Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom
Identifieur interne : 001D24 ( Ncbi/Merge ); précédent : 001D23; suivant : 001D25Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom
Auteurs : Xiaoming Song [République populaire de Chine] ; Weike Duan [République populaire de Chine] ; Zhinan Huang [République populaire de Chine] ; Gaofeng Liu [République populaire de Chine] ; Peng Wu [République populaire de Chine] ; Tongkun Liu [République populaire de Chine] ; Ying Li [République populaire de Chine] ; Xilin Hou [République populaire de Chine]Source :
- Scientific Reports [ 2045-2322 ] ; 2015.
Abstract
In plants, flowering is the most important transition from vegetative to reproductive growth. The flowering patterns of monocots and eudicots are distinctly different, but few studies have described the evolutionary patterns of the flowering genes in them. In this study, we analysed the evolutionary pattern, duplication and expression level of these genes. The main results were as follows: (i) characterization of flowering genes in monocots and eudicots, including the identification of family-specific, orthologous and collinear genes; (ii) full characterization of CONSTANS-like genes in
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DOI: 10.1038/srep14631
PubMed: 26416765
PubMed Central: 4586889
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom</title><author><name sortKey="Song, Xiaoming" sort="Song, Xiaoming" uniqKey="Song X" first="Xiaoming" last="Song">Xiaoming Song</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University</institution>, Nanjing 210095,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology</institution>, Tangshan, Hebei 063000,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Duan, Weike" sort="Duan, Weike" uniqKey="Duan W" first="Weike" last="Duan">Weike Duan</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University</institution>, Nanjing 210095,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Huang, Zhinan" sort="Huang, Zhinan" uniqKey="Huang Z" first="Zhinan" last="Huang">Zhinan Huang</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University</institution>, Nanjing 210095,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Liu, Gaofeng" sort="Liu, Gaofeng" uniqKey="Liu G" first="Gaofeng" last="Liu">Gaofeng Liu</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University</institution>, Nanjing 210095,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Wu, Peng" sort="Wu, Peng" uniqKey="Wu P" first="Peng" last="Wu">Peng Wu</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University</institution>, Nanjing 210095,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Liu, Tongkun" sort="Liu, Tongkun" uniqKey="Liu T" first="Tongkun" last="Liu">Tongkun Liu</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University</institution>, Nanjing 210095,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Li, Ying" sort="Li, Ying" uniqKey="Li Y" first="Ying" last="Li">Ying Li</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University</institution>, Nanjing 210095,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Hou, Xilin" sort="Hou, Xilin" uniqKey="Hou X" first="Xilin" last="Hou">Xilin Hou</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University</institution>, Nanjing 210095,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26416765</idno><idno type="pmc">4586889</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4586889</idno><idno type="RBID">PMC:4586889</idno><idno type="doi">10.1038/srep14631</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000451</idno><idno type="wicri:Area/Pmc/Curation">000450</idno><idno type="wicri:Area/Pmc/Checkpoint">000561</idno><idno type="wicri:Area/Ncbi/Merge">001D24</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom</title><author><name sortKey="Song, Xiaoming" sort="Song, Xiaoming" uniqKey="Song X" first="Xiaoming" last="Song">Xiaoming Song</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University</institution>, Nanjing 210095,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology</institution>, Tangshan, Hebei 063000,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Duan, Weike" sort="Duan, Weike" uniqKey="Duan W" first="Weike" last="Duan">Weike Duan</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University</institution>, Nanjing 210095,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Huang, Zhinan" sort="Huang, Zhinan" uniqKey="Huang Z" first="Zhinan" last="Huang">Zhinan Huang</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University</institution>, Nanjing 210095,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Liu, Gaofeng" sort="Liu, Gaofeng" uniqKey="Liu G" first="Gaofeng" last="Liu">Gaofeng Liu</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University</institution>, Nanjing 210095,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Wu, Peng" sort="Wu, Peng" uniqKey="Wu P" first="Peng" last="Wu">Peng Wu</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University</institution>, Nanjing 210095,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Liu, Tongkun" sort="Liu, Tongkun" uniqKey="Liu T" first="Tongkun" last="Liu">Tongkun Liu</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University</institution>, Nanjing 