1">19-5</td><td align="left" rowspan="1" colspan="1">XP_003549848</td><td align="left" rowspan="1" colspan="1">2.E-25</td><td align="left" rowspan="1" colspan="1">102</td><td align="left" rowspan="1" colspan="1"><italic>Glycine max</italic></td><td align="left" rowspan="1" colspan="1">274</td><td align="left" rowspan="1" colspan="1">Putative calcium-binding protein CML19-like</td><td align="left" rowspan="1" colspan="1">63%</td><td align="left" rowspan="1" colspan="1">1.00 c</td><td align="left" rowspan="1" colspan="1">1.42 bc</td><td align="left" rowspan="1" colspan="1">4.75 a</td><td align="left" rowspan="1" colspan="1">4.43 ab</td></tr><tr><td align="left" rowspan="1" colspan="1">89-2</td><td align="left" rowspan="1" colspan="1">NP_178383</td><td align="left" rowspan="1" colspan="1">1.E-43</td><td align="left" rowspan="1" colspan="1">156</td><td align="left" rowspan="1" colspan="1"><italic>Arabidopsis thaliana</italic></td><td align="left" rowspan="1" colspan="1">258</td><td align="left" rowspan="1" colspan="1">Protein kinase 2B</td><td align="left" rowspan="1" colspan="1">88%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.15 b</td><td align="left" rowspan="1" colspan="1">1.11 a</td><td align="left" rowspan="1" colspan="1">1.26 a</td></tr><tr><td align="left" rowspan="1" colspan="1">25-3</td><td align="left" rowspan="1" colspan="1">CAB63149</td><td align="left" rowspan="1" colspan="1">3.E-36</td><td align="left" rowspan="1" colspan="1">136</td><td align="left" rowspan="1" colspan="1"><italic>Arabidopsis thaliana</italic></td><td align="left" rowspan="1" colspan="1">222</td><td align="left" rowspan="1" colspan="1">MAP kinase</td><td align="left" rowspan="1" colspan="1">92%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.24 b</td><td align="left" rowspan="1" colspan="1">1.08 a</td><td align="left" rowspan="1" colspan="1">0.25 b</td></tr><tr><td align="left" rowspan="1" colspan="1">140-2</td><td align="left" rowspan="1" colspan="1">XP_006485632</td><td align="left" rowspan="1" colspan="1">6.E-07</td><td align="left" rowspan="1" colspan="1">54.7</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">219</td><td align="left" rowspan="1" colspan="1">Probable receptor-like protein kinase At5g47070-like isoform X1</td><td align="left" rowspan="1" colspan="1">96%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">1.06 a</td><td align="left" rowspan="1" colspan="1">1.08 a</td><td align="left" rowspan="1" colspan="1">0.35 b</td></tr><tr><td align="left" rowspan="1" colspan="1">246-3</td><td align="left" rowspan="1" colspan="1">XP_003534233</td><td align="left" rowspan="1" colspan="1">7.E-03</td><td align="left" rowspan="1" colspan="1">42.7</td><td align="left" rowspan="1" colspan="1"><italic>Glycine max</italic></td><td align="left" rowspan="1" colspan="1">221</td><td align="left" rowspan="1" colspan="1">SRSF protein kinase 1-like isoform 1</td><td align="left" rowspan="1" colspan="1">71%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.05 b</td><td align="left" rowspan="1" colspan="1">0.05 b</td><td align="left" rowspan="1" colspan="1">0.06 b</td></tr><tr><td align="left" rowspan="1" colspan="1">51-15</td><td align="left" rowspan="1" colspan="1">CAB90633</td><td align="left" rowspan="1" colspan="1">2.E-05</td><td align="left" rowspan="1" colspan="1">48.9</td><td align="left" rowspan="1" colspan="1"><italic>Fagus sylvatica</italic></td><td align="left" rowspan="1" colspan="1">116</td><td align="left" rowspan="1" colspan="1">protein phopsphatase 2C (PP2C)</td><td align="left" rowspan="1" colspan="1">81%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.21 b</td><td align="left" rowspan="1" colspan="1">0.23 b</td><td align="left" rowspan="1" colspan="1">0.24 b</td></tr><tr><td align="left" rowspan="1" colspan="1">131-1</td><td align="left" rowspan="1" colspan="1">XP_006350060</td><td align="left" rowspan="1" colspan="1">2.E-07</td><td align="left" rowspan="1" colspan="1">55.8</td><td align="left" rowspan="1" colspan="1"><italic>Solanum tuberosum</italic></td><td align="left" rowspan="1" colspan="1">288</td><td align="left" rowspan="1" colspan="1">Tetraspanin-8-like</td><td align="left" rowspan="1" colspan="1">66%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.05 b</td><td align="left" rowspan="1" colspan="1">0.06 b</td><td align="left" rowspan="1" colspan="1">0.05 b</td></tr><tr><td align="left" rowspan="1" colspan="1">138-6</td><td align="left" rowspan="1" colspan="1">NP_973890</td><td align="left" rowspan="1" colspan="1">1.E-11</td><td align="left" rowspan="1" colspan="1">67.8</td><td align="left" rowspan="1" colspan="1"><italic>Arabidopsis thaliana</italic></td><td align="left" rowspan="1" colspan="1">237</td><td align="left" rowspan="1" colspan="1">COP9 signalosome complex subunit 5a</td><td align="left" rowspan="1" colspan="1">89%</td><td align="left" rowspan="1" colspan="1">1.00 c</td><td align="left" rowspan="1" colspan="1">1.80 b</td><td align="left" rowspan="1" colspan="1">2.53 a</td><td align="left" rowspan="1" colspan="1">0.24 d</td></tr><tr><td align="left" rowspan="1" colspan="1">141-9</td><td align="left" rowspan="1" colspan="1">XP_006476047</td><td align="left" rowspan="1" colspan="1">6.E-12</td><td align="left" rowspan="1" colspan="1">68.9</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">183</td><td align="left" rowspan="1" colspan="1">Ankyrin repeat-containing protein At3g12360-like</td><td align="left" rowspan="1" colspan="1">79%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.33 b</td><td align="left" rowspan="1" colspan="1">0.35 b</td><td align="left" rowspan="1" colspan="1">0.35 b</td></tr><tr><td align="left" rowspan="1" colspan="1">87-7</td><td align="left" rowspan="1" colspan="1">XP_006468682</td><td align="left" rowspan="1" colspan="1">2.E-25</td><td align="left" rowspan="1" colspan="1">107</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">232</td><td align="left" rowspan="1" colspan="1">WD repeat-containing protein 26-like isoform X1</td><td align="left" rowspan="1" colspan="1">98%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">12.03 a</td><td align="left" rowspan="1" colspan="1">1.70 b</td><td align="left" rowspan="1" colspan="1">2.06 b</td></tr><tr><td align="left" rowspan="1" colspan="1">178-5</td><td align="left" rowspan="1" colspan="1">XP_006475371</td><td align="left" rowspan="1" colspan="1">4.E-19</td><td align="left" rowspan="1" colspan="1">87.8</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">149</td><td align="left" rowspan="1" colspan="1">IAA-amino acid hydrolase ILR1-like 4-like</td><td align="left" rowspan="1" colspan="1">98%</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">+</td></tr><tr><td colspan="4" align="left" rowspan="1"><bold><italic>Gene regulation</italic></bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">188-3</td><td align="left" rowspan="1" colspan="1">ADL36732</td><td align="left" rowspan="1" colspan="1">4.E-09</td><td align="left" rowspan="1" colspan="1">60.5</td><td align="left" rowspan="1" colspan="1"><italic>Malus domestica</italic></td><td align="left" rowspan="1" colspan="1">228</td><td align="left" rowspan="1" colspan="1">HSF domain class transcription factor</td><td align="left" rowspan="1" colspan="1">53%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">1.09 a</td><td align="left" rowspan="1" colspan="1">0.28 b</td><td align="left" rowspan="1" colspan="1">1.01 a</td></tr><tr><td align="left" rowspan="1" colspan="1">23-1</td><td align="left" rowspan="1" colspan="1">XP_006466606</td><td align="left" rowspan="1" colspan="1">3.E-30</td><td align="left" rowspan="1" colspan="1">117</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">198</td><td align="left" rowspan="1" colspan="1">Heat shock factor protein HSF24-like</td><td align="left" rowspan="1" colspan="1">97%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">3.36 a</td><td align="left" rowspan="1" colspan="1">3.27 a</td><td align="left" rowspan="1" colspan="1">3.20 a</td></tr><tr><td align="left" rowspan="1" colspan="1">138-4</td><td align="left" rowspan="1" colspan="1">XP_007018496</td><td align="left" rowspan="1" colspan="1">4.E-03</td><td align="left" rowspan="1" colspan="1">44.3</td><td align="left" rowspan="1" colspan="1"><italic>Theobroma cacao</italic></td><td align="left" rowspan="1" colspan="1">261</td><td align="left" rowspan="1" colspan="1">PHD finger transcription factor</td><td align="left" rowspan="1" colspan="1">44%</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">+</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">139-1</td><td align="left" rowspan="1" colspan="1">XP_006468886</td><td align="left" rowspan="1" colspan="1">5.E-74</td><td align="left" rowspan="1" colspan="1">246</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">375</td><td align="left" rowspan="1" colspan="1">Putative pentatricopeptide repeat-containing protein At2g01510-like</td><td align="left" rowspan="1" colspan="1">98%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.57 b</td><td align="left" rowspan="1" colspan="1">0.57 b</td><td align="left" rowspan="1" colspan="1">1.11 a</td></tr><tr><td align="left" rowspan="1" colspan="1">177-3</td><td align="left" rowspan="1" colspan="1">NP_195386</td><td align="left" rowspan="1" colspan="1">4.E-05</td><td align="left" rowspan="1" colspan="1">49.7</td><td align="left" rowspan="1" colspan="1"><italic>Arabidopsis thaliana</italic></td><td align="left" rowspan="1" colspan="1">235</td><td align="left" rowspan="1" colspan="1">Pentatricopeptide repeat-containing protein</td><td align="left" rowspan="1" colspan="1">73%</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">+</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">27-4</td><td align="left" rowspan="1" colspan="1">XP_006467029</td><td align="left" rowspan="1" colspan="1">7.E-27</td><td align="left" rowspan="1" colspan="1">112</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">186</td><td align="left" rowspan="1" colspan="1">DNA-directed RNA polymerase II subunit 1-like isoform X3</td><td align="left" rowspan="1" colspan="1">98%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.14 b</td><td align="left" rowspan="1" colspan="1">1.04 a</td><td align="left" rowspan="1" colspan="1">0.97 a</td></tr><tr><td align="left" rowspan="1" colspan="1">132-1</td><td align="left" rowspan="1" colspan="1">XP_006479511</td><td align="left" rowspan="1" colspan="1">2.E-39</td><td align="left" rowspan="1" colspan="1">149</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">245</td><td align="left" rowspan="1" colspan="1">DNA repair and recombination protein RAD26-like isoform X3</td><td align="left" rowspan="1" colspan="1">99%</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">+</td></tr><tr><td align="left" rowspan="1" colspan="1">219-4</td><td align="left" rowspan="1" colspan="1">XP_006472001</td><td align="left" rowspan="1" colspan="1">3.E-15</td><td align="left" rowspan="1" colspan="1">76.6</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">189</td><td align="left" rowspan="1" colspan="1">DNA excision