Functional divergence of duplicate genes several million years after gene duplication in Arabidopsis.
Identifieur interne : 000E88 ( Main/Exploration ); précédent : 000E87; suivant : 000E89Functional divergence of duplicate genes several million years after gene duplication in Arabidopsis.
Auteurs : Kousuke Hanada [Japon] ; Ayumi Tezuka [Japon] ; Masafumi Nozawa [Japon] ; Yutaka Suzuki [Japon] ; Sumio Sugano [Japon] ; Atsushi J. Nagano [Japon] ; Motomi Ito [Japon] ; Shin-Ichi Morinaga [Japon]Source :
- DNA research : an international journal for rapid publication of reports on genes and genomes [ 1756-1663 ] ; 2018.
Abstract
Lineage-specific duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selection pressures immediately after gene duplication is clear in the speciation process. Here, using Illumina DNA-sequencing reads from Arabidopsis halleri, which has multiple closely related species with high-quality genome assemblies (A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups in Brassicaceae. The duplication frequency of retained genes in the Arabidopsis lineage was ∼10 times higher than the duplication frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss (Physcomitrella patens). The difference of duplication frequencies can be explained by a rapid decay of anciently duplicated genes. To examine the degree of selection pressure on genes duplicated in either the A. halleri-lyrata or the A. halleri lineage, we examined positive and purifying selection in the A. halleri-lyrata and A. halleri lineages throughout the ratios of nonsynonymous to synonymous substitution rates (KA/KS). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. Interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication compared with immediately after gene duplication.
DOI: 10.1093/dnares/dsy005
PubMed: 29481587
PubMed Central: PMC6014284
Affiliations:
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Hanada</name><affiliation wicri:level="1"><nlm:affiliation>Department of Bioscience and Bioinformatics, Frontier Research Academy for Young Researchers, Kyusyu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Bioscience and Bioinformatics, Frontier Research Academy for Young Researchers, Kyusyu Institute of Technology, Iizuka, Fukuoka 820-8502</wicri:regionArea><wicri:noRegion>Fukuoka 820-8502</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>RIKEN Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa 230-0045, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>RIKEN Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa 230-0045</wicri:regionArea><wicri:noRegion>Kanagawa 230-0045</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>CREST, Japan Science and Technology Agency, Kawaguchi, 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first="Masafumi" last="Nozawa">Masafumi Nozawa</name><affiliation wicri:level="1"><nlm:affiliation>Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540</wicri:regionArea><wicri:noRegion>Shizuoka 411-8540</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Genetics, SOKENDAI, Mishima, Shizuoka 411-8540, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Genetics, SOKENDAI, Mishima, Shizuoka 411-8540</wicri:regionArea><wicri:noRegion>Shizuoka 411-8540</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Suzuki, Yutaka" sort="Suzuki, Yutaka" uniqKey="Suzuki Y" first="Yutaka" last="Suzuki">Yutaka Suzuki</name><affiliation wicri:level="4"><nlm:affiliation>Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562</wicri:regionArea><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Sugano, Sumio" sort="Sugano, Sumio" uniqKey="Sugano S" first="Sumio" last="Sugano">Sumio Sugano</name><affiliation wicri:level="4"><nlm:affiliation>Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562</wicri:regionArea><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Nagano, Atsushi J" sort="Nagano, Atsushi J" uniqKey="Nagano A" first="Atsushi J" last="Nagano">Atsushi J. Nagano</name><affiliation wicri:level="1"><nlm:affiliation>CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012</wicri:regionArea><wicri:noRegion>Saitama 332-0012</wicri:noRegion></affiliation><affiliation wicri:level="4"><nlm:affiliation>Center of Ecological Research, Kyoto University, Hirano, Otsu, Shiga 520-2113, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Center of Ecological Research, Kyoto University, Hirano, Otsu, Shiga 520-2113</wicri:regionArea><orgName type="university">Université de Kyoto</orgName><placeName><settlement type="city">Kyoto</settlement><region type="prefecture">Région du Kansai</region></placeName></affiliation></author><author><name sortKey="Ito, Motomi" sort="Ito, Motomi" uniqKey="Ito M" first="Motomi" last="Ito">Motomi Ito</name><affiliation wicri:level="4"><nlm:affiliation>Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Morinaga, Shin Ichi" sort="Morinaga, Shin Ichi" uniqKey="Morinaga S" first="Shin-Ichi" last="Morinaga">Shin-Ichi Morinaga</name><affiliation wicri:level="1"><nlm:affiliation>CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012</wicri:regionArea><wicri:noRegion>Saitama 332-0012</wicri:noRegion></affiliation><affiliation wicri:level="4"><nlm:affiliation>Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName><orgName