Assembly and comparative analysis of complete mitochondrial genome sequence of an economic plant Salix suchowensis.
Identifieur interne : 001516 ( Main/Exploration ); précédent : 001515; suivant : 001517Assembly and comparative analysis of complete mitochondrial genome sequence of an economic plant Salix suchowensis.
Auteurs : Ning Ye [République populaire de Chine] ; Xuelin Wang [République populaire de Chine] ; Juan Li [République populaire de Chine] ; Changwei Bi [République populaire de Chine] ; Yiqing Xu [République populaire de Chine] ; Dongyang Wu [République populaire de Chine] ; Qiaolin Ye [République populaire de Chine]Source :
- PeerJ [ 2167-8359 ] ; 2017.
Abstract
Willow is a widely used dioecious woody plant of Salicaceae family in China. Due to their high biomass yields, willows are promising sources for bioenergy crops. In this study, we assembled the complete mitochondrial (mt) genome sequence of S. suchowensis with the length of 644,437 bp using Roche-454 GS FLX Titanium sequencing technologies. Base composition of the S. suchowensis mt genome is A (27.43%), T (27.59%), C (22.34%), and G (22.64%), which shows a prevalent GC content with that of other angiosperms. This long circular mt genome encodes 58 unique genes (32 protein-coding genes, 23 tRNA genes and 3 rRNA genes), and 9 of the 32 protein-coding genes contain 17 introns. Through the phylogenetic analysis of 35 species based on 23 protein-coding genes, it is supported that Salix as a sister to Populus. With the detailed phylogenetic information and the identification of phylogenetic position, some ribosomal protein genes and succinate dehydrogenase genes are found usually lost during evolution. As a native shrub willow species, this worthwhile research of S. suchowensis mt genome will provide more desirable information for better understanding the genomic breeding and missing pieces of sex determination evolution in the future.
DOI: 10.7717/peerj.3148
PubMed: 28367378
PubMed Central: PMC5374973
Affiliations:
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Science and Technology, Nanjing Forestry University , Nanjing , Jiangsu , China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Information Science and Technology, Nanjing Forestry University , Nanjing , Jiangsu </wicri:regionArea><wicri:noRegion>Jiangsu </wicri:noRegion></affiliation></author><author><name sortKey="Wang, Xuelin" sort="Wang, Xuelin" uniqKey="Wang X" first="Xuelin" last="Wang">Xuelin Wang</name><affiliation wicri:level="1"><nlm:affiliation>College of Information Science and Technology, Nanjing Forestry University , Nanjing , Jiangsu , China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Information Science and Technology, Nanjing Forestry University , Nanjing , Jiangsu </wicri:regionArea><wicri:noRegion>Jiangsu </wicri:noRegion></affiliation></author><author><name sortKey="Li, Juan" sort="Li, Juan" uniqKey="Li J" first="Juan" last="Li">Juan Li</name><affiliation wicri:level="1"><nlm:affiliation>School of Electrical and Automatic Engineering, Nanjing Normal University , Nanjing , Jiangsu , China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Electrical and Automatic Engineering, Nanjing Normal University , Nanjing , Jiangsu </wicri:regionArea><wicri:noRegion>Jiangsu </wicri:noRegion></affiliation></author><author><name sortKey="Bi, Changwei" sort="Bi, Changwei" uniqKey="Bi C" first="Changwei" last="Bi">Changwei Bi</name><affiliation wicri:level="1"><nlm:affiliation>School of Biological Science and Medical Engineering, Southeast University , Nanjing , Jiangsu , China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Biological Science and Medical Engineering, Southeast University , Nanjing , Jiangsu </wicri:regionArea><wicri:noRegion>Jiangsu </wicri:noRegion></affiliation></author><author><name sortKey="Xu, Yiqing" sort="Xu, Yiqing" uniqKey="Xu Y" first="Yiqing" last="Xu">Yiqing Xu</name><affiliation wicri:level="1"><nlm:affiliation>College of Information Science and Technology, Nanjing Forestry University , Nanjing , Jiangsu , China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Information Science and Technology, Nanjing Forestry University , Nanjing , Jiangsu </wicri:regionArea><wicri:noRegion>Jiangsu </wicri:noRegion></affiliation></author><author><name sortKey="Wu, Dongyang" sort="Wu, Dongyang" uniqKey="Wu D" first="Dongyang" last="Wu">Dongyang Wu</name><affiliation wicri:level="1"><nlm:affiliation>College of Forest Resources and Environment, Nanjing Forestry University , Nanjing , Jiangsu , China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Forest Resources and Environment, Nanjing Forestry University , Nanjing , Jiangsu </wicri:regionArea><wicri:noRegion>Jiangsu </wicri:noRegion></affiliation></author><author><name sortKey="Ye, Qiaolin" sort="Ye, Qiaolin" uniqKey="Ye Q" first="Qiaolin" last="Ye">Qiaolin Ye</name><affiliation wicri:level="1"><nlm:affiliation>College of Information Science and Technology, Nanjing Forestry University , Nanjing , Jiangsu , China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Information Science and Technology, Nanjing Forestry University , Nanjing , Jiangsu </wicri:regionArea><wicri:noRegion>Jiangsu </wicri:noRegion></affiliation></author></analytic><series><title level="j">PeerJ</title><idno type="ISSN">2167-8359</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Willow is a widely used dioecious woody plant of <i>Salicaceae</i> family in China. Due to their high biomass yields, willows are promising sources for bioenergy crops. In this study, we assembled the complete mitochondrial (mt) genome sequence of <i>S. suchowensis</i> with the length of 644,437 bp using Roche-454 GS FLX Titanium sequencing technologies. Base composition of the <i>S. suchowensis</i> mt genome is A (27.43%), T (27.59%), C (22.34%), and G (22.64%), which shows a prevalent GC content with that of other angiosperms. This long circular mt genome encodes 58 unique genes (32 protein-coding genes, 23 tRNA genes and 3 rRNA genes), and 9 of the 32 protein-coding genes contain 17 introns. Through the phylogenetic analysis of 35 species based on 23 protein-coding genes, it is supported that <i>Salix</i> as a sister to <i>Populus</i>. With the detailed phylogenetic information and the identification of phylogenetic position, some ribosomal protein genes and succinate dehydrogenase genes are found usually lost during evolution. As a native shrub willow species, this worthwhile research of <i>S. suchowensis</i> mt genome will provide more desirable information for better understanding the genomic breeding and missing pieces of sex determination evolution in the future.