repair protein ERCC-1-like isoform X1</td><td align="left" rowspan="1" colspan="1">84%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">11.60 a</td><td align="left" rowspan="1" colspan="1">1.16 b</td><td align="left" rowspan="1" colspan="1">1.07 b</td></tr><tr><td align="left" rowspan="1" colspan="1">177-8</td><td align="left" rowspan="1" colspan="1">XP_006490371</td><td align="left" rowspan="1" colspan="1">1.E-10</td><td align="left" rowspan="1" colspan="1">65.5</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">165</td><td align="left" rowspan="1" colspan="1">DNA mismatch repair protein MSH3-like</td><td align="left" rowspan="1" colspan="1">97%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">1.02 a</td><td align="left" rowspan="1" colspan="1">0.22 b</td><td align="left" rowspan="1" colspan="1">0.21 b</td></tr><tr><td align="left" rowspan="1" colspan="1">134-13</td><td align="left" rowspan="1" colspan="1">BAK61840</td><td align="left" rowspan="1" colspan="1">2.E-16</td><td align="left" rowspan="1" colspan="1">82.8</td><td align="left" rowspan="1" colspan="1"><italic>Citrus unshiu</italic></td><td align="left" rowspan="1" colspan="1">182</td><td align="left" rowspan="1" colspan="1">Gag-pol polyprotein</td><td align="left" rowspan="1" colspan="1">70%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">0.04 c</td><td align="left" rowspan="1" colspan="1">0.04 c</td><td align="left" rowspan="1" colspan="1">3.25 a</td></tr><tr><td align="left" rowspan="1" colspan="1">134-4</td><td align="left" rowspan="1" colspan="1">XP_003614387</td><td align="left" rowspan="1" colspan="1">3.E-14</td><td align="left" rowspan="1" colspan="1">77.4</td><td align="left" rowspan="1" colspan="1"><italic>Medicago truncatula</italic></td><td align="left" rowspan="1" colspan="1">279</td><td align="left" rowspan="1" colspan="1">RRNA intron-encoded homing endonuclease</td><td align="left" rowspan="1" colspan="1">93%</td><td align="left" rowspan="1" colspan="1">+</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">246-2</td><td align="left" rowspan="1" colspan="1">XP_003614387</td><td align="left" rowspan="1" colspan="1">1.E-08</td><td align="left" rowspan="1" colspan="1">60.5</td><td align="left" rowspan="1" colspan="1"><italic>Medicago truncatula</italic></td><td align="left" rowspan="1" colspan="1">234</td><td align="left" rowspan="1" colspan="1">RRNA intron-encoded homing endonuclease</td><td align="left" rowspan="1" colspan="1">86%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">10.50 a</td><td align="left" rowspan="1" colspan="1">1.39 b</td><td align="left" rowspan="1" colspan="1">1.05 b</td></tr><tr><td align="left" rowspan="1" colspan="1">83-2</td><td align="left" rowspan="1" colspan="1">XP_003614389</td><td align="left" rowspan="1" colspan="1">3.E-22</td><td align="left" rowspan="1" colspan="1">97.1</td><td align="left" rowspan="1" colspan="1"><italic>Medicago truncatula</italic></td><td align="left" rowspan="1" colspan="1">210</td><td align="left" rowspan="1" colspan="1">RRNA intron-encoded homing endonuclease</td><td align="left" rowspan="1" colspan="1">87%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.13 b</td><td align="left" rowspan="1" colspan="1">1.13 a</td><td align="left" rowspan="1" colspan="1">0.12 b</td></tr><tr><td align="left" rowspan="1" colspan="1">162-5</td><td align="left" rowspan="1" colspan="1">XP_006473637</td><td align="left" rowspan="1" colspan="1">3.E-07</td><td align="left" rowspan="1" colspan="1">55.1</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">149</td><td align="left" rowspan="1" colspan="1">5'-3' exoribonuclease 3-like isoform X2</td><td align="left" rowspan="1" colspan="1">96%</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">+</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">246-5</td><td align="left" rowspan="1" colspan="1">XP_006472153</td><td align="left" rowspan="1" colspan="1">9.E-24</td><td align="left" rowspan="1" colspan="1">100</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">169</td><td align="left" rowspan="1" colspan="1">Pre-mRNA-splicing factor 38A-like</td><td align="left" rowspan="1" colspan="1">94%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">1.09 b</td><td align="left" rowspan="1" colspan="1">10.40 a</td><td align="left" rowspan="1" colspan="1">1.09 b</td></tr><tr><td colspan="4" align="left" rowspan="1"><bold><italic>Cell transport</italic></bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">175-7</td><td align="left" rowspan="1" colspan="1">XP_006489422.</td><td align="left" rowspan="1" colspan="1">3.E-06</td><td align="left" rowspan="1" colspan="1">49.7</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">136</td><td align="left" rowspan="1" colspan="1">Non-specific lipid-transfer protein-like protein At2g13820-like</td><td align="left" rowspan="1" colspan="1">96%</td><td align="left" rowspan="1" colspan="1">0 c</td><td align="left" rowspan="1" colspan="1">0 c</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.38 b</td></tr><tr><td align="left" rowspan="1" colspan="1">59-3</td><td align="left" rowspan="1" colspan="1">XP_007026766</td><td align="left" rowspan="1" colspan="1">7.E+00</td><td align="left" rowspan="1" colspan="1">33.9</td><td align="left" rowspan="1" colspan="1"><italic>Theobroma cacao</italic></td><td align="left" rowspan="1" colspan="1">243</td><td align="left" rowspan="1" colspan="1">Major facilitator superfamily protein, putative</td><td align="left" rowspan="1" colspan="1">32%</td><td align="left" rowspan="1" colspan="1">0 c</td><td align="left" rowspan="1" colspan="1">0 c</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.23 b</td></tr><tr><td align="left" rowspan="1" colspan="1">252-1</td><td align="left" rowspan="1" colspan="1">XP_006464865</td><td align="left" rowspan="1" colspan="1">4.E-34</td><td align="left" rowspan="1" colspan="1">126</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">275</td><td align="left" rowspan="1" colspan="1">Citrate-binding protein-like</td><td align="left" rowspan="1" colspan="1">77%</td><td align="left" rowspan="1" colspan="1">0 c</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0 c</td><td align="left" rowspan="1" colspan="1">0.35 b</td></tr><tr><td align="left" rowspan="1" colspan="1">141-8</td><td align="left" rowspan="1" colspan="1">XP_006473247</td><td align="left" rowspan="1" colspan="1">3.E-31</td><td align="left" rowspan="1" colspan="1">123</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">209</td><td align="left" rowspan="1" colspan="1">Patellin-2-like</td><td align="left" rowspan="1" colspan="1">84%</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">+</td></tr><tr><td align="left" rowspan="1" colspan="1">177-6</td><td align="left" rowspan="1" colspan="1">XP_007012650</td><td align="left" rowspan="1" colspan="1">2.E-03</td><td align="left" rowspan="1" colspan="1">43.5</td><td align="left" rowspan="1" colspan="1"><italic>Theobroma cacao</italic></td><td align="left" rowspan="1" colspan="1">202</td><td align="left" rowspan="1" colspan="1">Membrane lipoprotein</td><td align="left" rowspan="1" colspan="1">82%</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">+</td></tr><tr><td align="left" rowspan="1" colspan="1">134-5</td><td align="left" rowspan="1" colspan="1">XP_006469059</td><td align="left" rowspan="1" colspan="1">2.E-35</td><td align="left" rowspan="1" colspan="1">130</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">260</td><td align="left" rowspan="1" colspan="1">Ras-related protein RABA1f-like</td><td align="left" rowspan="1" colspan="1">95%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">3.37 a</td><td align="left" rowspan="1" colspan="1">0.16 c</td><td align="left" rowspan="1" colspan="1">2.79 a</td></tr><tr><td align="left" rowspan="1" colspan="1">19-3</td><td align="left" rowspan="1" colspan="1">XP_006467607</td><td align="left" rowspan="1" colspan="1">3.E-57</td><td align="left" rowspan="1" colspan="1">194</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">316</td><td align="left" rowspan="1" colspan="1">Protein transport protein Sec61 subunit alpha-like</td><td align="left" rowspan="1" colspan="1">94%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">7.14 a</td><td align="left" rowspan="1" colspan="1">6.69 a</td><td align="left" rowspan="1" colspan="1">6.77 a</td></tr><tr><td align="left" rowspan="1" colspan="1">180-2</td><td align="left" rowspan="1" colspan="1">XP_006480618</td><td align="left" rowspan="1" colspan="1">2.E-11</td><td align="left" rowspan="1" colspan="1">65.9</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">240</td><td align="left" rowspan="1" colspan="1">Syntaxin-71-like</td><td align="left" rowspan="1" colspan="1">79%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.06 b</td><td align="left" rowspan="1" colspan="1">1.14 a</td><td align="left" rowspan="1" colspan="1">0.05 b</td></tr><tr><td align="left" rowspan="1" colspan="1">162-4</td><td align="left" rowspan="1" colspan="1">XP_006487552</td><td align="left" rowspan="1" colspan="1">1.E-15</td><td align="left" rowspan="1" colspan="1">80.1</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">177</td><td align="left" rowspan="1" colspan="1">ADP-ribosylation factor GTPase-activating protein AGD3-like</td><td align="left" rowspan="1" colspan="1">100%</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">+</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">78-3</td><td align="left" rowspan="1" colspan="1">XP_006483372</td><td align="left" rowspan="1" colspan="1">3.E-11</td><td align="left" rowspan="1" colspan="1">66.2</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">147</td><td align="left" rowspan="1" colspan="1">Putative clathrin assembly protein At2g25430-like</td><td align="left" rowspan="1" colspan="1">97%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">1.02 a</td><td align="left" rowspan="1" colspan="1">1.06 a</td><td align="left" rowspan="1" colspan="1">0.10 b</td></tr><tr><td align="left" rowspan="1" colspan="1">136-8</td><td align="left" rowspan="1" colspan="1">XP_006472885</td><td align="left" rowspan="1" colspan="1">2.E-29</td><td align="left" rowspan="1" colspan="1">117</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">200</td><td align="left" rowspan="1" colspan="1">Target of Myb protein 1-like isoform X1</td><td align="left" rowspan="1" colspan="1">92%</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">+</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">87-5</td><td align="left" rowspan="1" colspan="1">AFX72760</td><td align="left" rowspan="1" colspan="1">5.E-32</td><td align="left" rowspan="1" colspan="1">124</td><td align="left" rowspan="1" colspan="1"><italic>Litchi chinensis</italic></td><td align="left" rowspan="1" colspan="1">236</td><td align="left" rowspan="1" colspan="1">ATP/ADP carrier protein, partial</td><td align="left" rowspan="1" colspan="1">97%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.16 b</td><td align="left" rowspan="1" colspan="1">0.10 b</td><td align="left" rowspan="1" colspan="1">0.13 b</td></tr><tr><td