Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots
Identifieur interne : 002057 ( Main/Exploration ); précédent : 002056; suivant : 002058Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots
Auteurs : Rui-Jiang Wang [République populaire de Chine, Taïwan] ; Chiao-Lei Cheng [Taïwan] ; Ching-Chun Chang [Taïwan] ; Chun-Lin Wu [Taïwan] ; Tian-Mu Su [Taïwan] ; Shu-Miaw Chaw [Taïwan]Source :
- BMC Evolutionary Biology [ 1471-2148 ] ; 2008.
Abstract
Various expansions or contractions of inverted repeats (IRs) in chloroplast genomes led to fluxes in the IR-LSC (large single copy) junctions. Previous studies revealed that some monocot IRs contain a
The organizations of genes flanking IR-LSC junctions in angiosperms can be classified into three types. Generally each IR of monocots contains a
Two hypotheses are proposed to account for the evolution of IR expansions in monocots. Based on our observations, the inclusion of a
Url:
DOI: 10.1186/1471-2148-8-36
PubMed: 18237435
PubMed Central: 2275221
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots</title><author><name sortKey="Wang, Rui Jiang" sort="Wang, Rui Jiang" uniqKey="Wang R" first="Rui-Jiang" last="Wang">Rui-Jiang Wang</name><affiliation wicri:level="1"><nlm:aff id="I1">South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou 510650, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou 510650</wicri:regionArea><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Research Center for Biodiversity, Academia Sinica, Taipei 115, Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Research Center for Biodiversity, Academia Sinica, Taipei 115</wicri:regionArea><wicri:noRegion>Taipei 115</wicri:noRegion></affiliation></author><author><name sortKey="Cheng, Chiao Lei" sort="Cheng, Chiao Lei" uniqKey="Cheng C" first="Chiao-Lei" last="Cheng">Chiao-Lei Cheng</name><affiliation wicri:level="1"><nlm:aff id="I2">Research Center for Biodiversity, Academia Sinica, Taipei 115, Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Research Center for Biodiversity, Academia Sinica, Taipei 115</wicri:regionArea><wicri:noRegion>Taipei 115</wicri:noRegion></affiliation></author><author><name sortKey="Chang, Ching Chun" sort="Chang, Ching Chun" uniqKey="Chang C" first="Ching-Chun" last="Chang">Ching-Chun Chang</name><affiliation wicri:level="1"><nlm:aff id="I3">Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Biotechnology, National Cheng Kung University, Tainan</wicri:regionArea><wicri:noRegion>Tainan</wicri:noRegion></affiliation></author><author><name sortKey="Wu, Chun Lin" sort="Wu, Chun Lin" uniqKey="Wu C" first="Chun-Lin" last="Wu">Chun-Lin Wu</name><affiliation wicri:level="1"><nlm:aff id="I2">Research Center for Biodiversity, Academia Sinica, Taipei 115, Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Research Center for Biodiversity, Academia Sinica, Taipei 115</wicri:regionArea><wicri:noRegion>Taipei 115</wicri:noRegion></affiliation></author><author><name sortKey="Su, Tian Mu" sort="Su, Tian Mu" uniqKey="Su T" first="Tian-Mu" last="Su">Tian-Mu Su</name><affiliation wicri:level="1"><nlm:aff id="I2">Research Center for Biodiversity, Academia Sinica, Taipei 115, Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Research Center for Biodiversity, Academia Sinica, Taipei 115</wicri:regionArea><wicri:noRegion>Taipei 115</wicri:noRegion></affiliation></author><author><name sortKey="Chaw, Shu Miaw" sort="Chaw, Shu Miaw" uniqKey="Chaw S" first="Shu-Miaw" last="Chaw">Shu-Miaw Chaw</name><affiliation wicri:level="1"><nlm:aff id="I2">Research Center for Biodiversity, Academia Sinica, Taipei 115, Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Research Center for Biodiversity, Academia Sinica, Taipei 115</wicri:regionArea><wicri:noRegion>Taipei 115</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18237435</idno><idno type="pmc">2275221</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275221</idno><idno type="RBID">PMC:2275221</idno><idno type="doi">10.1186/1471-2148-8-36</idno><date when="2008">2008</date><idno type="wicri:Area/Pmc/Corpus">000B03</idno><idno type="wicri:Area/Pmc/Curation">000B02</idno><idno type="wicri:Area/Pmc/Checkpoint">001077</idno><idno type="wicri:Area/Ncbi/Merge">000791</idno><idno type="wicri:Area/Ncbi/Curation">000791</idno><idno type="wicri:Area/Ncbi/Checkpoint">000791</idno><idno type="wicri:Area/Main/Merge">002115</idno><idno type="wicri:Area/Main/Curation">002057</idno><idno type="wicri:Area/Main/Exploration">002057</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots</title><author><name sortKey="Wang, Rui Jiang" sort="Wang, Rui Jiang" uniqKey="Wang R" first="Rui-Jiang" last="Wang">Rui-Jiang Wang</name><affiliation wicri:level="1"><nlm:aff id="I1">South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou 