PMRD: plant microRNA database
Identifieur interne : 001076 ( Pmc/Corpus ); précédent : 001075; suivant : 001077PMRD: plant microRNA database
Auteurs : Zhenhai Zhang ; Jingyin Yu ; Daofeng Li ; Zuyong Zhang ; Fengxia Liu ; Xin Zhou ; Tao Wang ; Yi Ling ; Zhen SuSource :
- Nucleic Acids Research [ 0305-1048 ] ; 2009.
Abstract
MicroRNAs (miRNA) are ∼21 nucleotide-long non-coding small RNAs, which function as post-transcriptional regulators in eukaryotes. miRNAs play essential roles in regulating plant growth and development. In recent years, research into the mechanism and consequences of miRNA action has made great progress. With whole genome sequence available in such plants as
Url:
DOI: 10.1093/nar/gkp818
PubMed: 19808935
PubMed Central: 2808885
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">PMRD: plant microRNA database</title><author><name sortKey="Zhang, Zhenhai" sort="Zhang, Zhenhai" uniqKey="Zhang Z" first="Zhenhai" last="Zhang">Zhenhai Zhang</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">State Key Laboratory of Plant Physiology and Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Yu, Jingyin" sort="Yu, Jingyin" uniqKey="Yu J" first="Jingyin" last="Yu">Jingyin Yu</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">State Key Laboratory of Plant Physiology and Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Li, Daofeng" sort="Li, Daofeng" uniqKey="Li D" first="Daofeng" last="Li">Daofeng Li</name><affiliation><nlm:aff id="AFF1">State Key Laboratory for Agricultural Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China</nlm:aff></affiliation></author><author><name sortKey="Zhang, Zuyong" sort="Zhang, Zuyong" uniqKey="Zhang Z" first="Zuyong" last="Zhang">Zuyong Zhang</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">State Key Laboratory of Plant Physiology and Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Liu, Fengxia" sort="Liu, Fengxia" uniqKey="Liu F" first="Fengxia" last="Liu">Fengxia Liu</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">State Key Laboratory of Plant Physiology and Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Zhou, Xin" sort="Zhou, Xin" uniqKey="Zhou X" first="Xin" last="Zhou">Xin Zhou</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">State Key Laboratory of Plant Physiology and Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Wang, Tao" sort="Wang, Tao" uniqKey="Wang T" first="Tao" last="Wang">Tao Wang</name><affiliation><nlm:aff id="AFF1">State Key Laboratory for Agricultural Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China</nlm:aff></affiliation></author><author><name sortKey="Ling, Yi" sort="Ling, Yi" uniqKey="Ling Y" first="Yi" last="Ling">Yi Ling</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">State Key Laboratory of Plant Physiology and Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Su, Zhen" sort="Su, Zhen" uniqKey="Su Z" first="Zhen" last="Su">Zhen Su</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">State Key Laboratory of Plant Physiology and Biochemistry</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">19808935</idno><idno type="pmc">2808885</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808885</idno><idno type="RBID">PMC:2808885</idno><idno type="doi">10.1093/nar/gkp818</idno><date when="2009">2009</date><idno type="wicri:Area/Pmc/Corpus">001076</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">PMRD: plant microRNA database</title><author><name sortKey="Zhang, Zhenhai" sort="Zhang, Zhenhai" uniqKey="Zhang Z" first="Zhenhai" last="Zhang">Zhenhai Zhang</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">State Key Laboratory of Plant Physiology and Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Yu, Jingyin" sort="Yu, Jingyin" uniqKey="Yu J" first="Jingyin" last="Yu">Jingyin Yu</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">State Key Laboratory of Plant Physiology and Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Li, Daofeng" sort="Li, Daofeng" uniqKey="Li D" first="Daofeng" last="Li">Daofeng Li</name><affiliation><nlm:aff id="AFF1">State Key Laboratory for Agricultural Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China</nlm:aff></affiliation></author><author><name sortKey="Zhang, Zuyong" sort="Zhang, Zuyong" uniqKey="Zhang Z" first="Zuyong" last="Zhang">Zuyong Zhang</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">State Key Laboratory of Plant Physiology and Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Liu, Fengxia" sort="Liu, Fengxia" uniqKey="Liu F" first="Fengxia" last="Liu">Fengxia Liu</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">State Key Laboratory of Plant Physiology and Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Zhou, Xin" sort="Zhou, Xin" uniqKey="Zhou X" first="Xin" last="Zhou">Xin Zhou</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">State Key Laboratory of Plant Physiology and Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Wang, Tao" sort="Wang, Tao" uniqKey="Wang T" first="Tao" last="Wang">Tao Wang</name><affiliation><nlm:aff id="AFF1">State Key Laboratory for Agricultural Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China</nlm:aff></affiliation></author><author><name sortKey="Ling, Yi" sort="Ling, Yi" uniqKey="Ling Y" first="Yi" last="Ling">Yi Ling</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">State Key Laboratory of Plant Physiology and Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Su, Zhen" sort="Su, Zhen" uniqKey="Su Z" first="Zhen" last="Su">Zhen Su</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">State Key Laboratory of Plant Physiology and Biochemistry</nlm:aff></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>MicroRNAs (miRNA) are ∼21 nucleotide-long non-coding small RNAs, which function as post-transcriptional regulators in eukaryotes. miRNAs play essential roles in regulating plant growth and development. In recent years, research into the mechanism and consequences of miRNA action has made great progress. With whole genome sequence available in such plants as <italic>Arabidopsis