Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae).
Identifieur interne : 002A95 ( Main/Exploration ); précédent : 002A94; suivant : 002A96Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae).
Auteurs : Chi-Chun Huang [Taïwan] ; Kuo-Hsiang Hung ; Wei-Kuang Wang ; Chuan-Wen Ho ; Chao-Li Huang ; Tsai-Wen Hsu ; Naoki Osada ; Chi-Chuan Hwang ; Tzen-Yuh ChiangSource :
- Gene [ 1879-0038 ] ; 2012.
Descripteurs français
- KwdFr :
- Arabidopsis (génétique), Brassicaceae (génétique), Flux des gènes (physiologie), Génome végétal (génétique), Marqueurs génétiques (génétique), Noyau de la cellule (génétique), Organites (génétique), Phylogenèse (MeSH), Populus (génétique), Spéciation génétique (MeSH), Taux de mutation (MeSH), Variation génétique (génétique), Variation génétique (physiologie), Évolution moléculaire (MeSH).
- MESH :
- génétique : Arabidopsis, Brassicaceae, Génome végétal, Marqueurs génétiques, Noyau de la cellule, Organites, Populus, Variation génétique.
- physiologie : Flux des gènes, Variation génétique.
- Phylogenèse, Spéciation génétique, Taux de mutation, Évolution moléculaire.
English descriptors
- KwdEn :
- Arabidopsis (genetics), Brassicaceae (genetics), Cell Nucleus (genetics), Evolution, Molecular (MeSH), Gene Flow (physiology), Genetic Markers (genetics), Genetic Speciation (MeSH), Genetic Variation (genetics), Genetic Variation (physiology), Genome, Plant (genetics), Mutation Rate (MeSH), Organelles (genetics), Phylogeny (MeSH), Populus (genetics).
- MESH :
- chemical , genetics : Genetic Markers.
- genetics : Arabidopsis, Brassicaceae, Cell Nucleus, Genetic Variation, Genome, Plant, Organelles, Populus.
- physiology : Gene Flow, Genetic Variation.
- Evolution, Molecular, Genetic Speciation, Mutation Rate, Phylogeny.
Abstract
Recovering the genetic divergence between species is one of the major interests in the evolutionary biology. It requires accurate estimation of the neutral substitution rates. Arabidopsis thaliana, the first whole-genome sequenced plant, and its out-crossing relatives provide an ideal model for examining the split between sister species. In the study, rates of molecular evolution at markers frequently used for systematics and population genetics, including 14 nuclear genes spanning most chromosomes, three noncoding regions of chloroplast genome, and one intron of mitochondrial genome, between A. thaliana and four relatives were estimated. No deviation from neutrality was detected in the genes examined. Based on the known divergence between A. thaliana and its sisters about 8.0-17.6 MYA, evolutionary rates of the eighteen genes were estimated. Accordingly, the ratio of rates of synonymous substitutions among mitochondrial, chloroplast and nuclear genes was calculated with an average and 95% confidence interval of 1 (0.25-1.75): 15.77 (7.48-114.09): 74.79 (36.27-534.61). Molecular evolutionary rates of nuclear genes varied, with a range of 0.383-0.856×10(-8) for synonymous substitutions per site per year and 0.036-0.081×10(-9) for nonsynonymous substitutions per site per year. Compared with orthologs in Populus, a long life-span tree, genes in Arabidopsis evolved faster in an order of magnitude at the gene level, agreeing with a generation time hypothesis. The estimated substitution rates of these genes can be used as a reference for molecular dating.