510650, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou 510650</wicri:regionArea><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Research Center for Biodiversity, Academia Sinica, Taipei 115, Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Research Center for Biodiversity, Academia Sinica, Taipei 115</wicri:regionArea><wicri:noRegion>Taipei 115</wicri:noRegion></affiliation></author><author><name sortKey="Cheng, Chiao Lei" sort="Cheng, Chiao Lei" uniqKey="Cheng C" first="Chiao-Lei" last="Cheng">Chiao-Lei Cheng</name><affiliation wicri:level="1"><nlm:aff id="I2">Research Center for Biodiversity, Academia Sinica, Taipei 115, Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Research Center for Biodiversity, Academia Sinica, Taipei 115</wicri:regionArea><wicri:noRegion>Taipei 115</wicri:noRegion></affiliation></author><author><name sortKey="Chang, Ching Chun" sort="Chang, Ching Chun" uniqKey="Chang C" first="Ching-Chun" last="Chang">Ching-Chun Chang</name><affiliation wicri:level="1"><nlm:aff id="I3">Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Biotechnology, National Cheng Kung University, Tainan</wicri:regionArea><wicri:noRegion>Tainan</wicri:noRegion></affiliation></author><author><name sortKey="Wu, Chun Lin" sort="Wu, Chun Lin" uniqKey="Wu C" first="Chun-Lin" last="Wu">Chun-Lin Wu</name><affiliation wicri:level="1"><nlm:aff id="I2">Research Center for Biodiversity, Academia Sinica, Taipei 115, Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Research Center for Biodiversity, Academia Sinica, Taipei 115</wicri:regionArea><wicri:noRegion>Taipei 115</wicri:noRegion></affiliation></author><author><name sortKey="Su, Tian Mu" sort="Su, Tian Mu" uniqKey="Su T" first="Tian-Mu" last="Su">Tian-Mu Su</name><affiliation wicri:level="1"><nlm:aff id="I2">Research Center for Biodiversity, Academia Sinica, Taipei 115, Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Research Center for Biodiversity, Academia Sinica, Taipei 115</wicri:regionArea><wicri:noRegion>Taipei 115</wicri:noRegion></affiliation></author><author><name sortKey="Chaw, Shu Miaw" sort="Chaw, Shu Miaw" uniqKey="Chaw S" first="Shu-Miaw" last="Chaw">Shu-Miaw Chaw</name><affiliation wicri:level="1"><nlm:aff id="I2">Research Center for Biodiversity, Academia Sinica, Taipei 115, Taiwan</nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Research Center for Biodiversity, Academia Sinica, Taipei 115</wicri:regionArea><wicri:noRegion>Taipei 115</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Evolutionary Biology</title><idno type="eISSN">1471-2148</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Various expansions or contractions of inverted repeats (IRs) in chloroplast genomes led to fluxes in the IR-LSC (large single copy) junctions. Previous studies revealed that some monocot IRs contain a <italic>trnH-rps19 </italic>gene cluster, and it has been speculated that this may be an evidence of a duplication event prior to the divergence of monocot lineages. Therefore, we compared the organizations of genes flanking two IR-LSC junctions in 123 angiosperm representatives to uncover the evolutionary dynamics of IR-LSC junctions in basal angiosperms and monocots.</p></sec><sec><title>Results</title><p>The organizations of genes flanking IR-LSC junctions in angiosperms can be classified into three types. Generally each IR of monocots contains a <italic>trnH-rps19 </italic>gene cluster near the IR-LSC junctions, which differs from those in non-monocot angiosperms. Moreover, IRs expanded more progressively in monocots than in non-monocot angiosperms. IR-LSC junctions commonly occurred at polyA tract or A-rich regions in angiosperms. Our RT-PCR assays indicate that in monocot IR<sub>A </sub>the <italic>trnH-rps19 </italic>gene cluster is regulated by two opposing promoters, <italic>S10</italic><sub><italic>A </italic></sub>and <italic>psbA</italic>.</p></sec><sec><title>Conclusion</title><p>Two hypotheses are proposed to account for the evolution of IR expansions in monocots. Based on our observations, the inclusion of a <italic>trnH-rps19 </italic>cluster in majority of monocot IRs could be reasonably explained by the hypothesis that a DSB event first occurred at IR<sub>B </sub>and led to the expansion of IRs to <italic>trnH</italic>, followed by a successive DSB event within IR<sub>A </sub>and lead to the expansion of IRs to <italic>rps19 </italic>or to <italic>rpl22 </italic>so far. This implies that the duplication of <italic>trnH-rps19 </italic>gene cluster was prior to the diversification of extant monocot lineages. The duplicated <italic>trnH </italic>genes in the IR<sub>B </sub>of most monocots and non-monocot angiosperms have distinct fates, which are likely regulated by different expression levels of <italic>S10</italic><sub><italic>A </italic></sub>and <italic>S10</italic><sub><italic>B </italic></sub>promoters. Further study is needed to unravel the evolutionary significance of IR expansion in more recently diverged monocots.