colspan="2" align="center" rowspan="1"><bold><italic>Cell wall modification</italic></bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">124-1</td><td align="left" rowspan="1" colspan="1">XP_006480190</td><td align="left" rowspan="1" colspan="1">1.E-12</td><td align="left" rowspan="1" colspan="1">70.1</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">149</td><td align="left" rowspan="1" colspan="1">Probable pectate lyase 8-like</td><td align="left" rowspan="1" colspan="1">94%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.08 b</td><td align="left" rowspan="1" colspan="1">1.03 a</td><td align="left" rowspan="1" colspan="1">0.07 b</td></tr><tr><td align="left" rowspan="1" colspan="1">17-1</td><td align="left" rowspan="1" colspan="1">XP_006493306</td><td align="left" rowspan="1" colspan="1">2.E-44</td><td align="left" rowspan="1" colspan="1">160</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">257</td><td align="left" rowspan="1" colspan="1">Probable pectinesterase/pectinesterase inhibitor 61-like</td><td align="left" rowspan="1" colspan="1">97%</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">+</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">51-1</td><td align="left" rowspan="1" colspan="1">XP_007042653</td><td align="left" rowspan="1" colspan="1">4.E-25</td><td align="left" rowspan="1" colspan="1">107</td><td align="left" rowspan="1" colspan="1"><italic>Theobroma cacao</italic></td><td align="left" rowspan="1" colspan="1">241</td><td align="left" rowspan="1" colspan="1">Glycosyl hydrolase family 10 protein, putative</td><td align="left" rowspan="1" colspan="1">65%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">0.11 c</td><td align="left" rowspan="1" colspan="1">0.09 c</td><td align="left" rowspan="1" colspan="1">1.64 a</td></tr><tr><td align="left" rowspan="1" colspan="1">148-1</td><td align="left" rowspan="1" colspan="1">XP_006469451</td><td align="left" rowspan="1" colspan="1">6.E-01</td><td align="left" rowspan="1" colspan="1">36.6</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">189</td><td align="left" rowspan="1" colspan="1">Fasciclin-like arabinogalactan protein 2-like</td><td align="left" rowspan="1" colspan="1">90%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">1.08 a</td><td align="left" rowspan="1" colspan="1">0.17 b</td><td align="left" rowspan="1" colspan="1">0.20 b</td></tr><tr><td colspan="4" align="left" rowspan="1"><bold><italic>Others (unknown/unclassified)</italic></bold></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"></td></tr><tr><td align="left" rowspan="1" colspan="1">204-2</td><td align="left" rowspan="1" colspan="1">XP_003588355</td><td align="left" rowspan="1" colspan="1">1.E-04</td><td align="left" rowspan="1" colspan="1">48.1</td><td align="left" rowspan="1" colspan="1"><italic>Medicago truncatula</italic></td><td align="left" rowspan="1" colspan="1">170</td><td align="left" rowspan="1" colspan="1">Mitochondrial protein, putative</td><td align="left" rowspan="1" colspan="1">88%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.59 b</td><td align="left" rowspan="1" colspan="1">1.09 a</td><td align="left" rowspan="1" colspan="1">0.57 b</td></tr><tr><td align="left" rowspan="1" colspan="1">149-1</td><td align="left" rowspan="1" colspan="1">XP_006480893</td><td align="left" rowspan="1" colspan="1">7.E-43</td><td align="left" rowspan="1" colspan="1">155</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">276</td><td align="left" rowspan="1" colspan="1">Uncharacterized protein LOC102616798</td><td align="left" rowspan="1" colspan="1">70%</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">+</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">159-2</td><td align="left" rowspan="1" colspan="1">XP_006468400.</td><td align="left" rowspan="1" colspan="1">2.E-13</td><td align="left" rowspan="1" colspan="1">73.2</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">219</td><td align="left" rowspan="1" colspan="1">Uncharacterized protein LOC102609810</td><td align="left" rowspan="1" colspan="1">78%</td><td align="left" rowspan="1" colspan="1">0 b</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0 b</td><td align="left" rowspan="1" colspan="1">0.99 a</td></tr><tr><td align="left" rowspan="1" colspan="1">179-1</td><td align="left" rowspan="1" colspan="1">NP_001169009</td><td align="left" rowspan="1" colspan="1">2.E-23</td><td align="left" rowspan="1" colspan="1">98.6</td><td align="left" rowspan="1" colspan="1"><italic>Zea mays</italic></td><td align="left" rowspan="1" colspan="1">318</td><td align="left" rowspan="1" colspan="1">Hypothetical protein</td><td align="left" rowspan="1" colspan="1">74%</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">+</td></tr><tr><td align="left" rowspan="1" colspan="1">180-5</td><td align="left" rowspan="1" colspan="1">XP_006421131</td><td align="left" rowspan="1" colspan="1">8.E-18</td><td align="left" rowspan="1" colspan="1">84.3</td><td align="left" rowspan="1" colspan="1"><italic>Citrus clementina</italic></td><td align="left" rowspan="1" colspan="1">260</td><td align="left" rowspan="1" colspan="1">Hypothetical protein CICLE_v10005475mg</td><td align="left" rowspan="1" colspan="1">87%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.06 b</td><td align="left" rowspan="1" colspan="1">0.07 b</td><td align="left" rowspan="1" colspan="1">0.07 b</td></tr><tr><td align="left" rowspan="1" colspan="1">187-2</td><td align="left" rowspan="1" colspan="1">XP_006492168</td><td align="left" rowspan="1" colspan="1">2.E-06</td><td align="left" rowspan="1" colspan="1">54.7</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">292</td><td align="left" rowspan="1" colspan="1">Uncharacterized protein LOC102628400</td><td align="left" rowspan="1" colspan="1">87%</td><td align="left" rowspan="1" colspan="1">1.00 c</td><td align="left" rowspan="1" colspan="1">4.51 b</td><td align="left" rowspan="1" colspan="1">1.23 c</td><td align="left" rowspan="1" colspan="1">9.38 a</td></tr><tr><td align="left" rowspan="1" colspan="1">19-2</td><td align="left" rowspan="1" colspan="1">NP_189331</td><td align="left" rowspan="1" colspan="1">7.E-18</td><td align="left" rowspan="1" colspan="1">85.9</td><td align="left" rowspan="1" colspan="1"><italic>Arabidopsis thaliana</italic></td><td align="left" rowspan="1" colspan="1">206</td><td align="left" rowspan="1" colspan="1">Uncharacterized protein</td><td align="left" rowspan="1" colspan="1">82%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">0.15 b</td><td align="left" rowspan="1" colspan="1">0.18 b</td><td align="left" rowspan="1" colspan="1">0.16 b</td></tr><tr><td align="left" rowspan="1" colspan="1">237-1</td><td align="left" rowspan="1" colspan="1">XP_006478809</td><td align="left" rowspan="1" colspan="1">2.E-46</td><td align="left" rowspan="1" colspan="1">163</td><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">263</td><td align="left" rowspan="1" colspan="1">Uncharacterized protein LOC102629577</td><td align="left" rowspan="1" colspan="1">100%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">5.24 a</td><td align="left" rowspan="1" colspan="1">1.19 b</td><td align="left" rowspan="1" colspan="1">5.21 a</td></tr><tr><td align="left" rowspan="1" colspan="1">249-1</td><td align="left" rowspan="1" colspan="1">XP_004499954</td><td align="left" rowspan="1" colspan="1">2.E-37</td><td align="left" rowspan="1" colspan="1">131</td><td align="left" rowspan="1" colspan="1"><italic>Cicer arietinum</italic></td><td align="left" rowspan="1" colspan="1">305</td><td align="left" rowspan="1" colspan="1">Uncharacterized protein LOC101515437</td><td align="left" rowspan="1" colspan="1">96%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">5.93 a</td><td align="left" rowspan="1" colspan="1">6.66 a</td><td align="left" rowspan="1" colspan="1">1.01 b</td></tr><tr><td align="left" rowspan="1" colspan="1">87-4</td><td align="left" rowspan="1" colspan="1">XP_006444509</td><td align="left" rowspan="1" colspan="1">4.E-14</td><td align="left" rowspan="1" colspan="1">74.3</td><td align="left" rowspan="1" colspan="1"><italic>Citrus clementina</italic></td><td align="left" rowspan="1" colspan="1">249</td><td align="left" rowspan="1" colspan="1">hypothetical protein CICLE_v10021318mg</td><td align="left" rowspan="1" colspan="1">97%</td><td align="left" rowspan="1" colspan="1">1.00 b</td><td align="left" rowspan="1" colspan="1">0.92 b</td><td align="left" rowspan="1" colspan="1">11.3 a</td><td align="left" rowspan="1" colspan="1">11.9 a</td></tr><tr><td align="left" rowspan="1" colspan="1">204-1</td><td align="left" rowspan="1" colspan="1">XP_003608262</td><td align="left" rowspan="1" colspan="1">1.E-09</td><td align="left" rowspan="1" colspan="1">60.5</td><td align="left" rowspan="1" colspan="1"><italic>Medicago truncatula</italic></td><td align="left" rowspan="1" colspan="1">252</td><td align="left" rowspan="1" colspan="1">hypothetical protein MTR_4g091430</td><td align="left" rowspan="1" colspan="1">76%</td><td align="left" rowspan="1" colspan="1">1.00 a</td><td align="left" rowspan="1" colspan="1">1.14 a</td><td align="left" rowspan="1" colspan="1">0.57 b</td><td align="left" rowspan="1" colspan="1">1.16 a</td></tr></tbody></table></alternatives><table-wrap-foot><fn id="t001fn001"><p><italic>Note</italic>. 2.5 B - Al: 2.5 μM B + 0 mM Al; 2.5 B + Al: 2.5 μM B + 1.2 mM Al; 20 B - Al: 20 μM B + 0 mM Al; 20 B + Al: 20 μM B + 1.2 mM Al.Ratio means the ratio of different treatments to control (set as 1). Usually, the control was 2.5 B - Al. If TDF was not detected in the treatment, the control would be 2.5 B + Al and so on.</p></fn><fn id="t001fn002"><p>0 means TDF was not detected in the treatment; + means TDF was detected only in the treatment.</p></fn><fn id="t001fn003"><p>Values are means of 3 replicates.</p></fn><fn id="t001fn004"><p>Differences among four treatments were analyzed by two (B) × two (Al) ANOVA.</p></fn><fn id="t001fn005"><p>Within a row, values followed by different letters indicate a significant difference at <italic>P</italic> < 0.05.</p></fn></table-wrap-foot></table-wrap><table-wrap id="pone.0115485.t002" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0115485.t002</object-id><label>Table 2</label><caption><title>Summary of differentially expressed TDFs in roots from <italic>Citrus grandis</italic> seedlings treated with two B (2.5 and 20 μM H<sub>3</sub>BO<sub>3</sub>) and two Al (0 and 1.2 mM AlCl<sub>3</sub>·6H<sub>2</sub>O) level.