thaliana</italic>, <italic>Oryza sativa</italic>, <italic>Populus trichocarpa</italic>, <italic>Glycine max</italic>, etc., it is desirable to develop a plant miRNA database through the integration of large amounts of information about publicly deposited miRNA data. The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser. In total, there are 8433 miRNAs collected from 121 plant species in PMRD, including model plants and major crops such as <italic>Arabidopsis</italic>, rice, wheat, soybean, maize, sorghum, barley, etc. For <italic>Arabidopsis</italic>, rice, poplar, soybean, cotton, medicago and maize, we included the possible target genes for each miRNA with a predicted interaction site in the database. Furthermore, we provided miRNA expression profiles in the PMRD, including our local rice oxidative stress related microarray data (LC Sciences miRPlants_10.1) and the recently published microarray data for poplar, <italic>Arabidopsis</italic>, tomato, maize and rice. The PMRD database was constructed by open source technology utilizing a user-friendly web interface, and multiple search tools. The PMRD is freely available at <ext-link ext-link-type="uri" xlink:href="http://bioinformatics.cau.edu.cn/PMRD">http://bioinformatics.cau.edu.cn/PMRD</ext-link>. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-id journal-id-type="iso-abbrev">Nucleic Acids Res</journal-id><journal-id journal-id-type="publisher-id">nar</journal-id><journal-id journal-id-type="hwp">nar</journal-id><journal-title-group><journal-title>Nucleic Acids Research</journal-title></journal-title-group><issn pub-type="ppub">0305-1048</issn><issn pub-type="epub">1362-4962</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">19808935</article-id><article-id pub-id-type="pmc">2808885</article-id><article-id pub-id-type="doi">10.1093/nar/gkp818</article-id><article-id pub-id-type="publisher-id">gkp818</article-id><article-categories><subj-group subj-group-type="heading"><subject>Articles</subject></subj-group></article-categories><title-group><article-title>PMRD: plant microRNA database</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Zhenhai</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Yu</surname><given-names>Jingyin</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Daofeng</given-names></name><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Zuyong</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Fengxia</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zhou</surname><given-names>Xin</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Tao</given-names></name><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ling</surname><given-names>Yi</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Su</surname><given-names>Zhen</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="corresp" rid="COR1">*</xref></contrib></contrib-group><aff id="AFF1"><sup>1</sup>State Key Laboratory of Plant Physiology and Biochemistry and<sup>2</sup>State Key Laboratory for Agricultural Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China</aff><author-notes><corresp id="COR1">*To whom correspondence should be addressed. Tel: <phone>+86 10 62731380</phone>; Fax: <fax>+86 10 62731214</fax>; Email: <email>zhensu@cau.edu.cn</email></corresp></author-notes><pub-date pub-type="ppub"><month>1</month><year>2010</year></pub-date><pub-date pub-type="epub"><day>6</day><month>10</month><year>2009</year></pub-date><pub-date pub-type="pmc-release"><day>6</day><month>10</month><year>2009</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>38</volume><issue>Database issue</issue><issue-title>Database issue</issue-title><fpage>D806</fpage><lpage>D813</lpage><history><date date-type="received"><day>4</day><month>7</month><year>2009</year></date><date date-type="rev-recd"><day>27</day><month>8</month><year>2009</year></date><date date-type="accepted"><day>16</day><month>9</month><year>2009</year></date></history><permissions><copyright-statement>© The Author(s) 2009. Published by Oxford University Press.</copyright-statement><copyright-year>2009</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/2.5/uk/"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/2.5/uk/">http://creativecommons.org/licenses/by-nc/2.5/uk/</ext-link>) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>MicroRNAs (miRNA) are ∼21 nucleotide-long non-coding small RNAs, which function as post-transcriptional regulators in eukaryotes. miRNAs play essential roles in regulating plant growth and development. In recent years, research into the mechanism and consequences of miRNA action has made great progress. With whole genome sequence available in such plants as <italic>Arabidopsis thaliana</italic>, <italic>Oryza sativa</italic>, <italic>Populus trichocarpa</italic>, <italic>Glycine max</italic>, etc., it is desirable to develop a plant miRNA database through the integration of large amounts of information about publicly deposited miRNA data. The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser. In total, there are 8433 miRNAs collected from 121 plant species in PMRD, including model plants and major crops such as <italic>Arabidopsis</italic>, rice, wheat, soybean, maize, sorghum, barley, etc. For <italic>Arabidopsis</italic>, rice, poplar, soybean, cotton, medicago and maize, we included the possible target genes for each miRNA with a predicted interaction site in the database. Furthermore, we provided miRNA expression profiles in the PMRD, including our local rice oxidative stress related microarray data (LC Sciences miRPlants_10.1) and the recently published microarray data for poplar, <italic>Arabidopsis</italic>, tomato, maize and rice. The PMRD database was constructed by open source technology utilizing a user-friendly web interface, and multiple search tools. The PMRD is freely available at <ext-link ext-link-type="uri" xlink:href="http://bioinformatics.cau.edu.cn/PMRD">http://bioinformatics.cau.edu.cn/PMRD</ext-link>. We expect PMRD to be a useful tool for scientists in the miRNA field in order to study the function of miRNAs and their target genes, especially in model plants and major crops.