210095,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Li, Ying" sort="Li, Ying" uniqKey="Li Y" first="Ying" last="Li">Ying Li</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University</institution>, Nanjing 210095,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Hou, Xilin" sort="Hou, Xilin" uniqKey="Hou X" first="Xilin" last="Hou">Xilin Hou</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University</institution>, Nanjing 210095,<country>China</country></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</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>In plants, flowering is the most important transition from vegetative to reproductive growth. The flowering patterns of monocots and eudicots are distinctly different, but few studies have described the evolutionary patterns of the flowering genes in them. In this study, we analysed the evolutionary pattern, duplication and expression level of these genes. The main results were as follows: (i) characterization of flowering genes in monocots and eudicots, including the identification of family-specific, orthologous and collinear genes; (ii) full characterization of CONSTANS-like genes in <italic>Brassica rapa</italic> (<italic>BraCOL</italic> genes), the key flowering genes; (iii) exploration of the evolution of <italic>COL</italic> genes in plant kingdom and construction of the evolutionary pattern of <italic>COL</italic> genes; (iv) comparative analysis of <italic>CO</italic> and <italic>FT</italic> genes between <italic>Brassicaceae</italic> and <italic>Grass</italic>, which identified several family-specific amino acids, and revealed that CO and FT protein structures were similar in <italic>B. rapa</italic> and <italic>Arabidopsis</italic> but different in rice; and (v) expression analysis of photoperiod pathway-related genes in <italic>B. rapa</italic> under different photoperiod treatments by RT-qPCR. This analysis will provide resources for understanding the flowering mechanisms and evolutionary pattern of <italic>COL</italic> genes. In addition, this genome-wide comparative study of <italic>COL</italic> genes may also provide clues for evolution of other flowering genes.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Putterill, J" uniqKey="Putterill J">J. Putterill</name></author><author><name sortKey="Laurie, R" uniqKey="Laurie R">R. Laurie</name></author><author><name sortKey="Macknight, R" uniqKey="Macknight R">R. Macknight</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mouhu, K" uniqKey="Mouhu K">K. Mouhu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Srikanth, A" uniqKey="Srikanth A">A. Srikanth</name></author><author><name sortKey="Schmid, M" uniqKey="Schmid M">M. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Sci Rep</journal-id><journal-id journal-id-type="iso-abbrev">Sci Rep</journal-id><journal-title-group><journal-title>Scientific Reports</journal-title></journal-title-group><issn pub-type="epub">2045-2322</issn><publisher><publisher-name>Nature Publishing Group</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26416765</article-id><article-id pub-id-type="pmc">4586889</article-id><article-id pub-id-type="pii">srep14631</article-id><article-id pub-id-type="doi">10.1038/srep14631</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Song</surname><given-names>Xiaoming</given-names></name><xref ref-type="aff" rid="a1">1</xref><xref ref-type="aff" rid="a2">2</xref><xref ref-type="author-notes" rid="n1">*</xref></contrib><contrib contrib-type="author"><name><surname>Duan</surname><given-names>Weike</given-names></name><xref ref-type="aff" rid="a1">1</xref><xref ref-type="author-notes" rid="n1">*</xref></contrib><contrib contrib-type="author"><name><surname>Huang</surname><given-names>Zhinan</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Gaofeng</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Wu</surname><given-names>Peng</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Tongkun</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Ying</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Hou</surname><given-names>Xilin</given-names></name><xref ref-type="corresp" rid="c1">a</xref><xref ref-type="aff" rid="a1">1</xref></contrib><aff id="a1"><label>1</label><institution>State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University</institution>, Nanjing 210095,<country>China</country></aff><aff id="a2"><label>2</label><institution>Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology</institution>, Tangshan, Hebei 063000,<country>China</country></aff></contrib-group><author-notes><corresp id="c1"><label>a</label><email>hxl@njau.edu.cn</email></corresp><fn id="n1"><label>*</label><p>These authors contributed equally to this work.</p></fn></author-notes><pub-date pub-type="epub"><day>29</day><month>09</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>5</volume><elocation-id>14631</elocation-id><history><date date-type="received"><day>05</day><month>03</month><year>2015</year></date><date date-type="accepted"><day>02</day><month>09</month><year>2015</year></date></history><permissions><copyright-statement>Copyright © 2015, Macmillan Publishers Limited</copyright-statement><copyright-year>2015</copyright-year><copyright-holder>Macmillan Publishers Limited</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><pmc-comment>author-paid</pmc-comment>