type="university">Université de Tokyo</orgName><placeName><settlement type="city">Tokyo</settlement><region type="province">Région de Kantō</region></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880</wicri:regionArea><wicri:noRegion>Kanagawa 252-0880</wicri:noRegion></affiliation></author></analytic><series><title level="j">DNA research : an international journal for rapid publication of reports on genes and genomes</title><idno type="eISSN">1756-1663</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Lineage-specific duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selection pressures immediately after gene duplication is clear in the speciation process. Here, using Illumina DNA-sequencing reads from Arabidopsis halleri, which has multiple closely related species with high-quality genome assemblies (A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups in Brassicaceae. The duplication frequency of retained genes in the Arabidopsis lineage was ∼10 times higher than the duplication frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss (Physcomitrella patens). The difference of duplication frequencies can be explained by a rapid decay of anciently duplicated genes. To examine the degree of selection pressure on genes duplicated in either the A. halleri-lyrata or the A. halleri lineage, we examined positive and purifying selection in the A. halleri-lyrata and A. halleri lineages throughout the ratios of nonsynonymous to synonymous substitution rates (KA/KS). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. Interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication compared with immediately after gene duplication.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">29481587</PMID><DateRevised><Year>2019</Year><Month>11</Month><Day>20</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1756-1663</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2018</Year><Month>Feb</Month><Day>21</Day></PubDate></JournalIssue><Title>DNA research : an international journal for rapid publication of reports on genes and genomes</Title><ISOAbbreviation>DNA Res</ISOAbbreviation></Journal><ArticleTitle>Functional divergence of duplicate genes several million years after gene duplication in Arabidopsis.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1093/dnares/dsy005</ELocationID><Abstract><AbstractText>Lineage-specific duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selection pressures immediately after gene duplication is clear in the speciation process. Here, using Illumina DNA-sequencing reads from Arabidopsis halleri, which has multiple closely related species with high-quality genome assemblies (A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups in Brassicaceae. The duplication frequency of retained genes in the Arabidopsis lineage was ∼10 times higher than the duplication frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss (Physcomitrella patens). The difference of duplication frequencies can be explained by a rapid decay of anciently duplicated genes. To examine the degree of selection pressure on genes duplicated in either the A. halleri-lyrata or the A. halleri lineage, we examined positive and purifying selection in the A. halleri-lyrata and A. halleri lineages throughout the ratios of nonsynonymous to synonymous substitution rates (KA/KS). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. Interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication compared with immediately after gene duplication.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hanada</LastName><ForeName>Kousuke</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Bioscience and Bioinformatics, Frontier Research Academy for Young Researchers, Kyusyu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>RIKEN Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa 230-0045, Japan.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tezuka</LastName><ForeName>Ayumi</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Bioscience and Bioinformatics, Frontier Research Academy for Young Researchers, Kyusyu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nozawa</LastName><ForeName>Masafumi</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Genetics, SOKENDAI, Mishima, Shizuoka 411-8540, Japan.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Suzuki</LastName><ForeName>Yutaka</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sugano</LastName><ForeName>Sumio</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nagano</LastName><ForeName>Atsushi J</ForeName><Initials>AJ</Initials><AffiliationInfo><Affiliation>CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center of Ecological Research, Kyoto University, Hirano, Otsu, Shiga 520-2113, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ito</LastName><ForeName>Motomi</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Morinaga</LastName><ForeName>Shin-Ichi</ForeName><Initials>SI</Initials><AffiliationInfo><Affiliation>CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>02</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>DNA 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