Comparative Genomics of Ten Solanaceous Plastomes
Identifieur interne : 001938 ( Ncbi/Curation ); précédent : 001937; suivant : 001939Comparative Genomics of Ten Solanaceous Plastomes
Auteurs : Harpreet Kaur [Inde] ; Bhupinder Pal Singh [Inde] ; Harpreet Singh [Inde] ; Avinash Kaur Nagpal [Inde]Source :
- Advances in Bioinformatics [ 1687-8027 ] ; 2014.
Abstract
Availability of complete plastid genomes of ten solanaceous species,
Url:
DOI: 10.1155/2014/424873
PubMed: 25477958
PubMed Central: 4248371
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Comparative Genomics of Ten Solanaceous Plastomes</title><author><name sortKey="Kaur, Harpreet" sort="Kaur, Harpreet" uniqKey="Kaur H" first="Harpreet" last="Kaur">Harpreet Kaur</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005</wicri:regionArea><wicri:noRegion>Amritsar 143005</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Bhupinder Pal" sort="Singh, Bhupinder Pal" uniqKey="Singh B" first="Bhupinder Pal" last="Singh">Bhupinder Pal Singh</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005</wicri:regionArea><wicri:noRegion>Amritsar 143005</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Harpreet" sort="Singh, Harpreet" uniqKey="Singh H" first="Harpreet" last="Singh">Harpreet Singh</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar 144008, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar 144008</wicri:regionArea><wicri:noRegion>Jalandhar 144008</wicri:noRegion></affiliation></author><author><name sortKey="Nagpal, Avinash Kaur" sort="Nagpal, Avinash Kaur" uniqKey="Nagpal A" first="Avinash Kaur" last="Nagpal">Avinash Kaur Nagpal</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005</wicri:regionArea><wicri:noRegion>Amritsar 143005</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25477958</idno><idno type="pmc">4248371</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248371</idno><idno type="RBID">PMC:4248371</idno><idno type="doi">10.1155/2014/424873</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000D84</idno><idno type="wicri:Area/Pmc/Curation">000D83</idno><idno type="wicri:Area/Pmc/Checkpoint">000880</idno><idno type="wicri:Area/Ncbi/Merge">001938</idno><idno type="wicri:Area/Ncbi/Curation">001938</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Comparative Genomics of Ten Solanaceous Plastomes</title><author><name sortKey="Kaur, Harpreet" sort="Kaur, Harpreet" uniqKey="Kaur H" first="Harpreet" last="Kaur">Harpreet Kaur</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005</wicri:regionArea><wicri:noRegion>Amritsar 143005</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Bhupinder Pal" sort="Singh, Bhupinder Pal" uniqKey="Singh B" first="Bhupinder Pal" last="Singh">Bhupinder Pal Singh</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005</wicri:regionArea><wicri:noRegion>Amritsar 143005</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Harpreet" sort="Singh, Harpreet" uniqKey="Singh H" first="Harpreet" last="Singh">Harpreet Singh</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar 144008, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar 144008</wicri:regionArea><wicri:noRegion>Jalandhar 144008</wicri:noRegion></affiliation></author><author><name sortKey="Nagpal, Avinash Kaur" sort="Nagpal, Avinash Kaur" uniqKey="Nagpal A" first="Avinash Kaur" last="Nagpal">Avinash Kaur Nagpal</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar 143005</wicri:regionArea><wicri:noRegion>Amritsar 143005</wicri:noRegion></affiliation></author></analytic><series><title level="j">Advances in Bioinformatics</title><idno type="ISSN">1687-8027</idno><idno type="eISSN">1687-8035</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Availability of complete plastid genomes of ten solanaceous species, <italic>Atropa belladonna</italic>, <italic>Capsicum annuum</italic>, <italic>Datura stramonium</italic>, <italic>Nicotiana sylvestris</italic>, <italic>Nicotiana tabacum</italic>, <italic>Nicotiana tomentosiformis</italic>, <italic>Nicotiana undulata</italic>, <italic>Solanum bulbocastanum</italic>, <italic>Solanum lycopersicum</italic>, and <italic>Solanum tuberosum</italic> provided us with an opportunity to conduct their <italic>in silico</italic> comparative analysis in depth. The size of complete chloroplast genomes and LSC and SSC regions of three species of <italic>Solanum</italic> is comparatively smaller than that of any other species studied till date (exception: SSC region of <italic>A. belladonna</italic>). AT content of coding regions was found to be less than noncoding regions. A duplicate copy of trnH gene in <italic>C. annuum</italic> and two alternative tRNA genes for proline in <italic>D. stramonium</italic> were observed for the first time in this analysis. Further, homology search revealed the presence of rps19 pseudogene and infA genes in <italic>A. belladonna</italic> and <italic>D. stramonium</italic>, a region identical to rps19 pseudogene in <italic>C. annum</italic> and orthologues of sprA gene in another six species. Among the eighteen intron-containing genes, 3 genes have two introns and 15 genes have one intron. The longest insertion was found in accD gene in <italic>C. annuum</italic>. Phylogenetic analysis using concatenated protein coding sequences gave two clades, one for <italic>Nicotiana</italic> species and another for <italic>Solanum</italic>, <italic>Capsicum</italic>, <italic>Atropa</italic>, and <italic>Datura</italic>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bausher, M G" uniqKey="Bausher M">M. G. Bausher</name></author><author><name sortKey="Singh, N D" uniqKey="Singh N">N. D. Singh</name></author><author><name sortKey="Lee, S B" uniqKey="Lee S">S.-B. Lee</name></author><author><name sortKey="Jansen, R K" uniqKey="Jansen R">R. K. Jansen</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H. Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hu, Z Y" uniqKey="Hu Z">Z. Y. Hu</name></author><author><name sortKey="Hua, W" uniqKey="Hua W">W. Hua</name></author><author><name sortKey="Huang, S M" uniqKey="Huang S">S. M. 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