<license-p>This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link></license-p></license></permissions><abstract><p>In plants, flowering is the most important transition from vegetative to reproductive growth. The flowering patterns of monocots and eudicots are distinctly different, but few studies have described the evolutionary patterns of the flowering genes in them. In this study, we analysed the evolutionary pattern, duplication and expression level of these genes. The main results were as follows: (i) characterization of flowering genes in monocots and eudicots, including the identification of family-specific, orthologous and collinear genes; (ii) full characterization of CONSTANS-like genes in <italic>Brassica rapa</italic> (<italic>BraCOL</italic> genes), the key flowering genes; (iii) exploration of the evolution of <italic>COL</italic> genes in plant kingdom and construction of the evolutionary pattern of <italic>COL</italic> genes; (iv) comparative analysis of <italic>CO</italic> and <italic>FT</italic> genes between <italic>Brassicaceae</italic> and <italic>Grass</italic>, which identified several family-specific amino acids, and revealed that CO and FT protein structures were similar in <italic>B. rapa</italic> and <italic>Arabidopsis</italic> but different in rice; and (v) expression analysis of photoperiod pathway-related genes in <italic>B. rapa</italic> under different photoperiod treatments by RT-qPCR. This analysis will provide resources for understanding the flowering mechanisms and evolutionary pattern of <italic>COL</italic> genes. In addition, this genome-wide comparative study of <italic>COL</italic> genes may also provide clues for evolution of other flowering genes.</p></abstract></article-meta></front><floats-group><fig id="f1"><label>Figure 1</label><caption><title>The comparative analysis of flowering-related genes in angiosperms.</title><p>(<bold>a</bold>) The number of genes in each flowering-related pathway in six eudicots, four monocots and one basal angiosperm. Information regarding genome duplication or triplication was obtained from the Plant Genome Duplication Database (PGDD)<xref ref-type="bibr" rid="b70">70</xref>. (<bold>b</bold>) The Venn diagram shows the number of common and specific gene families and genes in 11 angiosperms. The first number in the brackets represents the number of gene families, and the second number represents the number of genes. The abbreviations represent the species as follows: <italic>Ath, Arabidopsis thaliana</italic>; <italic>Bra, Brassica rapa</italic>; <italic>Tca, Theobroma cacao</italic>; <italic>Ptr, Populus trichocarpa</italic>; <italic>Mtr, Medicago truncatula</italic>; <italic>Vvi, Vitis vinifera</italic>; <italic>Bdi, Brachypodium distachyon</italic>; <italic>Osa, Oryza sativa</italic>; <italic>Sbi, Sorghum bicolor</italic>; <italic>Zma, Zea mays</italic>; <italic>Atr, Amborella trichopoda</italic>.</p></caption><graphic xlink:href="srep14631-f1"></graphic></fig><fig id="f2"><label>Figure 2</label><caption><title>The features of the <italic>COL</italic> genes in <italic>B. rapa</italic>.</title><p>(<bold>a</bold>) The distribution of <italic>BraCOL</italic> genes on ten chromosomes. The 8 ancestral blocks and three subgenomes, including the least fractionated (LF), medium fractionated (MF1), and most fractionated (MF2) subgenomes, were plotted as described by Cheng <italic>et al.</italic> (2013). AK represents the ancestral karyotype. The orange lines connect the duplicated <italic>BraCOL</italic> genes. (<bold>b</bold>) The following three maps were constructed based on the orthologous and paralogous pair positions: Chinese cabbage (A01–A10) and <italic>Arabidopsis</italic> chromosome (Chr1–Chr5) maps (left), Chinese cabbage (A01–A10) and rice chromosome (Chr1–Chr12) maps (middle), and <italic>Arabidopsis</italic> (Chr1–Chr5) and rice chromosome (Chr1–Chr12) maps (right). The red lines represent the orthologous pairs between Chinese cabbage and <italic>Arabidopsis</italic>, the purple lines represent the orthologous pairs between Chinese cabbage and rice, and the light blue lines represent the orthologous pairs between <italic>Arabidopsis</italic> and rice. The blue, green, and orange lines represent the paralogous pairs in Chinese cabbage, <italic>Arabidopsis</italic>, and rice, respectively.</p></caption><graphic xlink:href="srep14631-f2"></graphic></fig><fig id="f3"><label>Figure 3</label><caption><title>The analysis of the B-box domains in Bryophyta, Pteridophyta, Gymnospermae and basal Angiospermae.</title><p>Ab1 and Ab2 represent the two B-box domains of group A, Cb1 and Cb2 represent the two B-box domains of group C, and Bb represents the one B-box domain of group B. (<bold>a</bold>) The phylogenetic tree of these five B-box sequences. (<bold>b</bold>) The genetic distance among the five B-box sequences. (<bold>c</bold>) The multiple sequence alignment of the five B-box domains. The abbreviations represent the species as follows: <italic>Atr, Amborella trichopoda</italic>; <italic>Pta, Pinus taeda</italic>; <italic>Psi, Picea sitchensis</italic>; <italic>Pab, Picea abies</italic>; <italic>Smo, Selaginella moellendorffii</italic>; <italic>Ppa, Physcomitrella patens</italic>.