Assembly and analysis of the complete Salix purpurea L. (Salicaceae) mitochondrial genome sequence.
Identifieur interne : 000A99 ( Main/Corpus ); précédent : 000A98; suivant : 000B00Assembly and analysis of the complete Salix purpurea L. (Salicaceae) mitochondrial genome sequence.
Auteurs : Suyun Wei ; Xuelin Wang ; Changwei Bi ; Yiqing Xu ; Dongyang Wu ; Ning YeSource :
- SpringerPlus [ 2193-1801 ] ; 2016.
Abstract
Plant mitochondrial (mt) genomes possess several complex features, including a variable size, a dynamic genome structure, and complicated patterns of gene loss and gain throughout evolutionary history. Studies of plant mt genomes can, therefore, provide unique insights into organelle evolution. We assembled the complete Salix purpurea L. mt genome by screening genomic sequence reads generated by a Roche-454 pyrosequencing platform. The pseudo-molecule obtained has a typical circular structure 598,970 bp long, with an overall GC content of 55.06%. The S. purpurea mt genome contains 52 genes: 31 protein-coding, 18 tRNAs, and three rRNAs. Eighteen tandem repeats and 404 microsatellites are distributed unevenly throughout the S. purpurea mt genome. A phylogenetic tree of 23 representative terrestrial plants strongly supports S. purpurea inclusion in the Malpighiales clade. Our analysis contributes toward understanding the organization and evolution of organelle genomes in Salicaceae species.
DOI: 10.1186/s40064-016-3521-6
PubMed: 27843751
PubMed Central: PMC5084139
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(Salicaceae) mitochondrial genome sequence.</title><author><name sortKey="Wei, Suyun" sort="Wei, Suyun" uniqKey="Wei S" first="Suyun" last="Wei">Suyun Wei</name><affiliation><nlm:affiliation>College of Forestry, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Xuelin" sort="Wang, Xuelin" uniqKey="Wang X" first="Xuelin" last="Wang">Xuelin Wang</name><affiliation><nlm:affiliation>College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Bi, Changwei" sort="Bi, Changwei" uniqKey="Bi C" first="Changwei" last="Bi">Changwei Bi</name><affiliation><nlm:affiliation>College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Xu, Yiqing" sort="Xu, Yiqing" uniqKey="Xu Y" first="Yiqing" last="Xu">Yiqing Xu</name><affiliation><nlm:affiliation>College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; School of Computer Science and Engineering, Southeast University, Nanjing, 211189 Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Wu, Dongyang" sort="Wu, Dongyang" uniqKey="Wu D" first="Dongyang" last="Wu">Dongyang Wu</name><affiliation><nlm:affiliation>College of Forestry, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Ye, Ning" sort="Ye, Ning" uniqKey="Ye N" first="Ning" last="Ye">Ning Ye</name><affiliation><nlm:affiliation>The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2016">2016</date><idno type="RBID">pubmed:27843751</idno><idno type="pmid">27843751</idno><idno type="doi">10.1186/s40064-016-3521-6</idno><idno type="pmc">PMC5084139</idno><idno type="wicri:Area/Main/Corpus">000A99</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000A99</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Assembly and analysis of the complete <i>Salix purpurea</i> L. (Salicaceae) mitochondrial genome sequence.</title><author><name sortKey="Wei, Suyun" sort="Wei, Suyun" uniqKey="Wei S" first="Suyun" last="Wei">Suyun Wei</name><affiliation><nlm:affiliation>College of Forestry, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Xuelin" sort="Wang, Xuelin" uniqKey="Wang X" first="Xuelin" last="Wang">Xuelin Wang</name><affiliation><nlm:affiliation>College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Bi, Changwei" sort="Bi, Changwei" uniqKey="Bi C" first="Changwei" last="Bi">Changwei Bi</name><affiliation><nlm:affiliation>College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Xu, Yiqing" sort="Xu, Yiqing" uniqKey="Xu Y" first="Yiqing" last="Xu">Yiqing Xu</name><affiliation><nlm:affiliation>College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; School of Computer Science and Engineering, Southeast University, Nanjing, 211189 Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Wu, Dongyang" sort="Wu, Dongyang" uniqKey="Wu D" first="Dongyang" last="Wu">Dongyang Wu</name><affiliation><nlm:affiliation>College of Forestry, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China.</nlm:affiliation></affiliation></author><author><name sortKey="Ye, Ning" sort="Ye, Ning" uniqKey="Ye N" first="Ning" last="Ye">Ning Ye</name><affiliation><nlm:affiliation>The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China.