</p></abstract></article-meta></front><body><sec><title>INTRODUCTION</title><p>MicroRNAs (microRNA) are ∼21 nucleotide-long endogenetic non-coding small RNAs and function as post-transcriptional regulators in eukaryotes. The processing of miRNA is well studied and is comprised of a discrete series of steps (<xref ref-type="bibr" rid="B1">1</xref>). miRNA genes are transcribed and excised into miRNAs, then miRNA is recruited by RISC (RNA-induced silencing complex, including Argonaute and other proteins) which combines with mRNA to inhibit or degrade the target mRNA (<xref ref-type="bibr" rid="B1">1</xref>) and thus translation is interrupted.</p><p>MiRNAs play essential roles in regulating plant growth and development (<xref ref-type="bibr" rid="B2">2</xref>). Research into miRNA function on target genes has progressed at a very rapid rate in plants. As examples, Archak <italic>et al.</italic> (<xref ref-type="bibr" rid="B3">3</xref>) discovered that miRNAs may participate in diverse functions including transcription, catalysis, binding and transporter activity. Some miRNAs related to abiotic stress responses such as cold stress and nutrient deprivation were identified in <italic>Arabidopsis thaliana</italic> using transcriptome analysis (<xref ref-type="bibr" rid="B4">4</xref>,<xref ref-type="bibr" rid="B5">5</xref>); Lu <italic>et al.</italic> (<xref ref-type="bibr" rid="B6">6</xref>) analyzed miRNA regulatory roles in the response <italic>of Populus trichocarpa</italic> to the stressful environment incurred over their long-term growth; Morin <italic>et al.</italic> conducted comparative analyses on the conservation of miRNAs between <italic>Pinus contorta</italic> and <italic>Oryza sativa</italic> and discovered that important RNA silencing processes were highly developed in the earliest spermatophytes (<xref ref-type="bibr" rid="B7">7</xref>).</p><p>Recently, more and more miRNAs have been identified in plant genomes. Jones-Rhoades <italic>et al.</italic> (<xref ref-type="bibr" rid="B8">8</xref>) developed comparative genomic approaches to systematically identify both miRNAs and target genes, which enlarged the miRNAs family and the number of target genes in <italic>A. thaliana</italic>. Using high-throughput sequencing, Rajagopalan <italic>et al.</italic> (<xref ref-type="bibr" rid="B9">9</xref>) identified 38 new miRNAs in <italic>A. thaliana</italic>. Using a similar approach, a large number of miRNAs were recently identified in rice (<xref ref-type="bibr" rid="B10">10</xref>). Using support vector machine classification based on intra-genomic matching of potential miRNAs and their targets, Lindow <italic>et al.</italic> (<xref ref-type="bibr" rid="B11">11</xref>) predicted ∼1200, ∼2100 and ∼2500 miRNA candidate genes in <italic>A. thaliana</italic>, <italic>O. sativa</italic> and <italic>P. trichocarpa</italic>, respectively. Using EST analysis, Zhang <italic>et al.</italic> (<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>) identified numerous new miRNAs in many species. Finally, Ramanjulu Sunkar and Guru Jagadeeswaran (<xref ref-type="bibr" rid="B14">14</xref>) identified miRNAs in a large number of plant species.</p><p>With the discovery of a large number of miRNAs and their target genes, some public resources have been constructed: miRBase (<ext-link ext-link-type="uri" xlink:href="http://microrna.sanger.ac.uk/">http://microrna.sanger.ac.uk/</ext-link>), provides a set of precursor and mature miRNAs discovered in many plants (<xref ref-type="bibr" rid="B15">15</xref>); ASRP (<ext-link ext-link-type="uri" xlink:href="http://asrp.cgrb.oregonstate.edu/">http://asrp.cgrb.oregonstate.edu/</ext-link>) lists miRNAs and their target genes in <italic>Arabidopsis</italic> (<xref ref-type="bibr" rid="B16">16</xref>); CSRDB (<ext-link ext-link-type="uri" xlink:href="http://sundarlab.ucdavis.edu/smrnas/">http://sundarlab.ucdavis.edu/smrnas/</ext-link>) is a collection of miRNAs identified in maize and rice (<xref ref-type="bibr" rid="B17">17</xref>); Rfam (<ext-link ext-link-type="uri" xlink:href="http://rfam.sanger.ac.uk/">http://rfam.sanger.ac.uk/</ext-link>) provides secondary structures of miRNA precursors in many plant species (<xref ref-type="bibr" rid="B18">18</xref>,<xref ref-type="bibr" rid="B19">19</xref>). However, there are limitations to the current databases in this field. For example, miRBase only provides miRNA sequence data and annotation in 25 plant species; Rfam only contains miRNA precursor sequences from less than 50 plant species; the ASRP integrates miRNAs, precursor, target genes and genome browser only for <italic>Arabidopsis</italic>. It is necessary to develop a plant miRNA database through integration of the large amount of information about plant miRNAs available to the public. For this purpose, we developed a plant microRNA database (PMRD) to integrate the available data pertinent to plant miRNAs available from public resources. Uniquely, we provided miRNA expression profiles in the PMRD, including our local generated rice oxidative stress microarray data and the recent published microarray data generated from poplar, <italic>Arabidopsis</italic>, tomato, maize and rice.</p></sec><sec><title>DATABASE CONTENT</title><sec><title>miRNA data collection</title><p>The majority of our data was gleaned from miRBase, Rfam and literature published in recent years. The number of mature miRNAs that we immediately retrieved from the miRBase was 1931, 73 miRNAs came from Rfam, and other miRNAs were from the literature. As shown in <xref ref-type="table" rid="T1">Table 1</xref>, we integrated 8433 non-redundant miRNA sequences and their original resources. Annotation of miRNAs was mainly dependent on information present in miRBase, but in some particular instances, the annotation included information about the corresponding author who discovered the miRNA. Detailed information concerning the variety of miRNAs in PMRD is presented in <xref ref-type="table" rid="T1">Table 1</xref>.