DOI: 10.1016/j.gene.2012.02.037
PubMed: 22426291
Affiliations:
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Chuan Wen" uniqKey="Ho C" first="Chuan-Wen" last="Ho">Chuan-Wen Ho</name></author><author><name sortKey="Huang, Chao Li" sort="Huang, Chao Li" uniqKey="Huang C" first="Chao-Li" last="Huang">Chao-Li Huang</name></author><author><name sortKey="Hsu, Tsai Wen" sort="Hsu, Tsai Wen" uniqKey="Hsu T" first="Tsai-Wen" last="Hsu">Tsai-Wen Hsu</name></author><author><name sortKey="Osada, Naoki" sort="Osada, Naoki" uniqKey="Osada N" first="Naoki" last="Osada">Naoki Osada</name></author><author><name sortKey="Hwang, Chi Chuan" sort="Hwang, Chi Chuan" uniqKey="Hwang C" first="Chi-Chuan" last="Hwang">Chi-Chuan Hwang</name></author><author><name sortKey="Chiang, Tzen Yuh" sort="Chiang, Tzen Yuh" uniqKey="Chiang T" first="Tzen-Yuh" last="Chiang">Tzen-Yuh Chiang</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2012">2012</date><idno type="RBID">pubmed:22426291</idno><idno type="pmid">22426291</idno><idno type="doi">10.1016/j.gene.2012.02.037</idno><idno 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701</wicri:noRegion></affiliation></author><author><name sortKey="Hung, Kuo Hsiang" sort="Hung, Kuo Hsiang" uniqKey="Hung K" first="Kuo-Hsiang" last="Hung">Kuo-Hsiang Hung</name></author><author><name sortKey="Wang, Wei Kuang" sort="Wang, Wei Kuang" uniqKey="Wang W" first="Wei-Kuang" last="Wang">Wei-Kuang Wang</name></author><author><name sortKey="Ho, Chuan Wen" sort="Ho, Chuan Wen" uniqKey="Ho C" first="Chuan-Wen" last="Ho">Chuan-Wen Ho</name></author><author><name sortKey="Huang, Chao Li" sort="Huang, Chao Li" uniqKey="Huang C" first="Chao-Li" last="Huang">Chao-Li Huang</name></author><author><name sortKey="Hsu, Tsai Wen" sort="Hsu, Tsai Wen" uniqKey="Hsu T" first="Tsai-Wen" last="Hsu">Tsai-Wen Hsu</name></author><author><name sortKey="Osada, Naoki" sort="Osada, Naoki" uniqKey="Osada N" first="Naoki" last="Osada">Naoki Osada</name></author><author><name sortKey="Hwang, Chi Chuan" sort="Hwang, Chi Chuan" uniqKey="Hwang C" first="Chi-Chuan" last="Hwang">Chi-Chuan Hwang</name></author><author><name sortKey="Chiang, Tzen Yuh" sort="Chiang, Tzen Yuh" uniqKey="Chiang T" first="Tzen-Yuh" last="Chiang">Tzen-Yuh Chiang</name></author></analytic><series><title level="j">Gene</title><idno type="eISSN">1879-0038</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term><term>Brassicaceae (genetics)</term><term>Cell Nucleus (genetics)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Flow (physiology)</term><term>Genetic Markers (genetics)</term><term>Genetic Speciation (MeSH)</term><term>Genetic Variation (genetics)</term><term>Genetic Variation (physiology)</term><term>Genome, Plant (genetics)</term><term>Mutation Rate (MeSH)</term><term>Organelles (genetics)</term><term>Phylogeny (MeSH)</term><term>Populus (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Arabidopsis (génétique)</term><term>Brassicaceae (génétique)</term><term>Flux des gènes (physiologie)</term><term>Génome végétal (génétique)</term><term>Marqueurs génétiques (génétique)</term><term>Noyau de la cellule (génétique)</term><term>Organites (génétique)</term><term>Phylogenèse (MeSH)</term><term>Populus (génétique)</term><term>Spéciation génétique (MeSH)</term><term>Taux de mutation (MeSH)</term><term>Variation génétique (génétique)</term><term>Variation génétique (physiologie)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Brassicaceae</term><term>Cell Nucleus</term><term>Genetic Variation</term><term>Genome, Plant</term><term>Organelles</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Brassicaceae</term><term>Génome végétal</term><term>Marqueurs génétiques</term><term>Noyau de la cellule</term><term>Organites</term><term>Populus</term><term>Variation génétique</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Flux des gènes</term><term>Variation génétique</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Gene Flow</term><term>Genetic