</p></caption><graphic xlink:href="srep14631-f3"></graphic></fig><fig id="f4"><label>Figure 4</label><caption><title>The evolutionary history pattern of <italic>COL</italic> genes in the plant kingdom.</title><p>The tick and cross marks indicate that group B originated from G1. Ab and Cb represent the B-box domains of group A and group C genes that contained only one B-box domain.</p></caption><graphic xlink:href="srep14631-f4"></graphic></fig><fig id="f5"><label>Figure 5</label><caption><title>The comparative analysis of <italic>CO</italic> genes between <italic>Brassicaceae</italic> and <italic>Grass</italic> species.</title><p>(<bold>a</bold>) The multiple sequence alignment of <italic>CO</italic> genes. The orange solid rectangle represents the five <italic>Brassicaceae</italic> species, and the green solid rectangle represents the three <italic>Grass</italic> species. The red hollow rectangle indicates the family-specific amino acids. (<bold>b</bold>) The phylogenetic trees were constructed using the <italic>CO</italic> protein and gene sequences. The numbers on the branches of the phylogenetic tree represent the bootstrap supports provided by the NJ, ME and ML methods. (<bold>c</bold>) The genetic distance in <italic>Brassicaceae</italic> and <italic>Grass</italic> was estimated using the <italic>CO</italic> protein and gene sequences.</p></caption><graphic xlink:href="srep14631-f5"></graphic></fig><fig id="f6"><label>Figure 6</label><caption><title>The protein structure of CO in <italic>Arabidopsis</italic>, Chinese cabbage and rice.</title><p>The nine family-specific amino acids located in the two B-box domains are marked on the protein structure. The orange solid rectangle represents the hydrophilic amino acids, and the blue solid rectangle indicates the hydrophobic amino acids.</p></caption><graphic xlink:href="srep14631-f6"></graphic></fig><fig id="f7"><label>Figure 7</label><caption><title>The analysis of the expression of photoperiod pathway and circadian clock-related genes by RT-qPCR.</title><p>The bars correspond to the means ± S.D. from three independent experiments. D and N represent day and night, respectively. The RNA expression level relative to the <italic>actin</italic> gene was calculated using the 2<sup>−ΔΔCT</sup> method and was thenlog2-transformed. (<bold>a</bold>) The relative expression of <italic>CDF1</italic> and <italic>FKF1</italic> genes in Chinese cabbage under LD conditions over a one-day period. (<bold>b</bold>) The relative expression of <italic>CDF1</italic> and <italic>FKF1</italic> genes in Chinese cabbage under SD conditions over a one-day period. (<bold>c</bold>) The relative expression of <italic>CO</italic> and <italic>FT</italic> genes in Chinese cabbage under LD conditions over a one-day period. (<bold>d</bold>) The relative expression of <italic>CO</italic> and <italic>FT</italic> genes in Chinese cabbage under SD conditions over a one-day period.</p></caption><graphic xlink:href="srep14631-f7"></graphic></fig><table-wrap position="float" id="t1"><label>Table 1</label><caption><title>The numbers located below the diagonal represent the percentage of collinear ortholog pairs (collinear ortholog pairs number/number of all ortholog pairs) in the genomes of 11 angiosperms. The numbers located above the diagonal represent the percentage of collinear ortholog pairs in the flowering genes of 11 angiosperms.</title></caption><graphic xlink:href="srep14631-t1"></graphic><table-wrap-foot><fn id="t1-fn1"><p>Note: The abbreviations represent the species as follows: <italic>Ath, Arabidopsis thaliana; Bra, Brassica rapa; Tca, Theobroma cacao; Ptr, Populus trichocarpa; Mtr, Medicago truncatula; Vvi, Vitis vinifera; Bdi, Brachypodium distachyon; Osa, Oryza sativa; Sbi, Sorghum bicolor; Zma, Zea mays; Atr, Amborella trichopoda</italic>. The orange colour represents the percentage of collinear ortholog pairs within eudicot species, the green colour represents the percentage of collinear ortholog pairs within monocot species, the blue colour represents the percentage of collinear ortholog pairs between eudicot and monocot species, and the yellow colour represents the percentage of collinear ortholog pairs between Amborella trichopoda and other angiosperm species.</p></fn></table-wrap-foot></table-wrap><table-wrap position="float" id="t2"><label>Table 2</label><caption><title>Calculation of Ka/Ks and the divergence time of the duplicated <italic>COL</italic> gene pairs in Chinese cabbage and <italic>Arabidopsis</italic>.</title></caption><table frame="hsides" rules="groups" border="1"><colgroup><col align="left"></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="center"></col></colgroup><thead valign="bottom"><tr><th align="left" valign="top" charoff="50">Duplicated gene pairs</th><th align="center" valign="top" charoff="50">Ka</th><th align="center" valign="top" charoff="50">Ks</th><th align="center" valign="top" charoff="50">Ka/Ks</th><th align="center" valign="top" charoff="50"><italic>P-Value</italic>(Fisher)</th><th align="center" valign="top" charoff="50">Duplication type</th><th align="center" valign="top" charoff="50">Purify selection</th><th align="center" valign="top" charoff="50">Time (MYA)</th></tr></thead><tbody valign="top"><tr><td align="left" valign="top" charoff="50"><italic>BraCOL2-BraCOL1a</italic></td><td