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">28367378</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2167-8359</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><PubDate><Year>2017</Year></PubDate></JournalIssue><Title>PeerJ</Title><ISOAbbreviation>PeerJ</ISOAbbreviation></Journal><ArticleTitle>Assembly and comparative analysis of complete mitochondrial genome sequence of an economic plant <i>Salix suchowensis</i>.</ArticleTitle><Pagination><MedlinePgn>e3148</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.7717/peerj.3148</ELocationID><Abstract><AbstractText>Willow is a widely used dioecious woody plant of <i>Salicaceae</i> family in China. Due to their high biomass yields, willows are promising sources for bioenergy crops. In this study, we assembled the complete mitochondrial (mt) genome sequence of <i>S. suchowensis</i> with the length of 644,437 bp using Roche-454 GS FLX Titanium sequencing technologies. Base composition of the <i>S. suchowensis</i> mt genome is A (27.43%), T (27.59%), C (22.34%), and G (22.64%), which shows a prevalent GC content with that of other angiosperms. This long circular mt genome encodes 58 unique genes (32 protein-coding genes, 23 tRNA genes and 3 rRNA genes), and 9 of the 32 protein-coding genes contain 17 introns. Through the phylogenetic analysis of 35 species based on 23 protein-coding genes, it is supported that <i>Salix</i> as a sister to <i>Populus</i>. With the detailed phylogenetic information and the identification of phylogenetic position, some ribosomal protein genes and succinate dehydrogenase genes are found usually lost during evolution. As a native shrub willow species, this worthwhile research of <i>S. suchowensis</i> mt genome will provide more desirable information for better understanding the genomic breeding and missing pieces of sex determination evolution in the future.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Ning</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>College of Information Science and Technology, Nanjing Forestry University , Nanjing , 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 , Jiangsu , China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Juan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>School of Electrical and Automatic Engineering, Nanjing Normal University , Nanjing , Jiangsu , China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bi</LastName><ForeName>Changwei</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>School of Biological Science and Medical Engineering, Southeast University , Nanjing , 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 , Jiangsu , China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Dongyang</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>College of Forest Resources and Environment, Nanjing Forestry University , Nanjing , Jiangsu , China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Qiaolin</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>College of Information Science and Technology, Nanjing Forestry University , Nanjing , Jiangsu , China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>03</Month><Day>29</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PeerJ</MedlineTA><NlmUniqueID>101603425</NlmUniqueID><ISSNLinking>2167-8359</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Assembly</Keyword><Keyword MajorTopicYN="N">Mitochondrial genome</Keyword><Keyword MajorTopicYN="N">Phylogenetic analysis</Keyword><Keyword MajorTopicYN="N">Repeats</Keyword><Keyword MajorTopicYN="N">Salix suchowensis</Keyword></KeywordList><CoiStatement>The authors declare there are no competing interests.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>01</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>03</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>4</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>4</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>4</Month><Day>4</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28367378</ArticleId><ArticleId IdType="doi">10.7717/peerj.3148</ArticleId><ArticleId IdType="pii">3148</ArticleId><ArticleId 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Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Ye, Ning" sort="Ye, Ning" uniqKey="Ye N" first="Ning" last="Ye">Ning Ye</name></noRegion><name sortKey="Bi, Changwei" sort="Bi, Changwei" uniqKey="Bi C" first="Changwei" last="Bi">Changwei Bi</name><name sortKey="Li, Juan" sort="Li, Juan" uniqKey="Li J" first="Juan" last="Li">Juan Li</name><name sortKey="Wang, Xuelin" sort="Wang, Xuelin" uniqKey="Wang X" first="Xuelin" last="Wang">Xuelin Wang</name><name sortKey="Wu, Dongyang" sort="Wu, Dongyang" uniqKey="Wu D" first="Dongyang" last="Wu">Dongyang Wu</name><name sortKey="Xu, Yiqing" sort="Xu, Yiqing" uniqKey="Xu Y" first="Yiqing" last="Xu">Yiqing Xu</name><name sortKey="Ye, Qiaolin" sort="Ye, Qiaolin" uniqKey="Ye Q" first="Qiaolin" last="Ye">Qiaolin Ye</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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