<table-wrap id="T1" position="float"><label>Table 1.</label><caption><p>Species and sources for raw miRNA data</p></caption><table frame="hsides" rules="groups"><thead align="left"><tr><th rowspan="2" colspan="1">Species</th><th colspan="3" align="center" rowspan="1">Number of miRNAs<hr></hr></th><th rowspan="2" colspan="1">References</th></tr><tr><th rowspan="1" colspan="1">Total</th><th rowspan="1" colspan="1">Experimental</th><th rowspan="1" colspan="1">Computational</th></tr></thead><tbody align="left"><tr><td rowspan="1" colspan="1"><italic>Aegilops speltoides</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Aegilops tauschii</italic></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Alliaria petiolata</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Allium cepa</italic></td><td rowspan="1" colspan="1">7</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">7</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Annona cherimola</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Antirrhinum majus</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Arabidopsis arenosa</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Arabidopsis cebennensis</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Arabidopsis halleri</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Arabidopsis thaliana</italic></td><td rowspan="1" colspan="1">1427</td><td rowspan="1" colspan="1">207</td><td rowspan="1" colspan="1">1220</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B2">2</xref>,<xref ref-type="bibr" rid="B4">4</xref>,<xref ref-type="bibr" rid="B8">8</xref>,<xref ref-type="bibr" rid="B9">9</xref>,<xref ref-type="bibr" rid="B11 B12 B13">11–13</xref>,<xref ref-type="bibr" rid="B16">16</xref>,<xref ref-type="bibr" rid="B41 B42 B43 B44 B45 B46 B47 B48 B49 B50 B51 B52 B53 B54 B55 B56 B57 B58">41–58</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Arabis hirsuta</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Arachis hypogaea</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B59">59</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Australopyrum velutinum</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Avena sativa</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Barbarea vulgaris</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Boechera stricta</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B14">14</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Brachypodium distachyon</italic></td><td rowspan="1" colspan="1">12</td><td rowspan="1" colspan="1">12</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B25">25</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Brachypodium sylvaticum</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Brassica napus</italic></td><td rowspan="1" colspan="1">45</td><td rowspan="1" colspan="1">45</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B50">50</xref>,<xref ref-type="bibr" rid="B60">60</xref>,<xref ref-type="bibr" rid="B61">61</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Brassica oleracea</italic></td><td rowspan="1" colspan="1">9</td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">8</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B14">14</xref>,<xref ref-type="bibr" rid="B50">50</xref>,<xref ref-type="bibr" rid="B62">62</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Brassica rapa</italic></td><td rowspan="1" colspan="1">20</td><td rowspan="1" colspan="1">20</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B14">14</xref>,<xref ref-type="bibr" rid="B50">50</xref>,<xref ref-type="bibr" rid="B62">62</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Camelina microcarpa</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Capsella rubella</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Capsicum annuum</italic></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Carica papaya</italic></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B14">14</xref>,<xref ref-type="bibr" rid="B63">63</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Chlamydomonas reinhardtii</italic></td><td rowspan="1" colspan="1">84</td><td rowspan="1" colspan="1">84</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B64">64</xref>,<xref ref-type="bibr" rid="B65">65</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Citrus clementina</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B14">14</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td rowspan="1" colspan="1">5</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">5</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Citrus × paradisi × Poncirus trifoliata</italic></td><td rowspan="1" colspan="1">4</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">4</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B14">14</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Conringia orientalis</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Corylus avellana</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Cycas rumphii</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Descurainia sophia</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Dictyostelium discoideum</italic></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B66">66</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Erysimum cheiri</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Eschscholzia californica</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Festuca arundinacea</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B14">14</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Festuca glaucescens × Lolium multiflorum</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Fourraea alpina</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Glycine clandestina</italic></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>,<xref ref-type="bibr" rid="B22">22</xref>,<xref ref-type="bibr" rid="B23">23</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Glycine max</italic></td><td rowspan="1" colspan="1">166</td><td rowspan="1" colspan="1">80</td><td rowspan="1" colspan="1">86</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>,<xref ref-type="bibr" rid="B20 B21 B22 B23">20–23</xref>,<xref ref-type="bibr" rid="B59">59</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Glycine soja</italic></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B22">22</xref>,<xref ref-type="bibr" rid="B23">23</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Gossypium arboreum</italic></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Gossypium herbaceum</italic></td><td rowspan="1" colspan="1">4</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">4</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B32">32</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Gossypium hirsutum</italic></td><td rowspan="1" colspan="1">53</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">53</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B30 B31 B32">30–32</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Gossypium raimondii</italic></td><td rowspan="1" colspan="1">11</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">11</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>,<xref ref-type="bibr" rid="B30">30</xref>,<xref ref-type="bibr" rid="B32">32</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Hedyotis centranthoides</italic></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Hedyotis terminalis</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Helianthus annuus</italic></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Henrardia persica</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Heteranthelium piliferum</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Hordeum vulgare</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B14">14</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Hordeum vulgare subsp. Spontaneum</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Hordeum vulgare subsp. Vulgare</italic></td><td