align="center" valign="top" charoff="50">0.24</td><td align="center" valign="top" charoff="50">0.63</td><td align="center" valign="top" charoff="50">0.37</td><td align="center" valign="top" charoff="50">1.01E–09</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">21.14</td></tr><tr><td align="left" valign="top" charoff="50"><italic>BraCOL9b-BraCOL9c</italic></td><td align="center" valign="top" charoff="50">0.05</td><td align="center" valign="top" charoff="50">0.25</td><td align="center" valign="top" charoff="50">0.18</td><td align="center" valign="top" charoff="50">6.68E–14</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">8.49</td></tr><tr><td align="left" valign="top" charoff="50"><italic>BraCOL6b-BraCOL6a</italic></td><td align="center" valign="top" charoff="50">0.12</td><td align="center" valign="top" charoff="50">0.40</td><td align="center" valign="top" charoff="50">0.30</td><td align="center" valign="top" charoff="50">1.39E–13</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">13.23</td></tr><tr><td align="left" valign="top" charoff="50"><italic>BraCOL9c-BraCOL9a</italic></td><td align="center" valign="top" charoff="50">0.04</td><td align="center" valign="top" charoff="50">0.41</td><td align="center" valign="top" charoff="50">0.10</td><td align="center" valign="top" charoff="50">1.18E–28</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">13.79</td></tr><tr><td align="left" valign="top" charoff="50"><italic>BraCOL4b-BraCOL4a</italic></td><td align="center" valign="top" charoff="50">0.05</td><td align="center" valign="top" charoff="50">0.34</td><td align="center" valign="top" charoff="50">0.14</td><td align="center" valign="top" charoff="50">1.26E–21</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">11.39</td></tr><tr><td align="left" valign="top" charoff="50"><italic>BraCOL16b-BraCOL7</italic></td><td align="center" valign="top" charoff="50">0.20</td><td align="center" valign="top" charoff="50">0.38</td><td align="center" valign="top" charoff="50">0.54</td><td align="center" valign="top" charoff="50">8.07E–05</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">12.63</td></tr><tr><td align="left" valign="top" charoff="50"><italic>BraCOL16b-BraCOL16a</italic></td><td align="center" valign="top" charoff="50">0.08</td><td align="center" valign="top" charoff="50">0.36</td><td align="center" valign="top" charoff="50">0.22</td><td align="center" valign="top" charoff="50">1.81E–17</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">11.97</td></tr><tr><td align="left" valign="top" charoff="50"><italic>BraCOL15a-BraCOL15b</italic></td><td align="center" valign="top" charoff="50">0.12</td><td align="center" valign="top" charoff="50">0.34</td><td align="center" valign="top" charoff="50">0.35</td><td align="center" valign="top" charoff="50">1.34E–23</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">11.33</td></tr><tr><td align="left" valign="top" charoff="50"><italic>AthCOL2-AthCO</italic></td><td align="center" valign="top" charoff="50">0.17</td><td align="center" valign="top" charoff="50">0.61</td><td align="center" valign="top" charoff="50">0.29</td><td align="center" valign="top" charoff="50">1.23E–15</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">20.33</td></tr><tr><td align="left" valign="top" charoff="50"><italic>AthCOL9-AthCOL10</italic></td><td align="center" valign="top" charoff="50">0.18</td><td align="center" valign="top" charoff="50">0.87</td><td align="center" valign="top" charoff="50">0.21</td><td align="center" valign="top" charoff="50">3.35E–27</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">28.88</td></tr><tr><td align="left" valign="top" charoff="50"><italic>AthCOL2-BraCOL2</italic></td><td align="center" valign="top" charoff="50">0.11</td><td align="center" valign="top" charoff="50">0.31</td><td align="center" valign="top" charoff="50">0.34</td><td align="center" valign="top" charoff="50">2.67E–08</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">10.37</td></tr><tr><td align="left" valign="top" charoff="50"><italic>AthCOL2-BraCOL1b</italic></td><td align="center" valign="top" charoff="50">0.25</td><td align="center" valign="top" charoff="50">0.70</td><td align="center" valign="top" charoff="50">0.35</td><td align="center" valign="top" charoff="50">5.92E–12</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">23.4</td></tr><tr><td align="left" valign="top" charoff="50"><italic>AthCOL11-BraCOL12</italic></td><td align="center" valign="top" charoff="50">0.28</td><td align="center" valign="top" charoff="50">0.90</td><td align="center" valign="top" charoff="50">0.31</td><td align="center" valign="top" charoff="50">1.38E–15</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">30.04</td></tr><tr><td align="left" valign="top" charoff="50"><italic>AthCO-BraCOL2</italic></td><td align="center" valign="top" charoff="50">0.21</td><td align="center" valign="top" charoff="50">0.69</td><td align="center" valign="top" charoff="50">0.30</td><td align="center" valign="top" charoff="50">4.81E–14</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">23.17</td></tr><tr><td align="left" valign="top" charoff="50"><italic>AthCOL10-BraCOL10b</italic></td><td align="center" valign="top" charoff="50">0.10</td><td align="center" valign="top" charoff="50">0.52</td><td