</title></caption><alternatives><graphic id="pone.0115485.t002g" xlink:href="pone.0115485.t002"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col></colgroup><thead><tr><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1">Total differentially expressed TDFs</th><th colspan="4" align="left" rowspan="1">Al-toxicity-responsive TDFs</th><th colspan="4" align="left" rowspan="1">20 μM B-responsive TDFs</th></tr><tr><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th colspan="2" align="center" rowspan="1">2.5 μM B</th><th colspan="2" align="center" rowspan="1">20 μM B</th><th colspan="2" align="center" rowspan="1">0 mM Al</th><th colspan="2" align="center" rowspan="1">1.2 mM Al</th></tr><tr><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1"></th><th align="left" rowspan="1" colspan="1">Up</th><th align="left" rowspan="1" colspan="1">Down</th><th align="left" rowspan="1" colspan="1">Up</th><th align="left" rowspan="1" colspan="1">Down</th><th align="left" rowspan="1" colspan="1">Up</th><th align="left" rowspan="1" colspan="1">Down</th><th align="left" rowspan="1" colspan="1">Up</th><th align="left" rowspan="1" colspan="1">Down</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">Metabolism</td><td align="left" rowspan="1" colspan="1">21</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">10</td><td align="left" rowspan="1" colspan="1">10</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">13</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">4</td></tr><tr><td align="left" rowspan="1" colspan="1">Stress response</td><td align="left" rowspan="1" colspan="1">10</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">7</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">0</td></tr><tr><td align="left" rowspan="1" colspan="1">Autophagy and senescence</td><td align="left" rowspan="1" colspan="1">15</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">9</td><td align="left" rowspan="1" colspan="1">6</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">6</td><td align="left" rowspan="1" colspan="1">4</td></tr><tr><td align="left" rowspan="1" colspan="1">Signal transduction and hormone</td><td align="left" rowspan="1" colspan="1">12</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">6</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">3</td></tr><tr><td align="left" rowspan="1" colspan="1">Gene regulation</td><td align="left" rowspan="1" colspan="1">15</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">5</td></tr><tr><td align="left" rowspan="1" colspan="1">Cell transport</td><td align="left" rowspan="1" colspan="1">12</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">3</td></tr><tr><td align="left" rowspan="1" colspan="1">Cell wall modification</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">2</td></tr><tr><td align="left" rowspan="1" colspan="1">Others</td><td align="left" rowspan="1" colspan="1">11</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">1</td></tr><tr><td align="left" rowspan="1" colspan="1">Total</td><td align="left" rowspan="1" colspan="1">100</td><td align="left" rowspan="1" colspan="1">25</td><td align="left" rowspan="1" colspan="1">36</td><td align="left" rowspan="1" colspan="1">35</td><td align="left" rowspan="1" colspan="1">29</td><td align="left" rowspan="1" colspan="1">22</td><td align="left" rowspan="1" colspan="1">36</td><td align="left" rowspan="1" colspan="1">30</td><td align="left" rowspan="1" colspan="1">22</td></tr></tbody></table></alternatives></table-wrap></sec><sec id="sec013"><title>Validation of cDNA-AFLP data</title><p>To validate the reliabiability of cDNA-AFLP expression patterns, 13 TDFs were selected for qRT-PCR analysis. Among these TDFs, 11 TDFs (i.e., TDFs #19-3, 54-2, 60-1, 83-2, 87-7, 157-6, 162-5, 178-4, 219-2, 219-3 and 243-1) matched well with the expression profiles observed with cDNA-AFLP (<xref rid="pone.0115485.g003" ref-type="fig">Fig. 3</xref>). This technique was thus validated in 84.7% of cases. In addition, a linear regression analysis between qRT-PCR results and cDNA-AFLP data was performed. The correlation coefficient (<italic>r</italic>) was 0.8501, demonstrating that the qPCR and cDNA-AFLP results were highly correlated (<xref rid="pone.0115485.s002" ref-type="supplementary-material">S2 Fig.</xref>). It is worth noting that <italic>5'-3' exoribonuclease 3-like isoform X2</italic> (TDF #162-5) was not included in the analysis because the TDF was detected only in 2.5 μM B + 1.2 mM Al-treated roots.</p><fig id="pone.0115485.g003" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0115485.g003</object-id><label>Fig 3</label><caption><title>Relative expression levels of 13 genes in roots from <italic>C</italic>. <italic>grandis seedlings</italic> treated with different B and Al levels.</title><p>(A) Protein transport protein Sec61 subunit alpha-like (TDF #19-3); (B) 40S ribosomal protein S2 (TDF #54-2); (C) Thioredoxin M-type 4 (TDF #60-1); (D) RRNA intron-encoded homing endonuclease (TDF #83-2); (E) Dehydration responsive protein (TDF #83-5); (F) WD repeat-containing protein 26-like isoform X1 (TDF #87-7); (G) Ras-related protein RABA1f-like (TDF #134-5); (H) Flavonol synthase/flavanone 3-hydroxylase-like (TDF #157-6); (I) 5'-3' exoribonuclease 3-like isoform X2 (TDF #162-5); (J) Thiosulfate sulfurtransferase 18-like isoform X1 (TDF #178-4); (K) Putative senescence-associated protein (TDF #219-2); (L) Adenine nucleotide alpha hydrolases-like superfamily protein (TDF #219-3) and (M) 2-alkenal reductase (NADP<sup>+</sup>- dependent)-like (TDF #243-1). Bars represent means ± SE (<italic>n</italic> = 4). Samples for qRT-PCR were run in at least three biological replicates with two technical replicates. Relative gene expression was calculated using ddCt algorithm. For the normalization of gene, citrus <italic>actin</italic> (GU911361.1) was used as an internal standard and the roots from 2.5 μM B + 0 mM Al-treated plants was used as reference sample, which was set to 1. Differences among four treatments were analyzed by 2 (B levels) × 2 (Al levels) ANOVA. Different letters indicate a significant difference at <italic>P</italic> < 0.05.</p></caption><graphic xlink:href="pone.0115485.g003"></graphic></fig></sec></sec><sec sec-type="conclusions" id="sec014"><title>Discussion</title><sec id="sec015"><title>B-induced amelioration of Al-toxicity in <italic>C</italic>. <italic>grandis</italic></title><p>Our results showed that the effects of Al-toxicity on root DW, shoot DW and root DW/shoot DW ratio was less pronounced under 20 μM B than under 2.5 μM B (<xref rid="pone.0115485.g001" ref-type="fig">Fig. 1A-C</xref>), demonstrating that B alleviated Al-toxicity in <italic>C</italic>. <italic>grandis</italic> seedlings. Our data and previous study showed that Al-toxicity increased or did not affect B concentration in roots (<xref rid="pone.0115485.g001" ref-type="fig">Fig. 1E</xref>), stems and leaves [<xref rid="pone.0115485.ref006" ref-type="bibr">6</xref>], meaning that B-induced mitigation of Al-toxicity was not caused by an increase in plant B concentration, as previously obtained on <italic>C</italic>. <italic>grandis</italic> [<xref rid="pone.0115485.ref006" ref-type="bibr">6</xref>], flax [<xref rid="pone.0115485.ref007" ref-type="bibr">7</xref>] and soybean [<xref rid="pone.0115485.ref039" ref-type="bibr">39</xref>]. Al-induced secretion of OA anions from roots has been known to be a major mechanism of Al-tolerance in plants [<xref rid="pone.0115485.ref040" ref-type="bibr">40</xref>]. Our results showed that Al-induced secretion of malate and citrate from +Al or -Al excised roots was not affected by B supply (<xref rid="pone.0115485.g002" ref-type="fig">Fig. 2</xref>), indicating that B-induced alleviation of Al-toxicity was not explained in this way. Al-tolerance of plants is associated not only with low Al uptake, but also with relatively little Al translocation from roots to shoots [<xref rid="pone.0115485.ref037" ref-type="bibr">37</xref>,<xref rid="pone.0115485.ref041" ref-type="bibr">41</xref>]. In +Al seedlings, root Al concentration did not differ between two B treatments (<xref rid="pone.0115485.g001" ref-type="fig">Fig. 1D</xref>), while B supply decreased stem and leaf Al concentration [<xref rid="pone.0115485.ref006" ref-type="bibr">6</xref>], meaning that relatively less amount of Al was transported from roots to leaves (shoots). This might contribute to B-induced alleviation of Al-toxicity in <italic>C</italic>. <italic>grandis</italic> seedlings.</p></sec><sec id="sec016"><title>Genes related to metabolism</title><p>Twenty one TDFs involved in metabolism were altered by B and Al interactions (Tables <xref rid="pone.0115485.t001" ref-type="table">1</xref> and <xref rid="pone.0115485.t002" ref-type="table">2</xref>). Phenolic compounds particularly flavonoid type phenolics have been shown to confer plant Al-tolerance <italic>via</italic> the dual mechanisms of antioxidation and Al chelation [<xref rid="pone.0115485.ref040" ref-type="bibr">40</xref>]. Tolrà et al. [<xref rid="pone.0115485.ref042" ref-type="bibr">42</xref>] showed that root concentrations of caffeic acid, catechol and catechin were higher in Al-tolerant maize cultivar than in sensitive cultivar. Our finding that the expression of two genes [i.e., <italic>flavonol synthase/flavanone 3-hydroxylase-like</italic> (TDF #157-6) and <italic>flavanone 3 hydroxylase-like protein</italic> (TDF #134-14)] involved in flavonoid biosynthesis was induced by Al-toxicity except for similar root expression level of gene encoding lavanone 3 hydroxylase-like protein between two Al-treatments under 20 μM B (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>). This indicated that Al-toxicity might upregulate root biosynthesis of flavonoids, thus enhancing plant Al-tolerance. However, B-induced alleviation of Al-toxicity could not be explained by this way, because the expression levels of the two genes in Al-treated roots were not higher under 20 μM B than under 2.5 μM B (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>).</p><p>Four differentially expressed TDFs (i.e., TDFs #149-2, 216-2, 250-3 and 51-12) involved in lipid metabolism were isolated from roots (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>), demonstrating that B and Al interactions might alter root lipid metabolism. Carboxylesterases, which hydrolyze esters of short-chain fatty acids, play roles in plant defense, development, and secondary metabolism [<xref rid="pone.0115485.ref043" ref-type="bibr">43</xref>]. Our results showed that root expression of <italic>probable carboxylesterase 12-like</italic> (TDF #149-2) and <italic>carboxylesterase 1-like</italic> (TDF #216-2) kept unchanged and decreased in response to Al-toxicity under 2.5 μM B, respectively, but increased under 20 μM B, and that their expression level in Al-treated roots were higher under 20 μM B than under 2.5 μM B (TDF #149-2) or similar between the two B-treatments (TDF #216-2) depending on TDFs. The acylation of sterols has been thought to play a key role in maintaining free sterol homeostasis in the cell membranes. In <italic>Arabidopsis</italic>, sterol ester formation is catalyzed by phospholipid:sterol acyltransferase (PSAT), which displays homology with the mammalian lecithin-cholesterol acyltransferase (LCAT) [<xref rid="pone.0115485.ref044" ref-type="bibr">44</xref>]. Bouvier-Navé et al. [<xref rid="pone.0115485.ref045" ref-type="bibr">45</xref>] showed that the concentration of sterol esters decreased in leaves of <italic>Arabidopsis psat1</italic> mutants accompanied by an early leaf senescence phenotype, demonstrating the involvement of <italic>PSAT1</italic> in plant sterol homeostasis and leaf senescence. We found that root expression of gene encoding lecithin-cholesterol acyltransferase-like 4-like (TDF #250-3) in Al-treated roots decreased under 2.5 μM B, and kept unchanged under 20 μM B, and that its expression level in +Al roots was higher under 20 μM B than under 2.5 μM B (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>). The observed higher expression levels of genes encoding carboxylesterases and lecithin-cholesterol acyltransferase-like 4-like in 20 μM B + 1.2 mM Al-treated roots might contribute to the Al-tolerance of plants grown under 20 μM B.