rowspan="1" colspan="1">16</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">16</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Ipomoea batatas</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Ipomoea nil</italic></td><td rowspan="1" colspan="1">5</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">5</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Lactuca sativa</italic></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Liriodendron tulipifera</italic></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Lotus japonicus</italic></td><td rowspan="1" colspan="1">8</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">8</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>,<xref ref-type="bibr" rid="B22">22</xref>,<xref ref-type="bibr" rid="B59">59</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Lupinus luteus</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Malcolmia maritima</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Malus x domestica</italic></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Manihot esculenta</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B14">14</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Medicago truncatula</italic></td><td rowspan="1" colspan="1">76</td><td rowspan="1" colspan="1">36</td><td rowspan="1" colspan="1">40</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B13">13</xref>,<xref ref-type="bibr" rid="B20">20</xref>,<xref ref-type="bibr" rid="B22">22</xref>,<xref ref-type="bibr" rid="B59">59</xref>,<xref ref-type="bibr" rid="B67 B68 B69">67–69</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Nasturtium officinale</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Nicotiana benthamiana</italic></td><td rowspan="1" colspan="1">4</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">4</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Nicotiana sylvestris</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Nicotiana tabacum</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Nuphar advena</italic></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Oenocarpus bataua</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Oryza barthii</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Oryza brachyantha</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Oryza nivara</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Oryza rufipogon</italic></td><td rowspan="1" colspan="1">6</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">6</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Oryza sativa</italic></td><td rowspan="1" colspan="1">2540</td><td rowspan="1" colspan="1">269</td><td rowspan="1" colspan="1">2271</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B2">2</xref>,<xref ref-type="bibr" rid="B3">3</xref>,<xref ref-type="bibr" rid="B6 B7 B8">6–8</xref>,<xref ref-type="bibr" rid="B10 B11 B12 B13">10–13</xref>,<xref ref-type="bibr" rid="B28">28</xref>,<xref ref-type="bibr" rid="B52 B53 B54 B55">52–55</xref>,<xref ref-type="bibr" rid="B69 B70 B71 B72 B73 B74 B75 B76 B77 B78">69–78</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Panicum virgatum</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B14">14</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Pennisetum ciliare</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B14">14</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Pennisetum glaucum</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Peridictyon sanctum</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Persea americana</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Petunia x hybrida</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Phaseolus coccineus</italic></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Phaseolus vulgaris</italic></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B14">14</xref>,<xref ref-type="bibr" rid="B59">59</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Phleum pratense</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Physcomitrella patens</italic></td><td rowspan="1" colspan="1">282</td><td rowspan="1" colspan="1">281</td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B2">2</xref>,<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>,<xref ref-type="bibr" rid="B70">70</xref>,<xref ref-type="bibr" rid="B79 B80 B81 B82">79–82</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Picea glauca</italic></td><td rowspan="1" colspan="1">5</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">5</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Picea sitchensis</italic></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Pinus taeda</italic></td><td rowspan="1" colspan="1">40</td><td rowspan="1" colspan="1">24</td><td rowspan="1" colspan="1">16</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B6">6</xref>,<xref ref-type="bibr" rid="B7">7</xref>,<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>,<xref ref-type="bibr" rid="B77">77</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Populus tremula</italic></td><td rowspan="1" colspan="1">4</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">4</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Populus tremula × Populus tremuloides</italic></td><td rowspan="1" colspan="1">6</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">6</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B14">14</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Populus tremuloides</italic></td><td rowspan="1" colspan="1">7</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">7</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Populus trichocarpa</italic></td><td rowspan="1" colspan="1">2780</td><td rowspan="1" colspan="1">77</td><td rowspan="1" colspan="1">2703</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B2">2</xref>,<xref ref-type="bibr" rid="B6">6</xref>,<xref ref-type="bibr" rid="B11">11</xref>,<xref ref-type="bibr" rid="B13">13</xref>,<xref ref-type="bibr" rid="B83">83</xref>,<xref ref-type="bibr" rid="B84">84</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Populus trichocarpa × Populus deltoides</italic></td><td rowspan="1" colspan="1">5</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">5</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12 B13 B14">12–14</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Prunus armeniaca</italic></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Prunus persica</italic></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B14">14</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Prunus salicina</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Ricinus communis</italic></td><td rowspan="1" colspan="1">24</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">24</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Rorippa indica</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Saccharum officinarum</italic></td><td rowspan="1" colspan="1">32</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">32</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B14">14</xref>,<xref ref-type="bibr" rid="B20">20</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Saccharum sp</italic></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Schedonorus arundinaceus</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Secale cereale</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Selaginella moellendorffii</italic></td><td rowspan="1" colspan="1">64</td><td rowspan="1" colspan="1">64</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B79">79</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Sesamum indicum</italic></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Sibara virginica</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Solanum demissum</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Solanum lycopersicum</italic></td><td rowspan="1" colspan="1">37</td><td rowspan="1" colspan="1">21</td><td rowspan="1" colspan="1">16</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12 B13 