</nlm:affiliation></affiliation></author></analytic><series><title level="j">SpringerPlus</title><idno type="ISSN">2193-1801</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Plant mitochondrial (mt) genomes possess several complex features, including a variable size, a dynamic genome structure, and complicated patterns of gene loss and gain throughout evolutionary history. Studies of plant mt genomes can, therefore, provide unique insights into organelle evolution. We assembled the complete <i>Salix purpurea</i> L. mt genome by screening genomic sequence reads generated by a Roche-454 pyrosequencing platform. The pseudo-molecule obtained has a typical circular structure 598,970 bp long, with an overall GC content of 55.06%. The <i>S. purpurea</i> mt genome contains 52 genes: 31 protein-coding, 18 tRNAs, and three rRNAs. Eighteen tandem repeats and 404 microsatellites are distributed unevenly throughout the <i>S. purpurea</i> mt genome. A phylogenetic tree of 23 representative terrestrial plants strongly supports <i>S. purpurea</i> inclusion in the Malpighiales clade. Our analysis contributes toward understanding the organization and evolution of organelle genomes in Salicaceae species.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">27843751</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2193-1801</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><Issue>1</Issue><PubDate><Year>2016</Year></PubDate></JournalIssue><Title>SpringerPlus</Title><ISOAbbreviation>Springerplus</ISOAbbreviation></Journal><ArticleTitle>Assembly and analysis of the complete <i>Salix purpurea</i> L. (Salicaceae) mitochondrial genome sequence.</ArticleTitle><Pagination><MedlinePgn>1894</MedlinePgn></Pagination><Abstract><AbstractText>Plant mitochondrial (mt) genomes possess several complex features, including a variable size, a dynamic genome structure, and complicated patterns of gene loss and gain throughout evolutionary history. Studies of plant mt genomes can, therefore, provide unique insights into organelle evolution. We assembled the complete <i>Salix purpurea</i> L. mt genome by screening genomic sequence reads generated by a Roche-454 pyrosequencing platform. The pseudo-molecule obtained has a typical circular structure 598,970 bp long, with an overall GC content of 55.06%. The <i>S. purpurea</i> mt genome contains 52 genes: 31 protein-coding, 18 tRNAs, and three rRNAs. Eighteen tandem repeats and 404 microsatellites are distributed unevenly throughout the <i>S. purpurea</i> mt genome. A phylogenetic tree of 23 representative terrestrial plants strongly supports <i>S. purpurea</i> inclusion in the Malpighiales clade. Our analysis contributes toward understanding the organization and evolution of organelle genomes in Salicaceae species.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wei</LastName><ForeName>Suyun</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>College of Forestry, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Xuelin</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bi</LastName><ForeName>Changwei</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Yiqing</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; School of Computer Science and Engineering, Southeast University, Nanjing, 211189 Jiangsu China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Dongyang</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>College of Forestry, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Ning</ForeName><Initials>N</Initials><Identifier Source="ORCID">0000-0001-7249-8352</Identifier><AffiliationInfo><Affiliation>The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>10</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Springerplus</MedlineTA><NlmUniqueID>101597967</NlmUniqueID><ISSNLinking>2193-1801</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Genome assembly</Keyword><Keyword MajorTopicYN="N">Mitochondrial genome</Keyword><Keyword MajorTopicYN="N">Phylogenetic tree</Keyword><Keyword MajorTopicYN="N">Salicaceae</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>03</Month><Day>10</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>10</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>11</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>11</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>11</Month><Day>16</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27843751</ArticleId><ArticleId IdType="doi">10.1186/s40064-016-3521-6</ArticleId><ArticleId IdType="pii">3521</ArticleId><ArticleId IdType="pmc">PMC5084139</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>BMC Plant Biol. 2014 Feb 10;14:45</Citation><ArticleIdList><ArticleId IdType="pubmed">24512148</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 1995 Aug 15;92(17):7759-63</Citation><ArticleIdList><ArticleId IdType="pubmed">7644491</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2014 Oct;31(10):2586-91</Citation><ArticleIdList><ArticleId IdType="pubmed">24980738</ArticleId></ArticleIdList></Reference><Reference><Citation>Methods Mol Biol. 2015;1264:77-88</Citation><ArticleIdList><ArticleId IdType="pubmed">25631005</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2004 Nov 22;20(17):3252-5</Citation><ArticleIdList><ArticleId IdType="pubmed">15180927</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2013 Aug 05;8(8):e69476</Citation><ArticleIdList><ArticleId IdType="pubmed">23940520</ArticleId></ArticleIdList></Reference><Reference><Citation>Int J Mol Sci. 2012 Oct 03;13(10):12608-28</Citation><ArticleIdList><ArticleId IdType="pubmed">23202917</ArticleId></ArticleIdList></Reference><Reference><Citation>Theor Appl Genet. 