</p><p>As shown in <xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>, 10 TDFs (i.e., TDFs #136-3, 141-5, 87-2, 138-5, 138-3, 134-12, 18-2, 178-4, 54-2 and 80-2) related to amino acid and protein metabolism was altered by B and Al interactions. Adenosylhomocysteinase, which catalyzes the reversible hydrolysis of S-adenosyl-L-homocysteine (SAH, a strong inhibitor of transmethylation) to adenosine and L-homocysteine, is essential for maintaining the methyl cycling by the removal of SAH [<xref rid="pone.0115485.ref046" ref-type="bibr">46</xref>]. Zhao et al. [<xref rid="pone.0115485.ref047" ref-type="bibr">47</xref>] showed that 0.005 mM sodium nitroprusside (SNP) ameliorated Cd-induced toxicity in rice (<italic>Oryza sativa</italic>) and increased the abundance of adenosylhomocysteinase-like in Cd-treated rice roots. Our results showed that root expression of <italic>adenosylhomocysteinase-like</italic> (TDF #136-3) remained unchanged in response to Al-toxicity under 2.5 μM B and greatly increased under 20 μM B, and that its expression level in +Al roots was higher under 20 μM B than under 2.5 μM B (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>). Thus, adenosylhomocysteinase-like might play a role in B-induced alleviation of Al-toxicity. In addition, B and Al interactions also affected root expression of gene encoding S-adenosylmethionine-dependent methyltransferase At5g37990-like (TDF #141-5), which is involved in a variety of methylation reactions, and of gene encoding phosphomethylpyrimidine synthase (TDF, #87-2), which catalyzes the synthesis of 4-amino-2-methyl-5-phosphomethylpyrimidine from aminoimidazole ribotide in a radical S-adenosyl-L-methionine-dependent reaction (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>).</p><p>Nicotianamine (NA) aminotransferase (NAAT) plays a key role in the synthesis of mugineic acid family phytosiderophores (MAs) in graminaceous plants through catalyzing the amino group transfer of NA [<xref rid="pone.0115485.ref048" ref-type="bibr">48</xref>]. Takahashi et al. [<xref rid="pone.0115485.ref049" ref-type="bibr">49</xref>] showed that introduction of the barley NAAT gene into the nongraminaceous plant tobacco (<italic>Nicotiana tabacum</italic>), which produces NA but not phytosiderophores, caused a shortage of NA and decreases in the concentrations of Cu, Fe and Zn in leaves and floral organs of transgenic plants, indicating a role for NA in long-distance translocation of these metals. The Al-induced upregulation of root gene encoding nicotianamine aminotransferase A-like isoform X3 (TDF #138-5, <xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>) might contribute to Al-tolerance of plants by reducing Al concentration in stems and leaves. However, increased biosynthesis of NA in <italic>Arabidopsis</italic> and tobacco enhanced the tolerance of plants to high levels of metals [<xref rid="pone.0115485.ref050" ref-type="bibr">50</xref>].</p><p><sc>LL</sc>-diaminopimelate aminotransferase is an enzyme involved in <italic>meso</italic>-diaminopimelate, a precursor of cell wall peptidoglycan and <sc>l</sc>-lysine in plants [<xref rid="pone.0115485.ref051" ref-type="bibr">51</xref>]. Tyrosine transaminase (also known as tyrosine aminotransferase) catalyzes the conversion of tyrosine to 4-hydroxyphenylpyruvic acid, a precursor for homogenetisic acid, plastoquinones and tocopherols, the latter of which function as radical scavengers and protect the plants against various stresses [<xref rid="pone.0115485.ref052" ref-type="bibr">52</xref>]. In this study, we first observed that root expression levels of genes encoding LL-diaminopimelate aminotransferase (TDF #138-3) and tyrosine transaminase family protein (TDF #134-12) kept unchanged in response to Al-toxicity under 2.5 μM B and decreased by Al-toxicity under 20 μM B (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>). It is unclear whether the two genes play a role in B-induced alleviation of Al-toxicity. Further studies are needed to answer this question.</p><p>Thiosulfate sulfurtransferase, which catalyzes the cyanide-dependent cleavage of thiosulfate to form thiocyanate and sulfite, is involved in sulfur metabolism, removal of cyanide, regulation of redox homeostasis, protection against biotic and abiotic stresses [<xref rid="pone.0115485.ref053" ref-type="bibr">53</xref>]. In this study, we observed that root expression of <italic>thiosulfate sulfurtransferase 18-like isoform X1</italic> (TDFs #18-2 and 178-4) decreased in response to Al-toxicity under 2.5 μM B, but increased under 20 μM B (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>). This implied that the gene might be involved in B-induced alleviation of Al-toxicity.</p><p>As shown in <xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>, five TDFs (i.e., TDFs #201-1, 25-4, 29-2,134-9 and 51-9) related to energy and carbohydrate metabolism were altered by B and Al interactions. Onda et al. [<xref rid="pone.0115485.ref054" ref-type="bibr">54</xref>] proposed that the interaction of root ferredoxin (Fd)-NADP reductase (FNR) with FD III played a key role in the efficient electron allocations from NADPH to Fd-dependent metabolism in root plastids. We found that root expression of gene encoding FNR, root isozyme 2 (TDF #201-1) upregulated in response to Al-toxicity under 20 μM B, which might be an adaptive response of plants to Al-toxicity. However, the abundance of FNR in <italic>Lotus corniculatus</italic> roots decreased in response to Al-toxicity [<xref rid="pone.0115485.ref055" ref-type="bibr">55</xref>].</p></sec><sec id="sec017"><title>Genes related to stress response</title><p>Al-induced overproduction of reactive oxygen species (ROS) and lipid peroxidation have been observed in the roots of many plants including triticale [<xref rid="pone.0115485.ref056" ref-type="bibr">56</xref>], potato (<italic>Solanum tuberosum</italic>) [<xref rid="pone.0115485.ref057" ref-type="bibr">57</xref>], wheat [<xref rid="pone.0115485.ref058" ref-type="bibr">58</xref>], <italic>Plantago algarbiensis</italic> [<xref rid="pone.0115485.ref059" ref-type="bibr">59</xref>] and soybean [<xref rid="pone.0115485.ref060" ref-type="bibr">60</xref>]. To cope with the oxidative damage, plant cells are equipped with a scavenging system composed of antioxidants and antioxidant enzymes. Al-induced increases in both protein levels (activities) and expression levels of antioxidant enzyme genes have been reported in the roots of rice [<xref rid="pone.0115485.ref061" ref-type="bibr">61</xref>], triticale [<xref rid="pone.0115485.ref056" ref-type="bibr">56</xref>] and wheat [<xref rid="pone.0115485.ref025" ref-type="bibr">25</xref>]. Xu et al. [<xref rid="pone.0115485.ref058" ref-type="bibr">58</xref>] showed that Al treatment increased root activities of antioxidant enzymes, as well as the concentrations of antioxidants [i.e., AsA and reduced glutathione (GSH)] in two wheat genotypes: Yangmai-5 (Al-sensitive) and Jian-864 (Al-tolerant), and that Al-treated Jian-864 root tips had higher total antioxidant capacity and lower lipid peroxidation compared with Yangmai-5. They proposed that the total antioxidant capacity might play an important role in wheat plant Al-tolerance. Although the expression levels of <italic>glutathione reductase</italic> (GR) and <italic>cytosolic-like and glutathione peroxidase 6</italic> (TDFs #164-1 and 217-2) did not differ between 2.5 and 20 μM B-treated roots under Al-stress, the mRNA level of gene encoding glutathione S-transferase (GST) zeta class-like isoform X1 (TDF #78-4) in +Al roots was higher under 20 μM B than under 2.5 μM B (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>). Houde and Diallo [<xref rid="pone.0115485.ref025" ref-type="bibr">25</xref>] observed that GST expression level was higher in Al-tolerant than Al-sensitive wheat roots, concluding that GST might play a role in the detoxification of Al and ROS. Ezaki et al. [<xref rid="pone.0115485.ref062" ref-type="bibr">62</xref>] showed that overexpression of <italic>GST</italic> in transgenic <italic>Arabidopsis</italic> plants conferred tolerance to both Al and oxidative stresses. Thus, the observed higher expression level of <italic>GST</italic> in +Al roots under 20 μM B compared with under 2.5 μM B might enhance the tolerance of plants to Al.</p><p>Thioredoxins (Trxs) play a key role in redox balance regulation through thiol-disulfide exchange reactions [<xref rid="pone.0115485.ref063" ref-type="bibr">63</xref>]. Zhang et al. [<xref rid="pone.0115485.ref064" ref-type="bibr">64</xref>] found that transgenic rice plants overexpressing <italic>OsTRXh1</italic> (a subgroup I h-type Trx in rice) accumulated less H<sub>2</sub>O<sub>2</sub> under salt stress, whereas more H<sub>2</sub>O<sub>2</sub> was accumulated in the extracellular space of <italic>OsTRXh1</italic> knockdown plants compared with wild-type plants, demonstrating that <italic>OsTRXh1</italic> might play an important role in Trx-associated redox state regulation and plant stress responses. Lemaire et al. [<xref rid="pone.0115485.ref065" ref-type="bibr">65</xref>] showed that the expression of <italic>Trxs m</italic> and <italic>h</italic> in <italic>Chlamydomonas reinhardtii</italic> cells was induced by heavy metals such as Cd and Hg, concluding that Trxs was involved in defense mechanisms against heavy metals. Our results showed that the expression of <italic>Trx m-type 4</italic> (TDF #60-1) was induced by Al-toxicity only in 20 μM B-treated roots (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>), suggesting that <italic>Trx m-type 4</italic> might play a role in enhancing Al-tolerance by alleviating Al-induced oxidative stress under 20 μM B.</p><p>2-Alkenal reductase (AER) catalyzes the reduction of the α,β-unsaturated bond of 2-alkenals to produce <italic>n</italic>-alkanals. Transgenic tobacco plants overexpressing <italic>Arabidopsis AER</italic> displayed improved tolerance to photooxidative stress [<xref rid="pone.0115485.ref066" ref-type="bibr">66</xref>]. Recently, Yin et al. [<xref rid="pone.0115485.ref067" ref-type="bibr">67</xref>] showed that the suppression of lipid peroxide-derived aldehydes by AER provided an efficient defense mechanism against Al-toxicity. Thus, the Al-induced increase in root expression level of gene encoding 2-alkenal reductase (NADP<sup>+</sup>- dependent)-like (TDF #243-1, <xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>) might contribute to plant Al-tolerance by the detoxification of reactive carbonyls.