B14">12–14</xref>,<xref ref-type="bibr" rid="B34">34</xref>,<xref ref-type="bibr" rid="B85">85</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Solanum tuberosum</italic></td><td rowspan="1" colspan="1">14</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">14</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12 B13 B14">12–14</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Sorghum bicolor</italic></td><td rowspan="1" colspan="1">76</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">76</td><td rowspan="1" colspan="1">(12–14,<xref ref-type="bibr" rid="B20">20</xref>,<xref ref-type="bibr" rid="B27">27</xref>,<xref ref-type="bibr" rid="B86">86</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Sorghum propinquum</italic></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Theobroma cacao</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Thlaspi arvense</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Trifolium repens</italic></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Triticum aestivum</italic></td><td rowspan="1" colspan="1">85</td><td rowspan="1" colspan="1">71</td><td rowspan="1" colspan="1">14</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>,<xref ref-type="bibr" rid="B24">24</xref>,<xref ref-type="bibr" rid="B25">25</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Triticum monococcum</italic></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Triticum turgidum</italic></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Triticum urartu</italic></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B19">19</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Vigna unguiculata</italic></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B22">22</xref>,<xref ref-type="bibr" rid="B59">59</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Vitis vinifera</italic></td><td rowspan="1" colspan="1">142</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">142</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B13">13</xref>,<xref ref-type="bibr" rid="B22">22</xref>,<xref ref-type="bibr" rid="B87">87</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Zea mays</italic></td><td rowspan="1" colspan="1">207</td><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">205</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>,<xref ref-type="bibr" rid="B20">20</xref>,<xref ref-type="bibr" rid="B26 B27 B28 B29">26–29</xref>)</td></tr><tr><td rowspan="1" colspan="1"><italic>Zinnia elegans</italic></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1">(<xref ref-type="bibr" rid="B12">12</xref>,<xref ref-type="bibr" rid="B13">13</xref>)</td></tr></tbody></table><table-wrap-foot><fn><p>The curation of miRNAs that are not included in miRBase or that have not yet been named was performed using a special format that includes information about the corresponding author. An example is osa-miRf10000-akr, a rice miRNA discovered by Anders Krogh’s group (<xref ref-type="bibr" rid="B11">11</xref>).</p></fn></table-wrap-foot></table-wrap></p><p>Recently in PMRD, there are 1427, 2540 and 2780 mature miRNA entries for <italic>Arabidopsi</italic>s, rice and poplar, respectively, while in miRBase the entries for these three species are 207, 415 and 237, respectively. The other miRNAs we curated from these three species mainly come from Lindow <italic>et al.</italic> (<xref ref-type="bibr" rid="B11">11</xref>). There are 166 soybean entries in PMRD, of which 79 sequences came from miRBase (<xref ref-type="bibr" rid="B15">15</xref>,<xref ref-type="bibr" rid="B20 B21 B22">20–22</xref>), and the others were from Zhang <italic>et al.</italic> (<xref ref-type="bibr" rid="B13">13</xref>,<xref ref-type="bibr" rid="B23">23</xref>). For wheat we deposited 85 miRNAs in PMRD, of which 32 came from miRBase (<xref ref-type="bibr" rid="B15">15</xref>,<xref ref-type="bibr" rid="B24">24</xref>) and the others were from Yao <italic>et al.</italic> (<xref ref-type="bibr" rid="B24">24</xref>), Zhang <italic>et al.</italic> (<xref ref-type="bibr" rid="B13">13</xref>) and Wei <italic>et al.</italic> (<xref ref-type="bibr" rid="B25">25</xref>). As for maize, 207 entries were created in PMRD, including 98 from miRBase (<xref ref-type="bibr" rid="B13">13</xref>,<xref ref-type="bibr" rid="B15">15</xref>,<xref ref-type="bibr" rid="B20">20</xref>,<xref ref-type="bibr" rid="B26 B27 B28">26–28</xref>) and 109 from Zhang <italic>et al.</italic> (<xref ref-type="bibr" rid="B13">13</xref>,<xref ref-type="bibr" rid="B29">29</xref>). For cotton we deposited 53 mature sequences in PRMD, in which 13 items were from miRBase (<xref ref-type="bibr" rid="B15">15</xref>,<xref ref-type="bibr" rid="B30">30</xref>), and the others were from Qiu <italic>et al.</italic> (<xref ref-type="bibr" rid="B31">31</xref>) and Zhang <italic>et al.</italic> (<xref ref-type="bibr" rid="B32">32</xref>). In total, there were 8433 miRNAs taken from 121 plant species integrated into PMRD.</p></sec><sec><title>miRNA expression profiling</title><p>In our PMRD database, we had already added data concerning miRNA expression profiling for several public miRNA expression data sets including maize miRNA-seq results (<xref ref-type="bibr" rid="B33">33</xref>), poplar cold stress-responsive miRNAs (<xref ref-type="bibr" rid="B6">6</xref>) (sample data shown in <ext-link ext-link-type="uri" xlink:href="http://nar.oxfordjournals.org/cgi/content/full/gkp818/DC1">Supplementary Figure S1</ext-link>), tomato miRNA expression in leaf tissue (<xref ref-type="bibr" rid="B34">34</xref>), <italic>Arabidopsis</italic> stress (cold, salt and osmotic stresses) regulated miRNAs (<xref ref-type="bibr" rid="B35">35</xref>), maize miRNAs responding to salt stress in roots (<xref ref-type="bibr" rid="B36">36</xref>), miRNA expression profiles generated from <italic>Arabidopsis</italic> grown at different temperatures (GEO: GSE11535), and rice miRNAs responding to drought stress (GEO: GSE5986), etc.</p><p>For example, in the data set for poplar cold stress, there were 75 probes for 168 miRNAs, and a total of 21 samples including seven time points collected in triplicate. As shown in <ext-link ext-link-type="uri" xlink:href="http://nar.oxfordjournals.org/cgi/content/full/gkp818/DC1">Supplementary Figure S1</ext-link>, the ratio represented the fold-change of poplar ptc-miR474b expression between cold treatment and control. We highlighted time points demonstrating a significant change in miRNA expression using <italic>P</italic> ≤ 0.01 as the cut-off.</p><p>In addition, we added our local rice oxidative stress related microarray data into PMRD. In order to investigate differences in expression levels of miRNAs in response to oxidative stress in rice, we conducted a series of experiments using the miRPlants_10.1 small RNA chip (LC Sciences, Houston, TX). One-week-old 9311 (rice Indica variety) seedling plants were incubated in a solution containing 10 μM methyl viologen (MV) (paraquat, an herbicide that induces oxidative stresses in plants) using water as a mock-treatment control, for 24 h. A total of four samples were examined in these experiments: 9311-CK01 and 9311-CK02 were controls and 9311-MV01 and 9311-MV02 were two samples treated with MV. Quantile normalization (<xref ref-type="bibr" rid="B37">37</xref>) was used to analyze the miRNA expression data. Within the total of 653 probes related to 1773 miRNAs representing 14 species in the chip, 18 probes showed significant differential expression (<italic>P</italic> ≤ 0.05, listed in <xref ref-type="table" rid="T2">Table 2</xref>) between MV treatment and mock, including 12 probes that were up-regulated and 6 probes that were down-regulated after MV treatment. Detailed relative expression levels of each probe are presented in the Expression page in the PMRD database. In this article, we present the example of osa-miR159a as <ext-link ext-link-type="uri" xlink:href="http://nar.oxfordjournals.org/cgi/content/full/gkp818/DC1">Supplementary Figure S2</ext-link>.