align="center" valign="top" charoff="50">0.19</td><td align="center" valign="top" charoff="50">1.11E–22</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">17.29</td></tr><tr><td align="left" valign="top" charoff="50"><italic>AthCOL10-BraCOL10a</italic></td><td align="center" valign="top" charoff="50">0.12</td><td align="center" valign="top" charoff="50">0.61</td><td align="center" valign="top" charoff="50">0.20</td><td align="center" valign="top" charoff="50">1.24E–23</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">20.38</td></tr><tr><td align="left" valign="top" charoff="50"><italic>AthCOL4-BraCOL4a</italic></td><td align="center" valign="top" charoff="50">0.04</td><td align="center" valign="top" charoff="50">0.79</td><td align="center" valign="top" charoff="50">0.05</td><td align="center" valign="top" charoff="50">3.84E–56</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">26.21</td></tr><tr><td align="left" valign="top" charoff="50"><italic>AthCOL6-BraCOL6b</italic></td><td align="center" valign="top" charoff="50">0.12</td><td align="center" valign="top" charoff="50">0.40</td><td align="center" valign="top" charoff="50">0.30</td><td align="center" valign="top" charoff="50">5.03E–13</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">13.46</td></tr><tr><td align="left" valign="top" charoff="50"><italic>AthCOL8-BraCOL8</italic></td><td align="center" valign="top" charoff="50">0.15</td><td align="center" valign="top" charoff="50">0.35</td><td align="center" valign="top" charoff="50">0.43</td><td align="center" valign="top" charoff="50">7.58E–06</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">11.52</td></tr><tr><td align="left" valign="top" charoff="50"><italic>AthCOL6-BraCOL6a</italic></td><td align="center" valign="top" charoff="50">0.10</td><td align="center" valign="top" charoff="50">0.37</td><td align="center" valign="top" charoff="50">0.27</td><td align="center" valign="top" charoff="50">2.03E–14</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">12.38</td></tr><tr><td align="left" valign="top" charoff="50"><italic>AthCOL16-BraCOL7</italic></td><td align="center" valign="top" charoff="50">0.23</td><td align="center" valign="top" charoff="50">0.66</td><td align="center" valign="top" charoff="50">0.35</td><td align="center" valign="top" charoff="50">7.07E–14</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">21.9</td></tr><tr><td align="left" valign="top" charoff="50"><italic>AthCOL15-BraCOL15a</italic></td><td align="center" valign="top" charoff="50">0.16</td><td align="center" valign="top" charoff="50">0.73</td><td align="center" valign="top" charoff="50">0.23</td><td align="center" valign="top" charoff="50">5.14E–26</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">24.24</td></tr><tr><td align="left" valign="top" charoff="50"><italic>AthCOL16-BraCOL16a</italic></td><td align="center" valign="top" charoff="50">0.08</td><td align="center" valign="top" charoff="50">0.46</td><td align="center" valign="top" charoff="50">0.18</td><td align="center" valign="top" charoff="50">4.96E–25</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">15.3</td></tr><tr><td align="left" valign="top" charoff="50"><italic>AthCOL9-BraCOL9b</italic></td><td align="center" valign="top" charoff="50">0.07</td><td align="center" valign="top" charoff="50">0.39</td><td align="center" valign="top" charoff="50">0.18</td><td align="center" valign="top" charoff="50">9.26E–20</td><td align="center" valign="top" charoff="50">WGD or segmental</td><td align="center" valign="top" charoff="50">Yes</td><td align="center" valign="top" charoff="50">12.85</td></tr></tbody></table></table-wrap><table-wrap position="float" id="t3"><label>Table 3</label><caption><title>The statistics of the B-box domain lost in group A and group C <italic>COL</italic> genes of angiosperm species.</title></caption><table frame="hsides" rules="groups" border="1"><colgroup><col align="left"></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="center"></col><col align="center"></col></colgroup><thead valign="bottom"><tr><th align="left" valign="top" charoff="50"> </th><th colspan="2" align="center" valign="top" charoff="50">Group A</th><th align="center" valign="top" charoff="50">Group B</th><th colspan="2" align="center" valign="top" charoff="50">Group C</th><th align="center" valign="top" charoff="50">Total</th><th align="center" valign="top" charoff="50">Percentage<xref ref-type="fn" rid="t3-fn1">*</xref></th><th align="center" valign="top" charoff="50">Percentage<xref ref-type="fn" rid="t3-fn1">*</xref></th></tr><tr><th align="center" valign="top" charoff="50"><italic>Species</italic></th><th align="center" valign="top" charoff="50">Two B-box</th><th align="center" valign="top" charoff="50">One B-box</th><th align="center" valign="top" charoff="50">One B-box</th><th align="center" valign="top" charoff="50">Two B-box</th><th align="center" valign="top" charoff="50">One B-box</th><th align="center" valign="top" charoff="50">Gene Number</th><th align="center" valign="top" charoff="50">Group A-lost</th><th align="center" valign="top" charoff="50">Group C-lost</th></tr></thead><tbody valign="top"><tr><td align="left" valign="top" charoff="50"><italic>Aco</italic></td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">8</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Aly</italic></td><td align="center" valign="top" charoff="50">6</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">18</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">16.67</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Ath</italic></td><td align="center" valign="top" charoff="50">6</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">7</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">17</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Bdi</italic></td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">15</td><td align="center" valign="top" charoff="50">13.33</td><td align="center" valign="top" charoff="50">20.