</p><p>Heat shock proteins (HSPs)/chaperones have been known to play a key role in protecting plants against stress. Our results showed that root expression of gene encoding putative chaperone DnaJ-domain superfamily protein (TDF #178-1) downregulated in response to Al-toxicity under 2.5 μM B, and did not change under 20 μM B, and its expression level in +Al roots was higher under 20 μM B than under 2.5 μM B (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>), indicating that chaperones might play a role in B-induced alleviation of Al-toxicity.</p><p>Al-toxicity inhibits root growth by damaging the roots functionally and structurally, which consequently decreases water uptake, eventually resulting in dehydration stress in plant roots [<xref rid="pone.0115485.ref040" ref-type="bibr">40</xref>]. Consequently, the expression of some dehydration stress-related genes might be induced in Al-treated roots. As expected, root <italic>dehydration responsive protein</italic> (TDF #83-5) was strongly induced by Al-toxicity regardless of B concentration in the nutrient solution (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>). In addition, root expression level of gene encoding adenine nucleotide alpha hydrolases-like superfamily protein (TDF #219-3), a universal stress protein-like, was upregulated by Al-toxicity (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>). These data indicated that the two genes might play a role in plant Al-tolerance.</p><p>To conclude, our data demonstrated that in addition to enhancing the total ability to scavenge ROS, other mechanisms (i.e., ARE and chaperone DnaJ-domain superfamily protein) might be involved in B-induced alleviation of Al-toxicity.</p></sec><sec id="sec018"><title>Genes related to autophagy and senescence</title><p>Autophagy is a process of self-degradation of cellular components including protein and organelle in a molecule degradation process in which cells recycle cytoplasmic nutrients and other cellular components when under stress conditions or during developmental transitions. This process can help plants to adapt the changing environment [<xref rid="pone.0115485.ref068" ref-type="bibr">68</xref>]. <italic>RNAi-AtATG18a</italic> transgenic <italic>Arabidopsis</italic> plants usually senesce earlier and are more sensitive to a variety of stressful conditions such as drought, salt and oxidative stresses compared with wild-type plants [<xref rid="pone.0115485.ref068" ref-type="bibr">68</xref>,<xref rid="pone.0115485.ref069" ref-type="bibr">69</xref>]. The observed lower expression level of <italic>autophagy 18H-like protein</italic> (TDF #158-1, <xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>) implied that root autophagy might be damaged by Al-toxicity, hence lowering plant Al-tolerance. However, B-induced alleviation of Al-toxicity can not be explained in this way, because the gene expression level in Al-treated roots kept unchanged regardless of B concentration in the nutrient solution (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>).</p><p>Senescence is a form of programmed cell death (PCD) and many senescence-associated genes (SAGs) have been identified in plants [<xref rid="pone.0115485.ref070" ref-type="bibr">70</xref>]. Al-toxicity results in premature cell maturation and senescence in plants [<xref rid="pone.0115485.ref071" ref-type="bibr">71</xref>]. Zhan et al. [<xref rid="pone.0115485.ref072" ref-type="bibr">72</xref>] showed that Al-induced PCD was promoted by <italic>AhSAG</italic>, a senescence-associated gene in peanut (<italic>Arachis hypoganea</italic>). Transgenic tobacco plants overexpressing <italic>AhSAG</italic> displayed lower ability of Al-tolerance than in antisense transgenic plants. In this study, we isolated nine differentially expressed TDFs encoding putative senescence-associated proteins (i.e., TDFs #2-1, 5-3, 139-8, 156-3, 141-7, 209-1, 217-1, 219-2 and 223-1). Their expression levels increased, decreased or kept unchanged in response to Al-toxicity depending on B concentration (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>), indicating that the whole progression of senescence in +Al roots was disturbed.</p><p>Protein degradation is the main biochemical process that occurs during plant senescence. Senescence associated proteases not only are involved in nutrient recycling, but also are involved in the regulation of the senescence process [<xref rid="pone.0115485.ref073" ref-type="bibr">73</xref>]. Differentially expressed <italic>SAGs</italic> isolated in our study, which participate in cellular protein degradation processes, included: <italic>cysteine proteinase 15A-like</italic> (TDF #176-9), <italic>aspartic proteinase-like protein 1-like</italic> (TDF #246-9), <italic>serine-type peptidase</italic> (TDF #87-3), <italic>ubiquitin carboxyl-terminal hydrolase 22-like</italic> (TDF #179-4) and <italic>ubiquitin receptor RAD23c-like</italic> (TDF #78-2). Root expression levels of these genes decreased or did not significantly change in response to Al-toxicity regardless of B concentration in the nutrient solution except that <italic>ubiquitin carboxyl-terminal hydrolase 22-like</italic> expression in 20 μM B-treated roots was upregulated by Al-toxicity (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>). These data also support above inference that the whole progression of senescence in +Al roots was disturbed.</p></sec><sec id="sec019"><title>Genes related to signal transduction and hormone</title><p>Calmodulin, together with other calcium (Ca)-binding proteins, has been suggested to participate in heavy metal signaling by binding to Ca<sup>2+</sup> [<xref rid="pone.0115485.ref074" ref-type="bibr">74</xref>]. Transgenic tobacco plants expressing a calmodulin-binding tobacco plasma membrane protein gene (designated NtCBP4, for <italic>N</italic>. <italic>tabacum</italic> calmodulin-binding protein) displayed enhanced Ni tolerance [<xref rid="pone.0115485.ref075" ref-type="bibr">75</xref>]. Okekeogbu et al. [<xref rid="pone.0115485.ref076" ref-type="bibr">76</xref>] observed that several Ca-binding proteins were induced in Al-treated tomato (<italic>Solanum lycopersicum</italic>) radicles, concluding that Ca-binding proteins might play a role in enhancing tomato plant tolerance to the secondary cellular stresses induced by Al-stress. Generally speaking, root expression levels of <italic>putative Ca-binding protein CML19-like</italic> (TDFs #19-4 and 19-5) were higher under 20 μM B than under 2.5 μM B regardless of Al concentration in the nutrient solution. This might related to the fact that the ameliorative effect of 20 μM B was better than that of 2.5 μM B.</p><p>Protein phosphorylation, a versatile post-translational modification (PTM), is involved in response to various environmental stresses including heavy metals (i.e., Mn, Cu, Cd and Al) [<xref rid="pone.0115485.ref038" ref-type="bibr">38</xref>,<xref rid="pone.0115485.ref074" ref-type="bibr">74</xref>,<xref rid="pone.0115485.ref076" ref-type="bibr">76</xref>,<xref rid="pone.0115485.ref077" ref-type="bibr">77</xref>]. Jonak et al. [<xref rid="pone.0115485.ref077" ref-type="bibr">77</xref>] showed that different kinase belonging to the MAPK family in alfalfa roots were induced by excessive Cd and Cu. Okekeogbu et al. [<xref rid="pone.0115485.ref076" ref-type="bibr">76</xref>] reported that MAPK was strongly induced in Al-treated tomato radicles. Zhou et al. [<xref rid="pone.0115485.ref038" ref-type="bibr">38</xref>] observed that Mn-toxicity decreased the expression levels of genes associated with phosphorylation except for enhanced expression of a <italic>MAPK 1</italic> gene in <italic>C</italic>. <italic>grandis</italic> leaves. Our results showed that all these differentially expressed genes [i.e., <italic>protein kinase 2B</italic> (TDF #89-2), <italic>MAPK</italic> (TDF #25-3), <italic>probable receptor-like protein kinase At5g47070-like isoform X1</italic> (TDF #140-2) and <italic>SRSF protein kinase 1-like isoform 1</italic> (TDF #246-3)] involved in phosphorylation were downregulated or not significantly affected by Al-toxicity depending on B supply and the kinds of protein kinase. Thus, phosphorylation of some proteins might be impaired in +Al roots. Like protein kinase, the transcript level of a gene [i.e., <italic>protein phopsphatase 2C</italic> (PP2C, TDF #51-15)] involved in dephosphorylation decreased or did not change in response to Al-toxicity depending on B supply (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>). This agrees with our previous report that the expression of <italic>putative protein phosphatase 2a</italic>, <italic>regulatory subunit</italic> was downregulated by Mn-toxicity in <italic>C</italic>. <italic>grandis</italic> leaves [<xref rid="pone.0115485.ref038" ref-type="bibr">38</xref>].</p><p>Tetraspanins, also called tetraspans or the transmembrane 4 superfamily (TM4SF), contain four transmembrane domains linked by a small outer loop (EC1), a larger outer loop (EC2) and a small inner loop (IL) and are involved in signaling pathways [<xref rid="pone.0115485.ref078" ref-type="bibr">78</xref>,<xref rid="pone.0115485.ref079" ref-type="bibr">79</xref>]. Root expression level of <italic>tetraspanins-8-like</italic> did not differ among B and Al combination except for a significant increase under 2.5 μM B + 0 mM Al (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>).</p><p>COP9 signalosome (CSN) complex, composing of eight subunits named CSN1 to CSN8 according to protein size, plays a role in diverse plant signaling pathways and developmental processes through regulating protein ubiquitination and degradation [<xref rid="pone.0115485.ref080" ref-type="bibr">80</xref>,<xref rid="pone.0115485.ref081" ref-type="bibr">81</xref>]. For example, RNA silencing of the <italic>Arabidopsis</italic> CSN5 subunit led to decreased auxin signaling. Gusmaroli et al. [<xref rid="pone.0115485.ref080" ref-type="bibr">80</xref>] observed that mutations in <italic>CSN5A</italic> caused a pleiotropic dominant negative phenotype, concluding that CSN<sup>CSN5A</sup> was the major player in the derubylation of <italic>Arabidopsis</italic> Cullin1. As shown in <xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>, the expression of <italic>COP9 signalosome complex subunit 5A</italic> (CSN5A; TDF #138-6) was upregulated in -Al roots and downregulated in +Al roots by 20 μM B, respectively, and was enhanced in 2.5 μM B-treated roots and decreased in 20 μM B-treated roots by Al. Okekeogbu et al. [<xref rid="pone.0115485.ref076" ref-type="bibr">76</xref>] observed that the abundance of CSN6 was enhanced in Al-treated radicles of seeds derived from Al-treated tomato plants.