<table-wrap id="T2" position="float"><label>Table 2.</label><caption><p>Differentially expressed rice miRNAs after methyl viologen (MV) treatment</p></caption><table frame="hsides" rules="groups"><thead align="left"><tr><th rowspan="1" colspan="1">Probe ID</th><th rowspan="1" colspan="1">Log<sub>2</sub> ratio (MV/mock)</th><th rowspan="1" colspan="1"><italic>P</italic>-value</th><th rowspan="1" colspan="1">Target_Seq</th></tr></thead><tbody align="left"><tr><td rowspan="1" colspan="1">ptc-miR474c</td><td rowspan="1" colspan="1">2.17</td><td rowspan="1" colspan="1">3.67E−06</td><td rowspan="1" colspan="1">CAAAAGCUGUUGGGUUUGGCUGGG</td></tr><tr><td rowspan="1" colspan="1">ptc-miR474b</td><td rowspan="1" colspan="1">2.11</td><td rowspan="1" colspan="1">4.13E−05</td><td rowspan="1" colspan="1">CAAAAGUUGUUGGGUUUGGCUGGG</td></tr><tr><td rowspan="1" colspan="1">ptc-miR474a</td><td rowspan="1" colspan="1">2.08</td><td rowspan="1" colspan="1">1.49E−05</td><td rowspan="1" colspan="1">CAAAAGUUGCUGGGUUUGGCUGGG</td></tr><tr><td rowspan="1" colspan="1">tae-miR1125</td><td rowspan="1" colspan="1">1.66</td><td rowspan="1" colspan="1">1.12E−02</td><td rowspan="1" colspan="1">AACCAACGAGACCAACUGCGGCGG</td></tr><tr><td rowspan="1" colspan="1">ath-miR404</td><td rowspan="1" colspan="1">1.37</td><td rowspan="1" colspan="1">2.51E−05</td><td rowspan="1" colspan="1">AUUAACGCUGGCGGUUGCGGCAGC</td></tr><tr><td rowspan="1" colspan="1">ath-miR854a</td><td rowspan="1" colspan="1">0.80</td><td rowspan="1" colspan="1">7.00E−04</td><td rowspan="1" colspan="1">GAUGAGGAUAGGGAGGAGGAG</td></tr><tr><td rowspan="1" colspan="1">osa-miR169b</td><td rowspan="1" colspan="1">0.77</td><td rowspan="1" colspan="1">4.30E−02</td><td rowspan="1" colspan="1">CAGCCAAGGAUGACUUGCCGG</td></tr><tr><td rowspan="1" colspan="1">ppt-miR903</td><td rowspan="1" colspan="1">0.76</td><td rowspan="1" colspan="1">4.31E−02</td><td rowspan="1" colspan="1">GCUACUUCGGCGGGACAAGAGC</td></tr><tr><td rowspan="1" colspan="1">osa-miR529b</td><td rowspan="1" colspan="1">0.68</td><td rowspan="1" colspan="1">2.29E−03</td><td rowspan="1" colspan="1">GAGAAGAGAGAGAGUACAGC</td></tr><tr><td rowspan="1" colspan="1">osa-miR820a</td><td rowspan="1" colspan="1">0.66</td><td rowspan="1" colspan="1">7.61E−03</td><td rowspan="1" colspan="1">CGGCCUCGUGGAUGGACCAGG</td></tr><tr><td rowspan="1" colspan="1">ppt-miR900-5p</td><td rowspan="1" colspan="1">0.65</td><td rowspan="1" colspan="1">4.60E−02</td><td rowspan="1" colspan="1">UCCCAGGUACAAGAACACAGC</td></tr><tr><td rowspan="1" colspan="1">ppt-miR395</td><td rowspan="1" colspan="1">0.60</td><td rowspan="1" colspan="1">5.00E−03</td><td rowspan="1" colspan="1">CUGAAGCGUUUGGGGGAAGG</td></tr><tr><td rowspan="1" colspan="1">osa-miR159f</td><td rowspan="1" colspan="1">−0.76</td><td rowspan="1" colspan="1">5.86E−04</td><td rowspan="1" colspan="1">CUUGGAUUGAAGGGAGCUCUA</td></tr><tr><td rowspan="1" colspan="1">osa-miR396a</td><td rowspan="1" colspan="1">−0.81</td><td rowspan="1" colspan="1">2.72E−02</td><td rowspan="1" colspan="1">UUCCACAGCUUUCUUGAACUG</td></tr><tr><td rowspan="1" colspan="1">osa-miR159a</td><td rowspan="1" colspan="1">−0.83</td><td rowspan="1" colspan="1">1.19E−04</td><td rowspan="1" colspan="1">UUUGGAUUGAAGGGAGCUCUG</td></tr><tr><td rowspan="1" colspan="1">osa-miR397b</td><td rowspan="1" colspan="1">−0.99</td><td rowspan="1" colspan="1">6.99E−03</td><td rowspan="1" colspan="1">UUAUUGAGUGCAGCGUUGAUG</td></tr><tr><td rowspan="1" colspan="1">tae-miR1120</td><td rowspan="1" colspan="1">−1.08</td><td rowspan="1" colspan="1">2.36E−02</td><td rowspan="1" colspan="1">ACAUUCUUAUAUUAUGAGACGGAG</td></tr><tr><td rowspan="1" colspan="1">osa-miR396c</td><td rowspan="1" colspan="1">−1.22</td><td rowspan="1" colspan="1">1.36E−03</td><td rowspan="1" colspan="1">UUCCACAGCUUUCUUGAACUU</td></tr></tbody></table></table-wrap></p></sec><sec><title>miRNA target gene, genome browser and stem-loop information</title><p>In order to construct a collection of miRNA target genes, we mainly focused on <italic>Arabidopsis</italic>, rice, poplar, soybean, cotton, <italic>Medicago</italic> and maize. The target genes collection was curated from literature published in recent years. We also listed the location of interaction sites between miRNAs and target genes in <italic>Arabidopsis</italic> and rice [predicted by psRNATarget server (<xref ref-type="bibr" rid="B38">38</xref>,<xref ref-type="bibr" rid="B39">39</xref>)] in our database. Furthermore, we added information concerning miRNA action on target genes in <italic>Arabidopsis</italic>, rice and soybean into our local genome browser. We also provided the chromosomal location, secondary structure and dot matrix [generated by RNAfold (<xref ref-type="bibr" rid="B40">40</xref>)] of miRNA precursor sequences.