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Kolodner, R" uniqKey="Kolodner R">R Kolodner</name></author><author><name sortKey="Tewari, Kk" uniqKey="Tewari K">KK Tewari</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Palmer, Jd" uniqKey="Palmer J">JD Palmer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shinozaki, K" uniqKey="Shinozaki K">K Shinozaki</name></author><author><name sortKey="Ohme, M" uniqKey="Ohme M">M Ohme</name></author><author><name sortKey="Tanaka, M" uniqKey="Tanaka M">M Tanaka</name></author><author><name sortKey="Wakasugi, T" uniqKey="Wakasugi T">T Wakasugi</name></author><author><name sortKey="Hayashida, N" uniqKey="Hayashida N">N Hayashida</name></author><author><name sortKey="Matsubayashi, T" 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Tabata</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ravi, V" uniqKey="Ravi V">V Ravi</name></author><author><name sortKey="Khurana, Jp" uniqKey="Khurana J">JP Khurana</name></author><author><name sortKey="Tyagi, Ak" uniqKey="Tyagi A">AK Tyagi</name></author><author><name sortKey="Khurana, P" uniqKey="Khurana P">P Khurana</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goremykin, Vv" uniqKey="Goremykin V">VV Goremykin</name></author><author><name sortKey="Holland, B" uniqKey="Holland B">B Holland</name></author><author><name sortKey="Hirsch Ernst, Ki" uniqKey="Hirsch Ernst K">KI Hirsch-Ernst</name></author><author><name sortKey="Hellwig, Fh" uniqKey="Hellwig F">FH Hellwig</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Masooda, Ms" uniqKey="Masooda M">MS Masooda</name></author><author><name sortKey="Nishikawaa, T" uniqKey="Nishikawaa T">T Nishikawaa</name></author><author><name 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Smimada</name></author><author><name sortKey="Kadowaki, K" uniqKey="Kadowaki K">K Kadowaki</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ogihara, Y" uniqKey="Ogihara Y">Y Ogihara</name></author><author><name sortKey="Isono, K" uniqKey="Isono K">K Isono</name></author><author><name sortKey="Kojima, T" uniqKey="Kojima T">T Kojima</name></author><author><name sortKey="Endo, A" uniqKey="Endo A">A Endo</name></author><author><name sortKey="Hanaoka, M" uniqKey="Hanaoka M">M Hanaoka</name></author><author><name sortKey="Shiina, T" uniqKey="Shiina T">T Shiina</name></author><author><name sortKey="Terachi, T" uniqKey="Terachi T">T Terachi</name></author><author><name sortKey="Utsugi, S" uniqKey="Utsugi S">S Utsugi</name></author><author><name sortKey="Murata, M" uniqKey="Murata M">M Murata</name></author><author><name sortKey="Mori, N" uniqKey="Mori N">N Mori</name></author><author><name sortKey="Takumi, S" uniqKey="Takumi S">S Takumi</name></author><author><name sortKey="Ikeo, K" uniqKey="Ikeo K">K Ikeo</name></author><author><name sortKey="Gojobori, T" uniqKey="Gojobori T">T Gojobori</name></author><author><name sortKey="Murai, R" uniqKey="Murai R">R Murai</name></author><author><name sortKey="Murai, K" uniqKey="Murai K">K Murai</name></author><author><name sortKey="Matsuoka, Y" uniqKey="Matsuoka Y">Y Matsuoka</name></author><author><name sortKey="Ohnishi, Y" uniqKey="Ohnishi Y">Y Ohnishi</name></author><author><name sortKey="Tajiri, H" uniqKey="Tajiri H">H Tajiri</name></author><author><name sortKey="Tsunewaki, K" uniqKey="Tsunewaki K">K Tsunewaki</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li><li>Taïwan</li></country><region><li>Guangdong</li></region><settlement><li>Jiangmen</li></settlement></list><tree><country name="République populaire de Chine"><region name="Guangdong"><name sortKey="Wang, Rui Jiang" sort="Wang, Rui Jiang" uniqKey="Wang R" first="Rui-Jiang" last="Wang">Rui-Jiang Wang</name></region></country><country name="Taïwan"><noRegion><name sortKey="Wang, Rui Jiang" sort="Wang, Rui Jiang" uniqKey="Wang R" first="Rui-Jiang" last="Wang">Rui-Jiang Wang</name></noRegion><name sortKey="Chang, Ching Chun" sort="Chang, Ching Chun" uniqKey="Chang C" first="Ching-Chun" last="Chang">Ching-Chun Chang</name><name sortKey="Chaw, Shu Miaw" sort="Chaw, Shu Miaw" uniqKey="Chaw S" first="Shu-Miaw" last="Chaw">Shu-Miaw Chaw</name><name sortKey="Cheng, Chiao Lei" sort="Cheng, Chiao Lei" uniqKey="Cheng C" first="Chiao-Lei" last="Cheng">Chiao-Lei Cheng</name><name sortKey="Su, Tian Mu" sort="Su, Tian Mu" uniqKey="Su T" first="Tian-Mu" last="Su">Tian-Mu Su</name><name sortKey="Wu, Chun Lin" sort="Wu, Chun Lin" uniqKey="Wu C" first="Chun-Lin" last="Wu">Chun-Lin Wu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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