Identification, characterization, and utilization of single copy genes in 29 angiosperm genomes
Identifieur interne : 001734 ( Ncbi/Merge ); précédent : 001733; suivant : 001735Identification, characterization, and utilization of single copy genes in 29 angiosperm genomes
Auteurs : Fengming Han [République populaire de Chine] ; Yong Peng [République populaire de Chine] ; Lijia Xu [République populaire de Chine] ; Peigen Xiao [République populaire de Chine]Source :
- BMC Genomics [ 1471-2164 ] ; 2014.
Abstract
Single copy genes are common across angiosperm genomes. With the sufficiently high quality sequenced genomes, the identification of large-scale single copy genes among multiple species is possible. Although some characteristics have been reported, our study provides novel insights into single copy genes.
We identified single copy genes across 29 angiosperm genomes. A significant negative correlation was found between the number of duplicate blocks and the number of single copy genes. We found that a considerable number of single copy genes are located in organelles, showing a preference for binding and catalytic activity. The analysis of effective number of codons (Nc) illustrates that single copy genes have a stronger codon bias than non-single copy genes in eudicots. The relative high expression level of single copy genes was partially confirmed by the RNA-seq data, rather than the Codon Adaptation Index (CAI). Unlike in most other species, a strongly negatively correlation occurs between Nc and GC3 among single copy genes in grass genomes. When compared to all non-single copy genes, single copy genes indicate more conservation (as indicated by
Our analysis provides insight into the evolutionary characteristics of single copy genes across 29 angiosperm genomes. The results suggest that there are key differences in evolutionary constraints between single copy genes and non-single copy genes. And to some extent, these evolutionary constraints show some species-specific differences, especially between eudicots and monocots. Our preliminary evidence also suggests that the concatenated shared single copy genes are well suited for use in resolving phylogenetic relationships.
The online version of this article (doi:10.1186/1471-2164-15-504) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/1471-2164-15-504
PubMed: 24950957
PubMed Central: 4092219
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China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Xu, Lijia" sort="Xu, Lijia" uniqKey="Xu L" first="Lijia" last="Xu">Lijia Xu</name><affiliation wicri:level="3"><nlm:aff id="Aff14">Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Xiao, Peigen" sort="Xiao, Peigen" uniqKey="Xiao P" first="Peigen" last="Xiao">Peigen Xiao</name><affiliation wicri:level="3"><nlm:aff id="Aff14">Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24950957</idno><idno type="pmc">4092219</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4092219</idno><idno type="RBID">PMC:4092219</idno><idno type="doi">10.1186/1471-2164-15-504</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000571</idno><idno type="wicri:Area/Pmc/Curation">000570</idno><idno type="wicri:Area/Pmc/Checkpoint">000788</idno><idno type="wicri:Area/Ncbi/Merge">001734</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identification, characterization, and utilization of single copy genes in 29 angiosperm genomes</title><author><name sortKey="Han, Fengming" sort="Han, Fengming" uniqKey="Han F" first="Fengming" last="Han">Fengming Han</name><affiliation wicri:level="3"><nlm:aff id="Aff14">Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Peng, Yong" sort="Peng, Yong" uniqKey="Peng Y" first="Yong" last="Peng">Yong Peng</name><affiliation wicri:level="3"><nlm:aff id="Aff14">Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Xu, Lijia" sort="Xu, Lijia" uniqKey="Xu L" first="Lijia" last="Xu">Lijia Xu</name><affiliation wicri:level="3"><nlm:aff id="Aff14">Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Xiao, Peigen" sort="Xiao, Peigen" uniqKey="Xiao P" first="Peigen" last="Xiao">Peigen Xiao</name><affiliation wicri:level="3"><nlm:aff id="Aff14">Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 PR China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Single copy genes are common across angiosperm genomes. With the sufficiently high quality sequenced genomes, the identification of large-scale single copy genes among multiple species is possible. Although some characteristics have been reported, our study provides novel insights into single copy genes.</p></sec><sec><title>Results</title><p>We identified single copy genes across 29 angiosperm genomes. A significant negative correlation was found between the number of duplicate blocks and the number of single copy genes. We found that a considerable number of single copy genes are located in organelles, showing a preference for binding and catalytic activity. The analysis of effective number of codons (Nc) illustrates that single copy genes have a stronger codon bias than non-single copy genes in eudicots. The relative high expression level of single copy genes was partially confirmed by the RNA-seq data, rather than the Codon Adaptation Index (CAI). Unlike in most other species, a strongly negatively correlation occurs between Nc and GC3 among single copy genes in grass genomes. When compared to all non-single copy genes, single copy genes indicate more conservation (as indicated by <italic>Ka</italic> and <italic>Ks</italic> values). But our alternative splicing (AS) results reveal that selective constraints are weaker in single copy genes than in low copy family genes (1–10 in-paralogs) and stronger than high copy family genes (>10 in-paralogs). Using concatenated shared single copy genes, we obtained a well-resolved phylogenetic tree. With the addition of intron sequences, the branch support is improved, but striking incongruences are also evident. Therefore, it is noteworthy that inclusion of intron sequences seems more appropriate for the phylogenetic reconstruction at lower taxonomic levels.</p></sec><sec><title>Conclusions</title><p>Our analysis provides insight into the evolutionary characteristics of single copy genes across 29 angiosperm genomes. The results suggest that there are key differences in evolutionary constraints between single copy genes and non-single copy genes. And to some extent, these evolutionary constraints show some species-specific differences, especially between eudicots and monocots. Our preliminary evidence also suggests that the concatenated shared single copy genes are well suited for use in resolving phylogenetic relationships.