Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species
Identifieur interne : 001082 ( Pmc/Checkpoint ); précédent : 001081; suivant : 001083Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species
Auteurs : Tomonori Hirao [Japon] ; Atsushi Watanabe [Japon] ; Manabu Kurita [Japon] ; Teiji Kondo [Japon] ; Katsuhiko Takata [Japon]Source :
- BMC Plant Biology [ 1471-2229 ] ; 2008.
Abstract
The recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species,
The
The observed differences in genomic structure between
Url:
DOI: 10.1186/1471-2229-8-70
PubMed: 18570682
PubMed Central: 2443145
Affiliations:
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PMC:2443145Le document en format XML
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D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species</title>
<author><name sortKey="Hirao, Tomonori" sort="Hirao, Tomonori" uniqKey="Hirao T" first="Tomonori" last="Hirao">Tomonori Hirao</name>
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<author><name sortKey="Kurita, Manabu" sort="Kurita, Manabu" uniqKey="Kurita M" first="Manabu" last="Kurita">Manabu Kurita</name>
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<author><name sortKey="Kondo, Teiji" sort="Kondo, Teiji" uniqKey="Kondo T" first="Teiji" last="Kondo">Teiji Kondo</name>
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<author><name sortKey="Takata, Katsuhiko" sort="Takata, Katsuhiko" uniqKey="Takata K" first="Katsuhiko" last="Takata">Katsuhiko Takata</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Complete nucleotide sequence of the <italic>Cryptomeria japonica </italic>
D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species</title>
<author><name sortKey="Hirao, Tomonori" sort="Hirao, Tomonori" uniqKey="Hirao T" first="Tomonori" last="Hirao">Tomonori Hirao</name>
<affiliation wicri:level="1"><nlm:aff id="I1">Institute of Wood Technology, Akita Prefectural University, 11-1 Kaieisaka, Noshiro, Akita 016-0876, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
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<wicri:noRegion>Akita 016-0876</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="I2">Forestry and Forest Products Research Institute, Forest Tree Breeding Center, 3809-1 Ishi, Juo, Hitachi, Ibaraki 319-1301, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>Forestry and Forest Products Research Institute, Forest Tree Breeding Center, 3809-1 Ishi, Juo, Hitachi, Ibaraki 319-1301</wicri:regionArea>
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</affiliation>
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<author><name sortKey="Watanabe, Atsushi" sort="Watanabe, Atsushi" uniqKey="Watanabe A" first="Atsushi" last="Watanabe">Atsushi Watanabe</name>
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<country xml:lang="fr">Japon</country>
<wicri:regionArea>Forestry and Forest Products Research Institute, Forest Tree Breeding Center, 3809-1 Ishi, Juo, Hitachi, Ibaraki 319-1301</wicri:regionArea>
<wicri:noRegion>Ibaraki 319-1301</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Kurita, Manabu" sort="Kurita, Manabu" uniqKey="Kurita M" first="Manabu" last="Kurita">Manabu Kurita</name>
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<wicri:regionArea>Forestry and Forest Products Research Institute, Forest Tree Breeding Center, 3809-1 Ishi, Juo, Hitachi, Ibaraki 319-1301</wicri:regionArea>
<wicri:noRegion>Ibaraki 319-1301</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Kondo, Teiji" sort="Kondo, Teiji" uniqKey="Kondo T" first="Teiji" last="Kondo">Teiji Kondo</name>
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<wicri:regionArea>Forestry and Forest Products Research Institute, Forest Tree Breeding Center, 3809-1 Ishi, Juo, Hitachi, Ibaraki 319-1301</wicri:regionArea>
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</affiliation>
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<author><name sortKey="Takata, Katsuhiko" sort="Takata, Katsuhiko" uniqKey="Takata K" first="Katsuhiko" last="Takata">Katsuhiko Takata</name>
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<series><title level="j">BMC Plant Biology</title>
<idno type="eISSN">1471-2229</idno>
<imprint><date when="2008">2008</date>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>The recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species, <italic>Cycas taitungensis</italic>