</p><p>Ankyrin repeat-containing proteins, one of the most protein sequence motifs, play a role in cytoskeleton interactions, mitochondrial, toxins or signal transduction by mediating protein-protein interactions [<xref rid="pone.0115485.ref082" ref-type="bibr">82</xref>]. Shen et al. [<xref rid="pone.0115485.ref083" ref-type="bibr">83</xref>] observed that ankyrin repeat-containing protein 2A (AKR2A) played a key role in the biogenesis of <italic>A</italic>. <italic>thaliana</italic> ascorbate peroxidase 3 (APX3) by binding specifically to a sequence in APX3 (i.e., a transmembrane domain plus a few basic amino acid residues), concluding that AKR2A was an essential molecular for peroxisomal membrane-bound APX3. Our results showed that the expression of AKR At3g12360-like gene was higher in roots treated with 2.5 μM B + 0 mM Al than in other roots (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>), meaning that +Al roots might have lower or similar APX activity compared with -Al roots depending on B supply. This disagrees with the previous reports that the abundance of APX in wheat roots [<xref rid="pone.0115485.ref084" ref-type="bibr">84</xref>] and the activities of APX in <italic>Allium cepa</italic> roots [<xref rid="pone.0115485.ref085" ref-type="bibr">85</xref>] and ‘Cleopatra’ tangerine (<italic>Citrus reshni</italic>) leaves [<xref rid="pone.0115485.ref086" ref-type="bibr">86</xref>] increased in response to Al-toxicity. The difference between the expression level of APX gene and its activity (protein level) in response to Al might be due to PTMs.</p><p>WD (also known as Trp-Asp or WD40 or β-transducin) motifs are characterized by a conserved core of 40–60 amino acids, which usually form a tertiary propeller structure. WD repeat-containing proteins participate in a variety of cellular processes including signal transduction, vesicular trafficking, transcriptional regulation, apoptosis, cytoskeletal dynamics, ribosomal RNA biogenesis, and cell cycle control [<xref rid="pone.0115485.ref087" ref-type="bibr">87</xref>–<xref rid="pone.0115485.ref090" ref-type="bibr">90</xref>]. Mishra et al. [<xref rid="pone.0115485.ref091" ref-type="bibr">91</xref>] found that a <italic>SiWD40</italic> identified from foxtail millet, whose promoter interacted with the dehydration response element, was induced by various stresses such as salinity, dehydration and ABA, concluding that WD40 proteins might play a role in stress tolerance of foxtail millet. Lee et al. [<xref rid="pone.0115485.ref092" ref-type="bibr">92</xref>] demonstrated that a WD40 protein from <italic>Brassica napus</italic> might play a role in salt stress through ABA-dependent and/or -independent signaling pathways. Thus, Al-induced upregulation of <italic>WD repeat-containing protein 26-like isoform X1</italic> (TDF #87-7) in 2.5 μM B-treated roots might be involved in Al-tolerance.</p><p>Hormones are involved in plant Al-toxicity [<xref rid="pone.0115485.ref093" ref-type="bibr">93</xref>–<xref rid="pone.0115485.ref095" ref-type="bibr">95</xref>]. As shown in <xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>, <italic>IAA-amino acid hydrolase ILR1-like 4-like</italic> (TDF #178-5) expression was detected only in 20 μM B + 1.2 mM Al-treated roots. Chen et al. [<xref rid="pone.0115485.ref096" ref-type="bibr">96</xref>] reported that IAA-amino acid hydrolase ILR1-like 3 was induced in Hg-stressed rice roots. IAA-amino acid hydrolase ILR1, which was initially isolated in A. thaliana, releases active IAA from conjugates through cleaving IAA-amino acid conjugates [<xref rid="pone.0115485.ref097" ref-type="bibr">97</xref>]. Thus, free IAA level might be enhanced in 20 μM B + 1.2 mM Al-treated roots. This agrees with the report that Al treatments led to accumulation of endogenous IAA in wheat roots [<xref rid="pone.0115485.ref096" ref-type="bibr">96</xref>]. Zhou et al. [<xref rid="pone.0115485.ref095" ref-type="bibr">95</xref>] observed that IAA level increased in the base of the root and decreased in the root tips of 100 μM Al-treated alfalfa. Agami and Mohamed [<xref rid="pone.0115485.ref098" ref-type="bibr">98</xref>] reported that IAA pretreatment alleviated Cd-toxicity in wheat seedlings through enhancing the activities of antioxidant enzymes. Therefore, Al-induced expression of <italic>IAA-amino acid hydrolase ILR1-like 4-like</italic> in 20 μM B-treated roots might be an adaptive response of <italic>C</italic>. <italic>grandis</italic> plants to Al-toxicity. In addition, Yang et al. [<xref rid="pone.0115485.ref094" ref-type="bibr">94</xref>] showed that IAA increased the Al-induced secretion of malic acid anions from wheat roots. However, Al-induced secretion of malate and citrate did not differ between 2.5 and 20 μM B-treated <italic>C</italic>. <italic>grandis</italic> roots (<xref rid="pone.0115485.g002" ref-type="fig">Fig. 2</xref>).</p><p>In conclusion, signal transduction and hormone metabolism might be involved in B-induced alleviation of Al-toxicity.</p></sec><sec id="sec020"><title>Genes related to gene regulation</title><p>As shown in <xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>, 15 TDFs (i.e., TDFs #188-3, 23-1, 138-4, 139-1, 177-3, 27-4, 132-1, 219-4, 177-8, 134-13, 134-4, 246-2, 83-2, 162-5 and 246-5) related to transcriptional regulation was altered by B and Al interactions. Al-induced changes in proteins and genes involved in gene regulation have also been observed in roots of soybean [<xref rid="pone.0115485.ref099" ref-type="bibr">99</xref>] and <italic>Arabidopsis</italic> [<xref rid="pone.0115485.ref100" ref-type="bibr">100</xref>].</p><p>Plant heat stress transcription factors (Hsfs), which are modular transcription factors, are involved in protective responses to various environmental stresses such as heat [<xref rid="pone.0115485.ref101" ref-type="bibr">101</xref>], heavy metals [<xref rid="pone.0115485.ref102" ref-type="bibr">102</xref>,<xref rid="pone.0115485.ref103" ref-type="bibr">103</xref>], and oxidative stress [<xref rid="pone.0115485.ref102" ref-type="bibr">102</xref>]. Shim et al. [<xref rid="pone.0115485.ref103" ref-type="bibr">103</xref>] showed that two orthologs of the plant class A4 Hsfs conferred Cd-tolerance in wheat and rice by enhancing the expression of Cd-tolerance gene, metallothionein. Using a dominant-negative approach, Davletova et al. [<xref rid="pone.0115485.ref104" ref-type="bibr">104</xref>] demonstrated that Hsfs were important sensors for H<sub>2</sub>O<sub>2</sub> and were required at a relatively early stage of the oxidative stress acclimation response. Our results showed that Al treatment led to increased expression of <italic>heat shock factor protein HSF24-lik</italic>e (TDF #23-1) in 2.5 μM B-treated roots (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>). This indicated that Hsfs might play a role in the tolerance of plants to Al-toxicity. However, this could not explain why the ameliorative effect of 20 μM B was better than that of 2.5 μM B, because the gene expression level did not differ among roots treated with 2.5 μM B + 1.2 mM Al, 20 μM B + 1.2 mM Al, and 20 μM B + 0 mM Al (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>). In addition, the expression level of HSF domain class transcription factor (TDF #188-3) did not differ among four B and Al combinations except for a significant decrease under 20 μM B + 0 mM Al (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>). It appears that the response of Hsfs to Al-toxicity depends on B supply and Hsf member.</p><p>Pentatricopeptide repeat (PPR) proteins are required for a variety of post-transcriptional processes including RNA editing, RNA splicing, RNA cleavage and translation in plant organelles. Disruption of genes encoding PPR proteins often leads to severe phenotypes [<xref rid="pone.0115485.ref105" ref-type="bibr">105</xref>,<xref rid="pone.0115485.ref106" ref-type="bibr">106</xref>]. Our results showed that root expression of gene encoding putative pentatricopeptide repeat-containing protein At2g01510-like (TDF #139-1) decreased in response to Al under 2.5 μM B, and increased under 20 μM B, and that its expression level in +Al roots was higher under 20 μM B than under 2.5 μM B (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>), which might contribute to the tolerance of 20 μM B-treated plants to Al-toxicity. However, the expression of <italic>pentatricopeptide repeat-containing protein</italic> (TDF #177-3) was detected only in 2.5 μM B + 1.2 mM Al-treated roots (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>).</p><p>DNA-directed RNA polymerases catalyze the transcription of DNA into RNA. Our results showed that root expression of gene encoding DNA-directed RNA polymerase II subunit 1-like isoform X3 (TDF #27-4) was strongly downregulated by Al under 2.5 μM B and was not significantly affected under 20 μM B (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>), meaning that root transcription might be impaired by Al under 2.5 μM B, hence lowering the Al-tolerance of plants.</p><p>Al-toxicity leads to a degradation of DNA molecules and an apoptosis-like cell death in plant roots [<xref rid="pone.0115485.ref085" ref-type="bibr">85</xref>,<xref rid="pone.0115485.ref107" ref-type="bibr">107</xref>]. Shaked et al. [<xref rid="pone.0115485.ref108" ref-type="bibr">108</xref>] demonstrated the role of At5g63950/CHR24, a RAD26-like gene, in <italic>Arabidopsis</italic> DNA damage response and recombination. Our results showed that the expression of gene encoding DNA repair and recombination protein RAD26-like isoform X3 (TDF #132-1) was detected only in 20 μM B + 1.2 mM Al-treated roots (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>), which might contribute to the Al-tolerance of plants grown under 20 μM B. However, root expression of gene encoding DNA excision repair protein ERCC-1-like isoform X1 (TDF #219-4) was induced by Al-toxicity only under 2.5 μM B (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>).</p><p>Gag-Pol polyprotein is cleaved by proteases into functional peptides, which have been suggested to be essential for basic replication [<xref rid="pone.0115485.ref109" ref-type="bibr">109</xref>]. Our results showed that root expression of <italic>Gag-pol polyprotein</italic> (TDF #134-13) increased in response to Al under 20 μM B, and decreased under 2.5 μM B, and that its expression level in +Al roots was higher under 20 μM B than under 2.5 μM B (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>). This implied that <italic>Gag-pol polyprotein</italic> might be involved in B-induced alleviation of Al-toxicity.