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/1471-2164-15-504) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Zhang, J" uniqKey="Zhang J">J Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Birchler, Ja" uniqKey="Birchler J">JA Birchler</name></author><author><name sortKey="Newton, Kj" uniqKey="Newton K">KJ Newton</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Song, K" uniqKey="Song K">K Song</name></author><author><name sortKey="Lu, P" uniqKey="Lu P">P Lu</name></author><author><name sortKey="Tang, K" uniqKey="Tang K">K Tang</name></author><author><name 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<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Genomics</journal-id><journal-id journal-id-type="iso-abbrev">BMC Genomics</journal-id><journal-title-group><journal-title>BMC Genomics</journal-title></journal-title-group><issn pub-type="epub">1471-2164</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24950957</article-id><article-id pub-id-type="pmc">4092219</article-id><article-id pub-id-type="publisher-id">6214</article-id><article-id pub-id-type="doi">10.1186/1471-2164-15-504</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Identification, characterization, and utilization of single copy genes in 29 angiosperm genomes</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Han</surname><given-names>Fengming</given-names></name><address><email>hanfengming2004@163.com</email></address><xref ref-type="aff" rid="Aff14"></xref></contrib><contrib contrib-type="author"><name><surname>Peng</surname><given-names>Yong</given-names></name><address><email>ypeng@implad.ac.cn</email></address><xref ref-type="aff" rid="Aff14"></xref></contrib><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Lijia</given-names></name><address><email>ljxu@implad.ac.cn</email></address><xref ref-type="aff" rid="Aff14"></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Xiao</surname><given-names>Peigen</given-names></name><address><email>xiaopg@public.bta.net.cn</email></address><xref ref-type="aff" rid="Aff14"></xref></contrib><aff id="Aff14">Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 PR China</aff></contrib-group><pub-date pub-type="epub"><day>21</day><month>6</month><year>2014</year></pub-date><pub-date pub-type="pmc-release"><day>21</day><month>6</month><year>2014</year></pub-date><pub-date pub-type="collection"><year>2014</year></pub-date><volume>15</volume><issue>1</issue><elocation-id>504</elocation-id><history><date date-type="received"><day>19</day><month>11</month><year>2013</year></date><date date-type="accepted"><day>17</day><month>6</month><year>2014</year></date></history><permissions><copyright-statement>© Han et al.; licensee BioMed Central Ltd. 2014</copyright-statement><license license-type="open-access"><license-p>This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>) applies to the data made available in this article, unless otherwise stated.</license-p></license></permissions><abstract id="Abs1"><sec><title>Background</title><p>Single copy genes are common across angiosperm genomes. With the sufficiently high quality sequenced genomes, the identification of large-scale single copy genes among multiple species is possible. Although some characteristics have been reported, our study provides novel insights into single copy genes.</p></sec><sec><title>Results</title><p>We identified single copy genes across 29 angiosperm genomes. A significant negative correlation was found between the number of duplicate blocks and the number of single copy genes. We found that a considerable number of single copy genes are located in organelles, showing a preference for binding and catalytic activity. The analysis of effective number of codons (Nc) illustrates that single copy genes have a stronger codon bias than non-single copy genes in eudicots. The relative high expression level of single copy genes was partially confirmed by the RNA-seq data, rather than the Codon Adaptation Index (CAI). Unlike in most other species, a strongly negatively correlation occurs between Nc and GC3 among single copy genes in grass genomes. When compared to all non-single copy genes, single copy genes indicate more conservation (as indicated by <italic>Ka</italic> and <italic>Ks</italic> values). But our alternative splicing (AS) results reveal that selective constraints are weaker in single copy genes than in low copy family genes (1–10 in-paralogs) and stronger than high copy family genes (>10 in-paralogs). Using concatenated shared single copy genes, we obtained a well-resolved phylogenetic tree. With the addition of intron sequences, the branch support is improved, but striking incongruences are also evident. Therefore, it is noteworthy that inclusion of intron sequences seems more appropriate for the phylogenetic reconstruction at lower taxonomic levels.</p></sec><sec><title>Conclusions</title><p>Our analysis provides insight into the evolutionary characteristics of single copy genes across 29 angiosperm genomes. The results suggest that there are key differences in evolutionary constraints between single copy genes and non-single copy genes. And to some extent, these evolutionary constraints show some species-specific differences, especially between eudicots and monocots. Our preliminary evidence also suggests that the concatenated shared single copy genes are well suited for use in resolving phylogenetic relationships.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/1471-2164-15-504) contains supplementary material, which is available to authorized users.</p></sec></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd>Single copy gene</kwd><kwd>Duplication</kwd><kwd>Gene Ontology</kwd><kwd>Codon usage</kwd><kwd>GC3</kwd><kwd>Gene expression</kwd><kwd><italic>Ka</italic>/<italic>Ks</italic></kwd><kwd>Alternative splicing</kwd><kwd>Phylogeny</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2014</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc><affiliations><list><country><li>République populaire de Chine</li></country><settlement><li>Pékin</li></settlement></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Han, Fengming" sort="Han, Fengming" uniqKey="Han F" first="Fengming" last="Han">Fengming Han</name></noRegion><name sortKey="Peng, Yong" sort="Peng, Yong" uniqKey="Peng Y" first="Yong" last="Peng">Yong Peng</name><name sortKey="Xiao, Peigen" sort="Xiao, Peigen" uniqKey="Xiao P" first="Peigen" last="Xiao">Peigen Xiao</name><name sortKey="Xu, Lijia" sort="Xu, Lijia" uniqKey="Xu L" first="Lijia" last="Xu">Lijia Xu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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