Genome Survey Sequencing for the Characterization of the Genetic Background of Rosa roxburghii Tratt and Leaf Ascorbate Metabolism Genes
Identifieur interne : 000205 ( Main/Exploration ); précédent : 000204; suivant : 000206Genome Survey Sequencing for the Characterization of the Genetic Background of Rosa roxburghii Tratt and Leaf Ascorbate Metabolism Genes
Auteurs : Min Lu [République populaire de Chine] ; Huaming An [République populaire de Chine] ; Liangliang Li [République populaire de Chine]Source :
- PLoS ONE [ 1932-6203 ] ; 2016.
Abstract
Url:
DOI: 10.1371/journal.pone.0147530
PubMed: 26849133
PubMed Central: 4743950
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome Survey Sequencing for the Characterization of the Genetic Background of <italic>Rosa roxburghii</italic> Tratt and Leaf Ascorbate Metabolism Genes</title><author><name sortKey="Lu, Min" sort="Lu, Min" uniqKey="Lu M" first="Min" last="Lu">Min Lu</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Agricultural College, Guizhou University, Guiyang, Guizhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Agricultural College, Guizhou University, Guiyang, Guizhou</wicri:regionArea><wicri:noRegion>Guizhou</wicri:noRegion></affiliation></author><author><name sortKey="An, Huaming" sort="An, Huaming" uniqKey="An H" first="Huaming" last="An">Huaming An</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Agricultural College, Guizhou University, Guiyang, Guizhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Agricultural College, Guizhou University, Guiyang, Guizhou</wicri:regionArea><wicri:noRegion>Guizhou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Guizhou Engineering Research Center for Fruit Crops, Guiyang, Guizhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Guizhou Engineering Research Center for Fruit Crops, Guiyang, Guizhou</wicri:regionArea><wicri:noRegion>Guizhou</wicri:noRegion></affiliation></author><author><name sortKey="Li, Liangliang" sort="Li, Liangliang" uniqKey="Li L" first="Liangliang" last="Li">Liangliang Li</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Agricultural College, Guizhou University, Guiyang, Guizhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Agricultural College, Guizhou University, Guiyang, Guizhou</wicri:regionArea><wicri:noRegion>Guizhou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Guizhou Engineering Research Center for Fruit Crops, Guiyang, Guizhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Guizhou Engineering Research Center for Fruit Crops, Guiyang, Guizhou</wicri:regionArea><wicri:noRegion>Guizhou</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26849133</idno><idno type="pmc">4743950</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4743950</idno><idno type="RBID">PMC:4743950</idno><idno type="doi">10.1371/journal.pone.0147530</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000374</idno><idno type="wicri:Area/Pmc/Curation">000373</idno><idno type="wicri:Area/Pmc/Checkpoint">000168</idno><idno type="wicri:Area/Ncbi/Merge">001E99</idno><idno type="wicri:Area/Ncbi/Curation">001E99</idno><idno type="wicri:Area/Ncbi/Checkpoint">001E99</idno><idno type="wicri:Area/Main/Merge">000205</idno><idno type="wicri:Area/Main/Curation">000205</idno><idno type="wicri:Area/Main/Exploration">000205</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome Survey Sequencing for the Characterization of the Genetic Background of <italic>Rosa roxburghii</italic> Tratt and Leaf Ascorbate Metabolism Genes</title><author><name sortKey="Lu, Min" sort="Lu, Min" uniqKey="Lu M" first="Min" last="Lu">Min Lu</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Agricultural College, Guizhou University, Guiyang, Guizhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Agricultural College, Guizhou University, Guiyang, Guizhou</wicri:regionArea><wicri:noRegion>Guizhou</wicri:noRegion></affiliation></author><author><name sortKey="An, Huaming" sort="An, Huaming" uniqKey="An H" first="Huaming" last="An">Huaming An</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Agricultural College, Guizhou University, Guiyang, Guizhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Agricultural College, Guizhou University, Guiyang, Guizhou</wicri:regionArea><wicri:noRegion>Guizhou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Guizhou Engineering Research Center for Fruit Crops, Guiyang, Guizhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Guizhou Engineering Research Center for Fruit Crops, Guiyang, Guizhou</wicri:regionArea><wicri:noRegion>Guizhou</wicri:noRegion></affiliation></author><author><name sortKey="Li, Liangliang" sort="Li, Liangliang" uniqKey="Li L" first="Liangliang" last="Li">Liangliang Li</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Agricultural College, Guizhou University, Guiyang, Guizhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Agricultural College, Guizhou University, Guiyang, Guizhou</wicri:regionArea><wicri:noRegion>Guizhou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Guizhou Engineering Research Center for Fruit Crops, Guiyang, Guizhou, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Guizhou Engineering Research Center for Fruit Crops, Guiyang, Guizhou</wicri:regionArea><wicri:noRegion>Guizhou</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><italic>Rosa roxburghii</italic> Tratt is an important commercial horticultural crop in China that is recognized for its nutritional and medicinal values. In spite of the economic significance, genomic information on this rose species is currently unavailable. In the present research, a genome survey of <italic>R</italic>. <italic>roxburghii</italic> was carried out using next-generation sequencing (NGS) technologies. Total 30.29 Gb sequence data was obtained by HiSeq 2500 sequencing and an estimated genome size of <italic>R</italic>. <italic>roxburghii</italic> was 480.97 Mb, in which the guanine plus cytosine (GC) content was calculated to be 38.63%. All of these reads were technically assembled and a total of 627,554 contigs with a N50 length of 1.484 kb and furthermore 335,902 scaffolds with a total length of 409.36 Mb were obtained. Transposable elements (TE) sequence of 90.84 Mb which comprised 29.20% of the genome, and 167,859 simple sequence repeats (SSRs) were identified from the scaffolds. Among these, the mono-(66.30%), di-(25.67%), and tri-(6.64%) nucleotide repeats contributed to nearly 99% of the SSRs, and sequence motifs AG/CT (28.81%) and GAA/TTC (14.76%) were the most abundant among the dinucleotide and trinucleotide repeat motifs, respectively. Genome analysis predicted a total of 22,721 genes which have an average length of 2311.52 bp, an average exon length of 228.15 bp, and average intron length of 401.18 bp. Eleven genes putatively involved in ascorbate metabolism were identified and its expression in <italic>R</italic>. <italic>roxburghii</italic> leaves was validated by quantitative real-time PCR (qRT-PCR). 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Min" uniqKey="Lu M" first="Min" last="Lu">Min Lu</name></noRegion><name sortKey="An, Huaming" sort="An, Huaming" uniqKey="An H" first="Huaming" last="An">Huaming An</name><name sortKey="An, Huaming" sort="An, Huaming" uniqKey="An H" first="Huaming" last="An">Huaming An</name><name sortKey="Li, Liangliang" sort="Li, Liangliang" uniqKey="Li L" first="Liangliang" last="Li">Liangliang Li</name><name sortKey="Li, Liangliang" sort="Li, Liangliang" uniqKey="Li L" first="Liangliang" last="Li">Liangliang Li</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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