</p></sec></sec><sec><title>ACCESS TO THE DATABASE</title><p>The PMRD website was constructed using Hypertext Markup Language (HTML), perl CGI (<ext-link ext-link-type="uri" xlink:href="http://www.perl.com">http://www.perl.com</ext-link>), and the MySQL 4.0 (<ext-link ext-link-type="uri" xlink:href="http://www.mysql.com">http://www.mysql.com</ext-link>) database engine. The detailed architecture of the database tables is presented in <ext-link ext-link-type="uri" xlink:href="http://nar.oxfordjournals.org/cgi/content/full/gkp818/DC1">Supplementary Figure S3</ext-link>. These tables are divided into three sections: the first section concerns miRNAs, the second section is about target genes, and the last is a presentation of miRNA expression profiles. The whole database is run on a server managed by the LINUX operating system.</p><p>The PMRD database web interface enables users to view and analyze each miRNA through either the Browse page or Search page. Detail information page (shown as <xref ref-type="fig" rid="F1">Figure 1</xref>) displays basic information for each unique miRNA. The evidence for each entry is either experimental or computational. We listed the methods used for experimentally demonstrated miRNAs and the programs applied for computational prediction. Within the total 8433 miRNAs in PMRD, 1297 of them were experimentally demonstrated and 7136 of them were from computational predictions (the detailed number shown in <xref ref-type="table" rid="T1">Table 1</xref>). Users can view a miRNA display in the local Genome Browser (shown as <ext-link ext-link-type="uri" xlink:href="http://nar.oxfordjournals.org/cgi/content/full/gkp818/DC1">Supplementary Figure S4</ext-link>) in which users can extract information about <italic>Arabidopsis</italic>, rice and soybean. Through PMRD, users can also inspect miRNA expression profiles, target gene list and predicted interaction sites between miRNA and cDNA. In additional, the secondary structure of miRNA precursor could be predicted by using the prediction tool in our PMRD database. All miRNA sequences are available for downloading.
<fig id="F1" position="float"><label>Figure 1.</label><caption><p> Sample page for detailed information regarding each unique miRNA. Contents of this page are divided into four parts (miRNA ath-MIR168a was used as an example): the first section concerns miRNA precursor, including sequence, stem-loop information, miRNA family and location in the whole genome; the second section is about the mature miRNA, including sequence, evidence and expression patterns; the third section concerns target genes: for <italic>Arabidopsis</italic> and rice, the target genes and sites were predicted by psRNATarget server (<xref ref-type="bibr" rid="B38">38</xref>) in default parameters; for poplar, soybean, cotton, medicago and maize, the listed genes were collected from the references. The last section includes the related references. The miRNA family and the evidence were based on the definition from miRBase, Rfam and the references.</p></caption><graphic xlink:href="gkp818f1"></graphic></fig></p><p>Currently, we have collected thousands of miRNA sequences from <italic>Arabidopsis</italic>, rice and poplar in our database, but for other species such as soybean, maize, wheat, cotton and sorghum, etc., the identified miRNAs are limited. Since this field is progressing rapidly due to new deep sequencing technologies, many more plant miRNAs will be discovered, as well as their target genes and expression profiles. The PMRD will be updated and maintained in order to integrate the newest plant miRNA data.</p></sec><sec><title>SUPPLEMENTARY DATA</title><p><ext-link ext-link-type="uri" xlink:href="http://nar.oxfordjournals.org/cgi/content/full/gkp818/DC1">Supplementary Data</ext-link> are available at NAR Online.</p></sec><sec><title>FUNDING</title><p>Ministry of Science and Technology of China grants (2008AA02Z312 and 2006CB100105). Funding for open access charge: Ministry of Science and Technology of China (2008AA02Z312 and 2006CB100105).</p><p><italic>Conflict of interest statement</italic>. None declared.</p></sec></body><back><ack><title>ACKNOWLEDGEMENTS</title><p>The authors thank Ms Wenying Xu for critical suggestions. 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