Variation</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term><term>Genetic Speciation</term><term>Mutation Rate</term><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Phylogenèse</term><term>Spéciation génétique</term><term>Taux de mutation</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Recovering the genetic divergence between species is one of the major interests in the evolutionary biology. It requires accurate estimation of the neutral substitution rates. Arabidopsis thaliana, the first whole-genome sequenced plant, and its out-crossing relatives provide an ideal model for examining the split between sister species. In the study, rates of molecular evolution at markers frequently used for systematics and population genetics, including 14 nuclear genes spanning most chromosomes, three noncoding regions of chloroplast genome, and one intron of mitochondrial genome, between A. thaliana and four relatives were estimated. No deviation from neutrality was detected in the genes examined. Based on the known divergence between A. thaliana and its sisters about 8.0-17.6 MYA, evolutionary rates of the eighteen genes were estimated. Accordingly, the ratio of rates of synonymous substitutions among mitochondrial, chloroplast and nuclear genes was calculated with an average and 95% confidence interval of 1 (0.25-1.75): 15.77 (7.48-114.09): 74.79 (36.27-534.61). Molecular evolutionary rates of nuclear genes varied, with a range of 0.383-0.856×10(-8) for synonymous substitutions per site per year and 0.036-0.081×10(-9) for nonsynonymous substitutions per site per year. Compared with orthologs in Populus, a long life-span tree, genes in Arabidopsis evolved faster in an order of magnitude at the gene level, agreeing with a generation time hypothesis. The estimated substitution rates of these genes can be used as a reference for molecular dating.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22426291</PMID><DateCompleted><Year>2012</Year><Month>06</Month><Day>19</Day></DateCompleted><DateRevised><Year>2012</Year><Month>04</Month><Day>16</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1879-0038</ISSN><JournalIssue CitedMedium="Internet"><Volume>499</Volume><Issue>1</Issue><PubDate><Year>2012</Year><Month>May</Month><Day>10</Day></PubDate></JournalIssue><Title>Gene</Title><ISOAbbreviation>Gene</ISOAbbreviation></Journal><ArticleTitle>Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae).</ArticleTitle><Pagination><MedlinePgn>194-201</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.gene.2012.02.037</ELocationID><Abstract><AbstractText>Recovering the genetic divergence between species is one of the major interests in the evolutionary biology. It requires accurate estimation of the neutral substitution rates. Arabidopsis thaliana, the first whole-genome sequenced plant, and its out-crossing relatives provide an ideal model for examining the split between sister species. In the study, rates of molecular evolution at markers frequently used for systematics and population genetics, including 14 nuclear genes spanning most chromosomes, three noncoding regions of chloroplast genome, and one intron of mitochondrial genome, between A. thaliana and four relatives were estimated. No deviation from neutrality was detected in the genes examined. Based on the known divergence between A. thaliana and its sisters about 8.0-17.6 MYA, evolutionary rates of the eighteen genes were estimated. Accordingly, the ratio of rates of synonymous substitutions among mitochondrial, chloroplast and nuclear genes was calculated with an average and 95% confidence interval of 1 (0.25-1.75): 15.77 (7.48-114.09): 74.79 (36.27-534.61). Molecular evolutionary rates of nuclear genes varied, with a range of 0.383-0.856×10(-8) for synonymous substitutions per site per year and 0.036-0.081×10(-9) for nonsynonymous substitutions per site per year. Compared with orthologs in Populus, a long life-span tree, genes in Arabidopsis evolved faster in an order of magnitude at the gene level, agreeing with a generation time hypothesis. The estimated substitution rates of these genes can be used as a reference for molecular dating.