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Bra</italic></td><td align="center" valign="top" charoff="50">7</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">6</td><td align="center" valign="top" charoff="50">8</td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">25</td><td align="center" valign="top" charoff="50">4.00</td><td align="center" valign="top" charoff="50">12.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Ccl</italic></td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">8</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">14</td><td align="center" valign="top" charoff="50">7.14</td><td align="center" valign="top" charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Cpa</italic></td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">10</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Cru</italic></td><td align="center" valign="top" charoff="50">6</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">16</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">6.25</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Csa</italic></td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">13</td><td align="center" valign="top" charoff="50">7.69</td><td align="center" valign="top" charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Csi</italic></td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">12</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">18</td><td align="center" valign="top" charoff="50">5.56</td><td align="center" valign="top" charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Egr</italic></td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">10</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Fve</italic></td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">8</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">12.50</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Gma</italic></td><td align="center" valign="top" charoff="50">8</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">6</td><td align="center" valign="top" charoff="50">12</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">26</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Gra</italic></td><td align="center" valign="top" charoff="50">6</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">12</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">23</td><td align="center" valign="top" charoff="50">8.70</td><td align="center" valign="top" charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Lus</italic></td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">8</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">15</td><td align="center" valign="top" charoff="50">13.33</td><td align="center" valign="top" charoff="50">6.67</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Mdo</italic></td><td align="center" valign="top" charoff="50">6</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">6</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">17</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Mes</italic></td><td align="center" valign="top" charoff="50">7</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">7</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">18</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">5.56</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Mgu</italic></td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">12</td><td align="center" valign="top" charoff="50">8.33</td><td align="center" valign="top" charoff="50">8.33</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Mtr</italic></td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">10</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">10.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Osa</italic></td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">17</td><td align="center" valign="top" charoff="50">17.65</td><td align="center" valign="top" charoff="50">29.41</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Ppe</italic></td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">10</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Ptr</italic></td><td align="center" valign="top" charoff="50">6</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">7</td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">19</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">15.79</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Pvi</italic></td><td align="center" valign="top" charoff="50">6</td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">6</td><td align="center" valign="top" charoff="50">18</td><td align="center" valign="top" charoff="50">16.67</td><td align="center" valign="top" charoff="50">33.33</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Pvu</italic></td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">6</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">14</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Rco</italic></td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">10</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">10.