, <italic>Pinus thunbergii</italic>
, and <italic>Pinus koraiensis </italic>
have been established. The lack of information regarding the gene content and genomic structure of gymnosperm cp genomes may severely hamper further progress of plant and cp genome evolutionary studies. To address this need, we report here the complete nucleotide sequence of the cp genome of <italic>Cryptomeria japonica</italic>
, the first in the Cupressaceae sensu lato of gymnosperms, and provide a comparative analysis of their gene content and genomic structure that illustrates the unique genomic features of gymnosperms.</p>
</sec>
<sec><title>Results</title>
<p>The <italic>C. japonica </italic>
cp genome is 131,810 bp in length, with 112 single copy genes and two duplicated (<italic>trn</italic>
I-CAU, <italic>trn</italic>
Q-UUG) genes that give a total of 116 genes. Compared to other land plant cp genomes, the <italic>C. japonica </italic>
cp has lost one of the relevant large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperms, such as <italic>Cycas </italic>
and <italic>Gingko</italic>
, and additionally has completely lost its <italic>trn</italic>
R-CCG, partially lost its <italic>trn</italic>
T-GGU, and shows diversification of <italic>acc</italic>
D. The genomic structure of the <italic>C. japonica </italic>
cp genome also differs significantly from those of other plant species. For example, we estimate that a minimum of 15 inversions would be required to transform the gene organization of the <italic>Pinus thunbergii </italic>
cp genome into that of <italic>C. japonica</italic>
. In the <italic>C. japonica </italic>
cp genome, direct repeat and inverted repeat sequences are observed at the inversion and translocation endpoints, and these sequences may be associated with the genomic rearrangements.</p>
</sec>
<sec><title>Conclusion</title>
<p>The observed differences in genomic structure between <italic>C. japonica </italic>
and other land plants, including pines, strongly support the theory that the large IRs stabilize the cp genome. Furthermore, the deleted large IR and the numerous genomic rearrangements that have occurred in the <italic>C. japonica </italic>
cp genome provide new insights into both the evolutionary lineage of coniferous species in gymnosperm and the evolution of the cp genome.</p>
</sec>
</div>
</front>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Plant Biol</journal-id>
<journal-title>BMC Plant Biology</journal-title>
<issn pub-type="epub">1471-2229</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">18570682</article-id>
<article-id pub-id-type="pmc">2443145</article-id>
<article-id pub-id-type="publisher-id">1471-2229-8-70</article-id>
<article-id pub-id-type="doi">10.1186/1471-2229-8-70</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Complete nucleotide sequence of the <italic>Cryptomeria japonica </italic>
D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species</article-title>
</title-group>
<contrib-group><contrib id="A1" contrib-type="author"><name><surname>Hirao</surname>
<given-names>Tomonori</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>hiratomo@affrc.go.jp</email>
</contrib>
<contrib id="A2" contrib-type="author"><name><surname>Watanabe</surname>
<given-names>Atsushi</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>nabeatsu@affrc.go.jp</email>
</contrib>
<contrib id="A3" contrib-type="author"><name><surname>Kurita</surname>
<given-names>Manabu</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>mkuri@affrc.go.jp</email>
</contrib>
<contrib id="A4" contrib-type="author"><name><surname>Kondo</surname>
<given-names>Teiji</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>kontei@affrc.go.jp</email>
</contrib>
<contrib id="A5" corresp="yes" contrib-type="author"><name><surname>Takata</surname>
<given-names>Katsuhiko</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>katsu@iwt.akita-pu.ac.jp</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Institute of Wood Technology, Akita Prefectural University, 11-1 Kaieisaka, Noshiro, Akita 016-0876, Japan</aff>
<aff id="I2"><label>2</label>
Forestry and Forest Products Research Institute, Forest Tree Breeding Center, 3809-1 Ishi, Juo, Hitachi, Ibaraki 319-1301, Japan</aff>
<pub-date pub-type="collection"><year>2008</year>
</pub-date>
<pub-date pub-type="epub"><day>23</day>
<month>6</month>
<year>2008</year>