</AbstractText><CopyrightInformation>Copyright © 2012 Elsevier B.V. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Huang</LastName><ForeName>Chi-Chun</ForeName><Initials>CC</Initials><AffiliationInfo><Affiliation>Department of Life Sciences, National Cheng-Kung University, Tainan 701, Taiwan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hung</LastName><ForeName>Kuo-Hsiang</ForeName><Initials>KH</Initials></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Wei-Kuang</ForeName><Initials>WK</Initials></Author><Author ValidYN="Y"><LastName>Ho</LastName><ForeName>Chuan-Wen</ForeName><Initials>CW</Initials></Author><Author ValidYN="Y"><LastName>Huang</LastName><ForeName>Chao-Li</ForeName><Initials>CL</Initials></Author><Author ValidYN="Y"><LastName>Hsu</LastName><ForeName>Tsai-Wen</ForeName><Initials>TW</Initials></Author><Author ValidYN="Y"><LastName>Osada</LastName><ForeName>Naoki</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Hwang</LastName><ForeName>Chi-Chuan</ForeName><Initials>CC</Initials></Author><Author ValidYN="Y"><LastName>Chiang</LastName><ForeName>Tzen-Yuh</ForeName><Initials>TY</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2012</Year><Month>03</Month><Day>09</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Gene</MedlineTA><NlmUniqueID>7706761</NlmUniqueID><ISSNLinking>0378-1119</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019607" MajorTopicYN="N">Brassicaceae</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002467" MajorTopicYN="N">Cell Nucleus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D051456" MajorTopicYN="N">Gene Flow</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D049810" MajorTopicYN="N">Genetic Speciation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059645" MajorTopicYN="N">Mutation Rate</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015388" MajorTopicYN="N">Organelles</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2011</Year><Month>09</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2012</Year><Month>01</Month><Day>31</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2012</Year><Month>02</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2012</Year><Month>3</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2012</Year><Month>3</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2012</Year><Month>6</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">22426291</ArticleId><ArticleId IdType="pii">S0378-1119(12)00239-9</ArticleId><ArticleId IdType="doi">10.1016/j.gene.2012.02.037</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Taïwan</li></country></list><tree><noCountry><name sortKey="Chiang, Tzen Yuh" sort="Chiang, Tzen Yuh" uniqKey="Chiang T" first="Tzen-Yuh" last="Chiang">Tzen-Yuh Chiang</name><name sortKey="Ho, Chuan Wen" sort="Ho, Chuan Wen" uniqKey="Ho C" first="Chuan-Wen" last="Ho">Chuan-Wen Ho</name><name sortKey="Hsu, Tsai Wen" sort="Hsu, Tsai Wen" uniqKey="Hsu T" first="Tsai-Wen" last="Hsu">Tsai-Wen Hsu</name><name sortKey="Huang, Chao Li" sort="Huang, Chao Li" uniqKey="Huang C" first="Chao-Li" last="Huang">Chao-Li Huang</name><name sortKey="Hung, Kuo Hsiang" sort="Hung, Kuo Hsiang" uniqKey="Hung K" first="Kuo-Hsiang" last="Hung">Kuo-Hsiang Hung</name><name sortKey="Hwang, Chi Chuan" sort="Hwang, Chi Chuan" uniqKey="Hwang C" first="Chi-Chuan" last="Hwang">Chi-Chuan Hwang</name><name sortKey="Osada, Naoki" sort="Osada, Naoki" uniqKey="Osada N" first="Naoki" last="Osada">Naoki Osada</name><name sortKey="Wang, Wei Kuang" sort="Wang, Wei Kuang" uniqKey="Wang W" first="Wei-Kuang" last="Wang">Wei-Kuang Wang</name></noCountry><country name="Taïwan"><noRegion><name sortKey="Huang, Chi Chun" sort="Huang, Chi Chun" uniqKey="Huang C" first="Chi-Chun" last="Huang">Chi-Chun Huang</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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