Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species
Identifieur interne : 000851 ( Ncbi/Curation ); précédent : 000850; suivant : 000852Complete 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
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000975
- to stream Pmc, to step Curation: Pour aller vers cette notice dans l'étape Curation :000974
- to stream Pmc, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :001082
- to stream Ncbi, to step Merge: Pour aller vers cette notice dans l'étape Curation :000851
Links to Exploration step
PMC:2443145Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">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>
<wicri:regionArea>Institute of Wood Technology, Akita Prefectural University, 11-1 Kaieisaka, Noshiro, Akita 016-0876</wicri:regionArea>
<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>
<wicri:noRegion>Ibaraki 319-1301</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Watanabe, Atsushi" sort="Watanabe, Atsushi" uniqKey="Watanabe A" first="Atsushi" last="Watanabe">Atsushi Watanabe</name>
<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>
<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>
<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>
<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>
<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>
<wicri:noRegion>Ibaraki 319-1301</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Takata, Katsuhiko" sort="Takata, Katsuhiko" uniqKey="Takata K" first="Katsuhiko" last="Takata">Katsuhiko Takata</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>
<wicri:regionArea>Institute of Wood Technology, Akita Prefectural University, 11-1 Kaieisaka, Noshiro, Akita 016-0876</wicri:regionArea>
<wicri:noRegion>Akita 016-0876</wicri:noRegion>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">18570682</idno>
<idno type="pmc">2443145</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2443145</idno>
<idno type="RBID">PMC:2443145</idno>
<idno type="doi">10.1186/1471-2229-8-70</idno>
<date when="2008">2008</date>
<idno type="wicri:Area/Pmc/Corpus">000975</idno>
<idno type="wicri:Area/Pmc/Curation">000974</idno>
<idno type="wicri:Area/Pmc/Checkpoint">001082</idno>
<idno type="wicri:Area/Ncbi/Merge">000851</idno>
<idno type="wicri:Area/Ncbi/Curation">000851</idno>
</publicationStmt>
<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>
<wicri:regionArea>Institute of Wood Technology, Akita Prefectural University, 11-1 Kaieisaka, Noshiro, Akita 016-0876</wicri:regionArea>
<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>
<wicri:noRegion>Ibaraki 319-1301</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Watanabe, Atsushi" sort="Watanabe, Atsushi" uniqKey="Watanabe A" first="Atsushi" last="Watanabe">Atsushi Watanabe</name>
<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>
<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>
<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>
<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>
<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>
<wicri:noRegion>Ibaraki 319-1301</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Takata, Katsuhiko" sort="Takata, Katsuhiko" uniqKey="Takata K" first="Katsuhiko" last="Takata">Katsuhiko Takata</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>
<wicri:regionArea>Institute of Wood Technology, Akita Prefectural University, 11-1 Kaieisaka, Noshiro, Akita 016-0876</wicri:regionArea>
<wicri:noRegion>Akita 016-0876</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">BMC Plant Biology</title>
<idno type="eISSN">1471-2229</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>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>
<back><div1 type="bibliography"><listBibl><biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
</listBibl>
</div1>
</back>
</TEI>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Bois/explor/OrangerV1/Data/Ncbi/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000851 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd -nk 000851 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Wicri/Bois |area= OrangerV1 |flux= Ncbi |étape= Curation |type= RBID |clé= PMC:2443145 |texte= Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/RBID.i -Sk "pubmed:18570682" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd \ | NlmPubMed2Wicri -a OrangerV1
This area was generated with Dilib version V0.6.25. |