Genome Survey Sequencing for the Characterization of the Genetic Background of Rosa roxburghii Tratt and Leaf Ascorbate Metabolism Genes
Identifieur interne : 000168 ( Pmc/Checkpoint ); précédent : 000167; suivant : 000169Genome 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></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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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, CA USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26849133</article-id><article-id pub-id-type="pmc">4743950</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0147530</article-id><article-id pub-id-type="publisher-id">PONE-D-15-32707</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Genomics</subject><subj-group><subject>Plant Genomics</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Biotechnology</subject><subj-group><subject>Plant Biotechnology</subject><subj-group><subject>Plant Genomics</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Plant Science</subject><subj-group><subject>Plant Biotechnology</subject><subj-group><subject>Plant Genomics</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Plant Genetics</subject><subj-group><subject>Plant Genomics</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Plant Science</subject><subj-group><subject>Plant Genetics</subject><subj-group><subject>Plant Genomics</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Molecular Biology</subject><subj-group><subject>Molecular Biology Techniques</subject><subj-group><subject>Sequencing Techniques</subject><subj-group><subject>Sequence Analysis</subject><subj-group><subject>Sequence Motif Analysis</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject><subj-group><subject>Molecular Biology Techniques</subject><subj-group><subject>Sequencing Techniques</subject><subj-group><subject>Sequence Analysis</subject><subj-group><subject>Sequence Motif Analysis</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Genomics</subject><subj-group><subject>Genomic Medicine</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and life sciences</subject><subj-group><subject>Molecular biology</subject><subj-group><subject>Molecular biology techniques</subject><subj-group><subject>DNA construction</subject><subj-group><subject>DNA library construction</subject><subj-group><subject>Genomic Library Construction</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Research and analysis methods</subject><subj-group><subject>Molecular biology techniques</subject><subj-group><subject>DNA construction</subject><subj-group><subject>DNA library construction</subject><subj-group><subject>Genomic Library Construction</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Computational Biology</subject><subj-group><subject>Genome Analysis</subject><subj-group><subject>Sequence Assembly Tools</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Genomics</subject><subj-group><subject>Genome Analysis</subject><subj-group><subject>Sequence Assembly Tools</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject><subj-group><subject>Database and Informatics Methods</subject><subj-group><subject>Biological Databases</subject><subj-group><subject>Genomic Databases</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Computational Biology</subject><subj-group><subject>Genome Analysis</subject><subj-group><subject>Genomic Databases</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Genetics</subject><subj-group><subject>Genomics</subject><subj-group><subject>Genome Analysis</subject><subj-group><subject>Genomic Databases</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject><subj-group><subject>Molecular Biology</subject><subj-group><subject>Molecular Biology Techniques</subject><subj-group><subject>Sequencing Techniques</subject><subj-group><subject>Genome Sequencing</subject></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject><subj-group><subject>Molecular Biology Techniques</subject><subj-group><subject>Sequencing Techniques</subject><subj-group><subject>Genome Sequencing</subject></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Physical sciences</subject><subj-group><subject>Chemistry</subject><subj-group><subject>Chemical compounds</subject><subj-group><subject>Organic compounds</subject><subj-group><subject>Vitamins</subject><subj-group><subject>Vitamin C</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v3"><subject>Physical sciences</subject><subj-group><subject>Chemistry</subject><subj-group><subject>Organic chemistry</subject><subj-group><subject>Organic compounds</subject><subj-group><subject>Vitamins</subject><subj-group><subject>Vitamin C</subject></subj-group></subj-group></subj-group></subj-group></subj-group></subj-group></article-categories><title-group><article-title>Genome Survey Sequencing for the Characterization of the Genetic Background of <italic>Rosa roxburghii</italic> Tratt and Leaf Ascorbate Metabolism Genes</article-title><alt-title alt-title-type="running-head">Genome Survey Sequencing for <italic>Rosa roxburghii</italic> and Ascorbate Metabolism</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Lu</surname><given-names>Min</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>An</surname><given-names>Huaming</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff002"><sup>2</sup></xref><xref ref-type="corresp" rid="cor001">*</xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Liangliang</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib></contrib-group><aff id="aff001"><label>1</label><addr-line>Agricultural College, Guizhou University, Guiyang, Guizhou, China</addr-line></aff><aff id="aff002"><label>2</label><addr-line>Guizhou Engineering Research Center for Fruit Crops, Guiyang, Guizhou, China</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Jain</surname><given-names>Mukesh</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Jawaharlal Nehru University, INDIA</addr-line></aff><author-notes><fn fn-type="conflict" id="coi001"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con" id="contrib001"><p>Conceived and designed the experiments: HMA. Performed the experiments: ML LLL. Analyzed the data: ML HMA. Contributed reagents/materials/analysis tools: ML LLL. Wrote the paper: ML HMA.</p></fn><corresp id="cor001">* E-mail: <email>anhuaming@hotmail.com</email></corresp></author-notes><pub-date pub-type="epub"><day>5</day><month>2</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>11</volume><issue>2</issue><elocation-id>e0147530</elocation-id><history><date date-type="received"><day>30</day><month>7</month><year>2015</year></date><date date-type="accepted"><day>5</day><month>1</month><year>2016</year></date></history><permissions><copyright-statement>© 2016 Lu et al</copyright-statement><copyright-year>2016</copyright-year><copyright-holder>Lu et al</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:type="simple" xlink:href="pone.0147530.pdf"></self-uri><abstract><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). This is the first report of genome-wide characterization of this rose species.</p></abstract><funding-group><funding-statement>This work was supported by grants from the National Natural Science Foundation of China (31360475, AHM), <ext-link ext-link-type="uri" xlink:href="http://www.nsfc.gov.cn">http://www.nsfc.gov.cn</ext-link>; the special project of major science and technology in Guizhou Province, P. R. China (20136006-1, AHM), <ext-link ext-link-type="uri" xlink:href="http://kjt.gzst.gov.cn">http://kjt.gzst.gov.cn</ext-link>; and the natural science foundation in Guizhou Province, P. R. China (20122169, LM), <ext-link ext-link-type="uri" xlink:href="http://www.nsfc.gov.cn">http://www.nsfc.gov.cn</ext-link>. The funders provided support in the form of salaries for authors [AMH and LM], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.</funding-statement></funding-group><counts><fig-count count="8"></fig-count><table-count count="6"></table-count><page-count count="17"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>The genome sequence reads obtained by Illumina Hiseq 2500 are available at NCBI-SRA. The Bioproject accession number is PRJNA304925 (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/bioproject/304925">http://www.ncbi.nlm.nih.gov/bioproject/304925</ext-link>) and the Biosample accession number is SAMN04309304 (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/biosample/4309304">http://www.ncbi.nlm.nih.gov/biosample/4309304</ext-link>). The Experiment number: SRX1459983/Rosa roxburghii and Run number: SRR2970602.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>The genome sequence reads obtained by Illumina Hiseq 2500 are available at NCBI-SRA. The Bioproject accession number is PRJNA304925 (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/bioproject/304925">http://www.ncbi.nlm.nih.gov/bioproject/304925</ext-link>) and the Biosample accession number is SAMN04309304 (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/biosample/4309304">http://www.ncbi.nlm.nih.gov/biosample/4309304</ext-link>). The Experiment number: SRX1459983/Rosa roxburghii and Run number: SRR2970602.</p></notes></front></pmc><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Lu, Min" sort="Lu, 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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