</p></sec><sec id="sec021"><title>Genes related to cell transport</title><p>Twelve TDFs (i.e., TDFs #175-7, 59-3, 252-1, 141-8, 177-6, 134-5, 19-3, 180-2, 162-4, 78-3, 136-8 and 87-5) associated with cell transport in roots were altered by B and Al interactions (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>). Plant non-specific lipid transfer proteins (nsLTPs) are termed some LTPs which participate in the transfer of a broad range of lipids between membranes. Plant nsLTPs have been shown to play a role in mediating phospholipid transfer and the adaptation of plants to various environmental conditions [<xref rid="pone.0115485.ref110" ref-type="bibr">110</xref>]. Previous studies showed that root expression level of <italic>nsLTP</italic> (E30131) increased in response to Al-toxicity in Al-tolerant rice cultivar (Azucena), and decreased in Al-sensitive one (IR1552) [<xref rid="pone.0115485.ref111" ref-type="bibr">111</xref>], and that root mRNA level of <italic>LTPs</italic> was higher in Al-tolerant than in Al-sensitive soybean genotype [<xref rid="pone.0115485.ref021" ref-type="bibr">21</xref>]. The major facilitator superfamily (MFS), a class of membrane transport proteins, plays a role in plant metal homeostasis [<xref rid="pone.0115485.ref112" ref-type="bibr">112</xref>]. Haydon and Cobbett [<xref rid="pone.0115485.ref113" ref-type="bibr">113</xref>] showed that an <italic>Arabidopsis</italic> MFS member, Zinc-Induced Facilitator 1 (ZIF1) localized at the tonoplast, was involved in Zn-tolerance, demonstrating that MFS transporters might influence plant ion homeostasis. In addition, plant MFS transporters, which belong to the Pht1 and Pht4 families, regulate high- and low-affinity inorganic phosphate transport, respectively [<xref rid="pone.0115485.ref114" ref-type="bibr">114</xref>,<xref rid="pone.0115485.ref115" ref-type="bibr">115</xref>]. Our results showed that genes encoding non-specific lipid-transfer protein-like protein At2g13820-like (TDF #175-7) and putative MFS protein (TDF #59-3) were expressed only in 20 μM B-treated roots (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>), suggesting that the two genes might play a role in B-induced alleviation of Al-toxicity.</p><p>Citrate binding protein (CBP) is involved in plant vacuolar citrate transport [<xref rid="pone.0115485.ref116" ref-type="bibr">116</xref>]. Our finding that root expression level of citrate-binding protein-like gene (TDF #252-1) increased in response to Al-toxicity (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>) agrees with our results that Al-toxicity induced the secretion of citrate from roots (<xref rid="pone.0115485.g002" ref-type="fig">Fig. 2A</xref>). Interestingly, Al-induced upregulation of citrate-binding protein-like gene was lower under 20 μM B than under 2.5 μM B, which could be due to the amelioration of Al-toxicity by B.</p><p>Membrane traffic is required for normal cellular function by which molecules are transported between organelles in the post-Golgi network [<xref rid="pone.0115485.ref117" ref-type="bibr">117</xref>]. Peiter et al. [<xref rid="pone.0115485.ref118" ref-type="bibr">118</xref>] proposed a mechanism for metal tolerance involving membrane trafficking. Our results showed that root expression levels of genes encoding patellin-2-like, membrane lipoprotein, ADP-ribosylation factor GTPase-activating protein AGD3-like, Ras-related protein RABA1f-like and protein transport protein Sec61 subunit alpha-like (TDFs #141-8, 177-6, 162-4, 134-5 and 19-3) increased or kept unchanged in response to Al toxicity depending on B concentration in the nutrient solution (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>), indicating that the membrane traffic might be enhanced in Al-treated roots, thus conferring plant Al-tolerance. However, root expression levels of genes encoding syntaxin-71-like, putative clathrin assembly protein and target of Myb protein 1-like isoform X1 (TDFs #180-2, 78-3 and 136-8) decreased or did not change in response to Al-toxicity (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>).</p></sec><sec id="sec022"><title>Genes related to cell wall modification</title><p>Cell wall has been considered as the major site of Al-toxicity [<xref rid="pone.0115485.ref119" ref-type="bibr">119</xref>]. As expected, four TDFs (i.e. 124-1, 17-1, 51-1 and 148-1) involved in cell wall modification in roots were altered by B and Al interactions (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>). Our results showed that root expression of gene encoding putative glycosyl hydrolase family 10 protein (TDF #51-1), a family of glycoside hydrolases, decreased in response to Al-toxicity under 2.5 μM B and increased under 20 μM B, and that its expression level in +Al roots was higher under 20 μM B than under 2.5 μM B (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>). Duressa et al. [<xref rid="pone.0115485.ref021" ref-type="bibr">21</xref>] showed that the expression level of gene encoding glycosyl hydrolase family 3 protein/o-glycosyl cpds was higher in Al-tolerant than in Al-sensitive soybean genotype. Thus, glycosyl hydrolase might be involved in B-induced alleviation of Al-toxicity.</p><p>Pectate lyases degrade plant cell walls, causing tissue maceration and death [<xref rid="pone.0115485.ref120" ref-type="bibr">120</xref>]. We found that the expression of <italic>probable pectate lyase 8-like</italic> (TDF #124-1) in roots was down-regulated by Al-toxicity (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>), as previously obtained on Al-treated roots of aspen (<italic>Populus tremula</italic>) [<xref rid="pone.0115485.ref024" ref-type="bibr">24</xref>], indicating that pectate lyases might play a role in plant Al-tolerance. By contrast, the expression of gene encoding probable pectinesterase/pectinesterase inhibitor 61-like (TDF #17-1) was detected only in 2.5 μM B + 1.2 mM Al-treated roots (<xref rid="pone.0115485.t001" ref-type="table">Table 1</xref>), which disagrees with the previous report that Al downregulated alfalfa root expression of pectinesterase inhibitor gene [<xref rid="pone.0115485.ref022" ref-type="bibr">22</xref>].</p><p>In conclusion, we demonstrated the alleviation of Al-toxicity by B in <italic>C</italic>. <italic>grandis</italic> seedlings. The alleviation might be associated with relatively little Al transport from roots to leaves (shoots) rather than through increasing B concentration in roots and leaves, because its concentration was higher in +Al roots and leaves than in -Al ones. The molecular mechanisms underlying these processes are only beginning to understand. In this study, we first used the cDNA-AFLP to investigate the gene expression patterns in <italic>C</italic>. <italic>grandis</italic> roots in response to B and Al interactions, and successfully isolated 100 differentially expressed TDFs including some novel B-Al interaction responsive genes. B appears to alleviate Al-toxicity in <italic>C</italic>. <italic>grandis</italic> roots by the following several aspects: (<italic>a</italic>) improving the total ability to scavenge ROS and aldehydes; (<italic>b</italic>) increasing the expression levels of genes related to lipid (i.e., <italic>carboxylesterases and lecithin-cholesterol acyltransferase-like 4-like</italic>), amino acid (i.e., <italic>nicotianamine aminotransferase A-like isoform X3</italic>), S (i.e., <italic>thiosulfate sulfurtransferase 18-like isoform X1</italic>) and energy (<italic>i</italic>.<italic>e</italic>., FNR, root isozyme 2) metabolisms; and (<italic>c</italic>) upregulating gene expression related to cell transport (i.e., <italic>non-specific lipid-transfer protein-like protein At2g13820-like</italic> and <italic>MFS protein</italic>). In addition, genes related to Ca signal and hormone, gene regulation, and cell wall modification might also play a role in B-induced alleviation of Al-toxicity. Therefore, our study reveals some novel evidence for the B-induced alleviation of Al-toxicity at the transcriptional level, and increases our understanding of the molecular mechanisms on B-induced alleviation of Al-toxicity. Our results also are useful to us for obtaining the key genes responsible for plant Al-tolerance.</p></sec></sec><sec sec-type="supplementary-material" id="sec023"><title>Supporting Information</title><supplementary-material content-type="local-data" id="pone.0115485.s001"><label>S1 Fig</label><caption><title>A representative picture of a silver-stained cDNA-AFLP gel showing the differentially expressed TDFs in C. grandis roots in response to B and Al interactions using one EcoR I selective primer (EcoR I-AG) and nine Mes I selective primers (Mes I-CC, CG, CT, CA, GC, GG, GT, GA and TC).</title><p>1: 2.5 μM B + 0 mM Al; 2: 2.5 μM B + 1.2 mM Al; 3: 20 μM B + 0 mM Al; 4: 20 μM B + 1.2 mM Al. Arrows indicate differentially expressed TDFs.</p><p>(DOC)</p></caption><media xlink:href="pone.0115485.s001.doc"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="pone.0115485.s002"><label>S2 Fig</label><caption><title>Correlation analysis of qRT-PCR results and cDNA-AFLP data for selected genes.</title><p>Gene encoding 5'-3' exoribonuclease 3-like isoform X2 (TDF #162–5) was not included in the analysis because the TDF was detected only in 2.5 μM B + 1.2 mM Al-treated roots.</p><p>(DOC)</p></caption><media xlink:href="pone.0115485.s002.doc"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="pone.0115485.s003"><label>S1 Table</label><caption><title>Specific primer pairs used for qRT-PCR expression analysis.</title><p>(DOC)</p></caption><media xlink:href="pone.0115485.s003.doc"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material></sec></body><back><ref-list><title>References</title><ref id="pone.0115485.ref001"><label>1</label><mixed-citation publication-type="journal"><name><surname>Foy</surname><given-names>CD</given-names></name>, <name><surname>Chaney</surname><given-names>RL</given-names></name>, <name><surname>White</surname><given-names>MC</given-names></name> (<year>1978</year>) <article-title>The physiology of metal toxicity in plants</article-title>. <source>Annu Rev Plant Physiol</source><volume>29</volume>: <fpage>511</fpage>–<lpage>566</lpage>.</mixed-citation></ref><ref id="pone.0115485.ref002"><label>2</label><mixed-citation publication-type="journal"><name><surname>Kochian</surname><given-names>LV</given-names></name> (<year>1995</year>) <article-title>Cellular mechanism of aluminum toxicity and resistance in plants</article-title>. <source>Annu Rev Plant Physiol Plant Mol Biol</source><volume>46</volume>: <fpage>237</fpage>–<lpage>260</lpage>.</mixed-citation></ref><ref id="pone.0115485.ref003"><label>3</label><mixed-citation publication-type="journal"><name><surname>Rezaee</surname><given-names>F</given-names></name>, <name><surname>Ghanati</surname><given-names>F</given-names></name>, <name><surname>Behmanesh</surname><given-names>M</given-names></name> (<year>2013</year>) <article-title>Antioxidant activity and expression of catalase gene of (Eustoma grandiflorum L) in response to boron and aluminum</article-title>. <source>South Afr J Bot</source><volume>84</volume>: <fpage>13</fpage>–<lpage>18</lpage>.</mixed-citation></ref><ref id="pone.0115485.ref004"><label>4</label><mixed-citation publication-type="journal"><name><surname>LeNoble</surname><given-names>ME</given-names></name>, <name><surname>Blevins</surname><given-names>DG</given-names></name>, <name><surname>Sharp</surname><given-names>RE</given-names></name>, <name><surname>Cumbie</surname><given-names>BG</given-names></name> (<year>1996</year>) <article-title>Prevention of aluminum toxicity with supplemental boron.1. 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