2006 May;112(7):1248-57</Citation><ArticleIdList><ArticleId IdType="pubmed">16474971</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 1990 Jul 11;18(13):3689-96</Citation><ArticleIdList><ArticleId IdType="pubmed">2374706</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Genet. 1997 Jan;15(1):57-61</Citation><ArticleIdList><ArticleId IdType="pubmed">8988169</ArticleId></ArticleIdList></Reference><Reference><Citation>G3 (Bethesda). 2014 Jan 10;4(1):67-78</Citation><ArticleIdList><ArticleId IdType="pubmed">24192840</ArticleId></ArticleIdList></Reference><Reference><Citation>DNA Res. 2011 Apr;18(2):93-105</Citation><ArticleIdList><ArticleId IdType="pubmed">21444340</ArticleId></ArticleIdList></Reference><Reference><Citation>Curr Biol. 2002 Jan 22;12(2):R62-4</Citation><ArticleIdList><ArticleId IdType="pubmed">11818081</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Genet Genomics. 2002 Dec;268(4):434-45</Citation><ArticleIdList><ArticleId IdType="pubmed">12471441</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 1999 Jan 15;27(2):573-80</Citation><ArticleIdList><ArticleId IdType="pubmed">9862982</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2013 Dec;30(12):2725-9</Citation><ArticleIdList><ArticleId IdType="pubmed">24132122</ArticleId></ArticleIdList></Reference><Reference><Citation>Trends Genet. 1993 Aug;9(8):275-80</Citation><ArticleIdList><ArticleId IdType="pubmed">8104363</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2013;8(2):e56502</Citation><ArticleIdList><ArticleId IdType="pubmed">23431381</ArticleId></ArticleIdList></Reference><Reference><Citation>Theor Appl Genet. 2004 Apr;108(6):1151-61</Citation><ArticleIdList><ArticleId IdType="pubmed">14760486</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2015 Apr 07;10(4):e0121020</Citation><ArticleIdList><ArticleId IdType="pubmed">25849557</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2012;7(1):e30531</Citation><ArticleIdList><ArticleId IdType="pubmed">22291979</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2010 Jun;27(6):1436-48</Citation><ArticleIdList><ArticleId IdType="pubmed">20118192</ArticleId></ArticleIdList></Reference><Reference><Citation>Front Plant Sci. 2015 May 18;6:344</Citation><ArticleIdList><ArticleId IdType="pubmed">26042135</ArticleId></ArticleIdList></Reference><Reference><Citation>Trends Ecol Evol. 2001 Mar 1;16(3):142-147</Citation><ArticleIdList><ArticleId IdType="pubmed">11179578</ArticleId></ArticleIdList></Reference><Reference><Citation>Am J Bot. 2011 May;98(5):e123-6</Citation><ArticleIdList><ArticleId IdType="pubmed">21613178</ArticleId></ArticleIdList></Reference><Reference><Citation>Biochimie. 2014 May;100:107-20</Citation><ArticleIdList><ArticleId IdType="pubmed">24075874</ArticleId></ArticleIdList></Reference><Reference><Citation>Curr Genet. 2007 Nov;52(5-6):267-74</Citation><ArticleIdList><ArticleId IdType="pubmed">17957369</ArticleId></ArticleIdList></Reference><Reference><Citation>Z Naturforsch C. 2007 May-Jun;62(5-6):417-26</Citation><ArticleIdList><ArticleId IdType="pubmed">17708449</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell. 2011 Jul;23(7):2499-513</Citation><ArticleIdList><ArticleId IdType="pubmed">21742987</ArticleId></ArticleIdList></Reference><Reference><Citation>New Phytol. 2015 Apr;206(1):397-410</Citation><ArticleIdList><ArticleId IdType="pubmed">25420631</ArticleId></ArticleIdList></Reference><Reference><Citation>Curr Biol. 2006 Jul 25;16(14 ):R551-60</Citation><ArticleIdList><ArticleId IdType="pubmed">16860735</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2011 Jan 20;6(1):e16404</Citation><ArticleIdList><ArticleId IdType="pubmed">21283772</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 1994 Nov 11;22(22):4673-80</Citation><ArticleIdList><ArticleId IdType="pubmed">7984417</ArticleId></ArticleIdList></Reference><Reference><Citation>Am J Bot. 2012 Jun;99(6):e240-4</Citation><ArticleIdList><ArticleId IdType="pubmed">22615305</ArticleId></ArticleIdList></Reference><Reference><Citation>Annu Rev Biochem. 2007;76:701-22</Citation><ArticleIdList><ArticleId IdType="pubmed">17227225</ArticleId></ArticleIdList></Reference><Reference><Citation>Theor Appl Genet. 2003 Feb;106(3):411-22</Citation><ArticleIdList><ArticleId IdType="pubmed">12589540</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome. 2011 Aug;54(8):663-73</Citation><ArticleIdList><ArticleId IdType="pubmed">21793699</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2012;7(5):e36869</Citation><ArticleIdList><ArticleId IdType="pubmed">22606302</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W686-9</Citation><ArticleIdList><ArticleId IdType="pubmed">15980563</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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