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Sbi</italic></td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">16</td><td align="center" valign="top" charoff="50">6.25</td><td align="center" valign="top" charoff="50">25.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Sit</italic></td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">15</td><td align="center" valign="top" charoff="50">6.67</td><td align="center" valign="top" charoff="50">6.67</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Sly</italic></td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">13</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Stu</italic></td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">9</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">16</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Tca</italic></td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">6</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">12</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Tha</italic></td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">7</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">16</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">6.25</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Vvi</italic></td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">3</td><td align="center" valign="top" charoff="50">0</td><td align="center" valign="top" charoff="50">6</td><td align="center" valign="top" charoff="50">0.00</td><td align="center" valign="top" charoff="50">0.00</td></tr><tr><td align="left" valign="top" charoff="50"><italic>Zma</italic></td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">2</td><td align="center" valign="top" charoff="50">5</td><td align="center" valign="top" charoff="50">4</td><td align="center" valign="top" charoff="50">1</td><td align="center" valign="top" charoff="50">17</td><td align="center" valign="top" charoff="50">11.76</td><td align="center" valign="top" charoff="50">5.88</td></tr></tbody></table><table-wrap-foot><fn id="t3-fn1"><p>Note: The abbreviations represent the species as follows: <italic>Aco, Aquilegia coerulea</italic>; <italic>Aly, Arabidopsis lyrata</italic>; <italic>Ath, Arabidopsis thaliana</italic>; <italic>Bdi, Brachypodium distachyon</italic>; <italic>Bra, Brassica rapa</italic>; <italic>Ccl, Citrus clementina</italic>; <italic>Cpa, Carica papaya</italic>; <italic>Cru, Capsella rubella</italic>; <italic>Csa, Cucumis sativus</italic>; <italic>Csi, Citrus sinensis</italic>; <italic>Egr, Eucalyptus grandis</italic>; <italic>Fve, Fragaria vesca</italic>; <italic>Gma, Glycine max</italic>; <italic>Gra, Gossypium raimondii</italic>; <italic>Lus, Linum usitatissimum</italic>; <italic>Mdo, Malus domestica</italic>; <italic>Mes, Manihot esculenta</italic>; <italic>Mgu, Mimulus guttatus</italic>; <italic>Mtr, Medicago truncatula</italic>; <italic>Osa, Oryza sativa</italic>; <italic>Ppe, Prunus persica</italic>; <italic>Ptr, Populus trichocarpa</italic>; <italic>Pvi, Panicum virgatum</italic>; <italic>Pvu, Phaseolus vulgaris</italic>; <italic>Rco, Ricinus communis</italic>; <italic>Sbi, Sorghum bicolor</italic>; <italic>Sit, Setaria italica</italic>; <italic>Sly, Solanum lycopersicum</italic>; <italic>Stu, Solanum tuberosum</italic>; <italic>Tca, Theobroma cacao</italic>; <italic>Tha, Thellungiella halophila</italic>; <italic>Vvi, Vitis vinifera</italic>; <italic>Zma, Zea mays</italic>.</p></fn><fn id="t3-fn2"><p><sup>*</sup>The percentage of B-box loss in Group A or Group C = Number of genes that contained only one B-box domain in Group A or Group C/All the <italic>COL</italic> genes in the species.</p></fn></table-wrap-foot></table-wrap></floats-group></pmc><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Song, Xiaoming" sort="Song, Xiaoming" uniqKey="Song X" first="Xiaoming" last="Song">Xiaoming Song</name></noRegion><name sortKey="Duan, Weike" sort="Duan, Weike" uniqKey="Duan W" first="Weike" last="Duan">Weike Duan</name><name sortKey="Hou, Xilin" sort="Hou, Xilin" uniqKey="Hou X" first="Xilin" last="Hou">Xilin Hou</name><name sortKey="Huang, Zhinan" sort="Huang, Zhinan" uniqKey="Huang Z" first="Zhinan" last="Huang">Zhinan Huang</name><name sortKey="Li, Ying" sort="Li, Ying" uniqKey="Li Y" first="Ying" last="Li">Ying Li</name><name sortKey="Liu, Gaofeng" sort="Liu, Gaofeng" uniqKey="Liu G" first="Gaofeng" last="Liu">Gaofeng Liu</name><name sortKey="Liu, Tongkun" sort="Liu, Tongkun" uniqKey="Liu T" first="Tongkun" last="Liu">Tongkun Liu</name><name sortKey="Song, Xiaoming" sort="Song, Xiaoming" uniqKey="Song X" first="Xiaoming" last="Song">Xiaoming Song</name><name sortKey="Wu, Peng" sort="Wu, Peng" uniqKey="Wu P" first="Peng" last="Wu">Peng Wu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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