</pub-date>
<volume>8</volume>
<fpage>70</fpage>
<lpage>70</lpage>
<ext-link ext-link-type="uri" xlink:href="http://www.biomedcentral.com/1471-2229/8/70"></ext-link>
<history><date date-type="received"><day>23</day>
<month>1</month>
<year>2008</year>
</date>
<date date-type="accepted"><day>23</day>
<month>6</month>
<year>2008</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2008 Hirao et al; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2008</copyright-year>
<copyright-holder>Hirao et al; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><p>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"></ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p>
<pmc-comment>
Hirao
Tomonori
hiratomo@affrc.go.jp
Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species
2008 BMC Plant Biology 8(1): 70-. (2008) 1471-2229(2008)8:1<70> urn:ISSN:1471-2229 </pmc-comment>
</license>
</permissions>
<abstract><sec><title>Background</title>
<p>The recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species, <italic>Cycas taitungensis</italic>
, <italic>Pinus thunbergii</italic>
, and <italic>Pinus koraiensis </italic>
have been established. The lack of information regarding the gene content and genomic structure of gymnosperm cp genomes may severely hamper further progress of plant and cp genome evolutionary studies. To address this need, we report here the complete nucleotide sequence of the cp genome of <italic>Cryptomeria japonica</italic>
, the first in the Cupressaceae sensu lato of gymnosperms, and provide a comparative analysis of their gene content and genomic structure that illustrates the unique genomic features of gymnosperms.</p>
</sec>
<sec><title>Results</title>
<p>The <italic>C. japonica </italic>
cp genome is 131,810 bp in length, with 112 single copy genes and two duplicated (<italic>trn</italic>
I-CAU, <italic>trn</italic>
Q-UUG) genes that give a total of 116 genes. Compared to other land plant cp genomes, the <italic>C. japonica </italic>
cp has lost one of the relevant large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperms, such as <italic>Cycas </italic>
and <italic>Gingko</italic>
, and additionally has completely lost its <italic>trn</italic>
R-CCG, partially lost its <italic>trn</italic>
T-GGU, and shows diversification of <italic>acc</italic>
D. The genomic structure of the <italic>C. japonica </italic>
cp genome also differs significantly from those of other plant species. For example, we estimate that a minimum of 15 inversions would be required to transform the gene organization of the <italic>Pinus thunbergii </italic>
cp genome into that of <italic>C. japonica</italic>
. In the <italic>C. japonica </italic>
cp genome, direct repeat and inverted repeat sequences are observed at the inversion and translocation endpoints, and these sequences may be associated with the genomic rearrangements.</p>
</sec>
<sec><title>Conclusion</title>
<p>The observed differences in genomic structure between <italic>C. japonica </italic>
and other land plants, including pines, strongly support the theory that the large IRs stabilize the cp genome. Furthermore, the deleted large IR and the numerous genomic rearrangements that have occurred in the <italic>C. japonica </italic>
cp genome provide new insights into both the evolutionary lineage of coniferous species in gymnosperm and the evolution of the cp genome.</p>
</sec>
</abstract>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Japon</li>
</country>
</list>
<tree><country name="Japon"><noRegion><name sortKey="Hirao, Tomonori" sort="Hirao, Tomonori" uniqKey="Hirao T" first="Tomonori" last="Hirao">Tomonori Hirao</name>
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<name sortKey="Hirao, Tomonori" sort="Hirao, Tomonori" uniqKey="Hirao T" first="Tomonori" last="Hirao">Tomonori Hirao</name>
<name sortKey="Kondo, Teiji" sort="Kondo, Teiji" uniqKey="Kondo T" first="Teiji" last="Kondo">Teiji Kondo</name>
<name sortKey="Kurita, Manabu" sort="Kurita, Manabu" uniqKey="Kurita M" first="Manabu" last="Kurita">Manabu Kurita</name>
<name sortKey="Takata, Katsuhiko" sort="Takata, Katsuhiko" uniqKey="Takata K" first="Katsuhiko" last="Takata">Katsuhiko Takata</name>
<name sortKey="Watanabe, Atsushi" sort="Watanabe, Atsushi" uniqKey="Watanabe A" first="Atsushi" last="Watanabe">Atsushi Watanabe</name>
</country>
</tree>
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