The 206 kbp mitochondrial genome of Phanerochaete carnosa reveals dynamics of introns, accumulation of repeat sequences and plasmid-derived genes.
Identifieur interne : 000006 ( Main/Exploration ); précédent : 000005; suivant : 000007The 206 kbp mitochondrial genome of Phanerochaete carnosa reveals dynamics of introns, accumulation of repeat sequences and plasmid-derived genes.
Auteurs : Xu Wang [République populaire de Chine] ; Andong Song [République populaire de Chine] ; Fengqin Wang [République populaire de Chine] ; Mingyue Chen [République populaire de Chine] ; Xiao Li [République populaire de Chine] ; Qiang Li [République populaire de Chine] ; Na Liu [République populaire de Chine]Source :
- International journal of biological macromolecules [ 1879-0003 ] ; 2020.
Abstract
In this study, the mitogenome of Phanerochaete carnosa was sequenced and assembled by the next-generation sequencing. The P. carnosa mitogenome was composed of circular DNA molecules, with a total size of 206,437 bp. Intron sequence, repeat sequence and plasmid-derived genes together promoted the P. carnosa mitogenome to become the second largest mitogenome in Basidiomycota. Gene arrangement analysis revealed large-scale gene rearrangements between Polyporales mitogenomes, and P. carnosa contained a unique gene order. The number and position classes of introns varied between 14 Polyporales species tested, indicated numerous intron loss/gain events occurred in the evolution of Polyporales. Most core PCGs in the 14 Polyporales species we tested were found subjected to purifying selection. However, the Ka/Ks values of rps3 gene were found >1 between some Polyporales species, indicating pressure of positive selection may exist. Phylogenetic analysis based on the combined mitochondrial gene set obtained well-supported tree topologies, and P. carnosa was identified as a sister species to Phlebia radiata. This study served as the first report on the mitogenome in the family Phanerochaetaceae, which will promote the understanding of the phylogeny, population genetics, and evolution of this white-rot fungus and related fungi.
DOI: 10.1016/j.ijbiomac.2020.06.142
PubMed: 32562727
Affiliations:
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Electronic address: naliu@henau.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002</wicri:regionArea><wicri:noRegion>Henan 450002</wicri:noRegion></affiliation></author></analytic><series><title level="j">International journal of biological macromolecules</title><idno type="eISSN">1879-0003</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">In this study, the mitogenome of Phanerochaete carnosa was sequenced and assembled by the next-generation sequencing. The P. carnosa mitogenome was composed of circular DNA molecules, with a total size of 206,437 bp. Intron sequence, repeat sequence and plasmid-derived genes together promoted the P. carnosa mitogenome to become the second largest mitogenome in Basidiomycota. Gene arrangement analysis revealed large-scale gene rearrangements between Polyporales mitogenomes, and P. carnosa contained a unique gene order. The number and position classes of introns varied between 14 Polyporales species tested, indicated numerous intron loss/gain events occurred in the evolution of Polyporales. Most core PCGs in the 14 Polyporales species we tested were found subjected to purifying selection. However, the Ka/Ks values of rps3 gene were found >1 between some Polyporales species, indicating pressure of positive selection may exist. Phylogenetic analysis based on the combined mitochondrial gene set obtained well-supported tree topologies, and P. carnosa was identified as a sister species to Phlebia radiata. This study served as the first report on the mitogenome in the family Phanerochaetaceae, which will promote the understanding of the phylogeny, population genetics, and evolution of this white-rot fungus and related fungi.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32562727</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>06</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1879-0003</ISSN><JournalIssue CitedMedium="Internet"><Volume>162</Volume><PubDate><Year>2020</Year><Month>Nov</Month><Day>01</Day></PubDate></JournalIssue><Title>International journal of biological macromolecules</Title><ISOAbbreviation>Int J Biol Macromol</ISOAbbreviation></Journal><ArticleTitle>The 206 kbp mitochondrial genome of Phanerochaete carnosa reveals dynamics of introns, accumulation of repeat sequences and plasmid-derived genes.</ArticleTitle><Pagination><MedlinePgn>209-219</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S0141-8130(20)33586-8</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.ijbiomac.2020.06.142</ELocationID><Abstract><AbstractText>In this study, the mitogenome of Phanerochaete carnosa was sequenced and assembled by the next-generation sequencing. The P. carnosa mitogenome was composed of circular DNA molecules, with a total size of 206,437 bp. Intron sequence, repeat sequence and plasmid-derived genes together promoted the P. carnosa mitogenome to become the second largest mitogenome in Basidiomycota. Gene arrangement analysis revealed large-scale gene rearrangements between Polyporales mitogenomes, and P. carnosa contained a unique gene order. The number and position classes of introns varied between 14 Polyporales species tested, indicated numerous intron loss/gain events occurred in the evolution of Polyporales. Most core PCGs in the 14 Polyporales species we tested were found subjected to purifying selection. However, the Ka/Ks values of rps3 gene were found >1 between some Polyporales species, indicating pressure of positive selection may exist. Phylogenetic analysis based on the combined mitochondrial gene set obtained well-supported tree topologies, and P. carnosa was identified as a sister species to Phlebia radiata. This study served as the first report on the mitogenome in the family Phanerochaetaceae, which will promote the understanding of the phylogeny, population genetics, and evolution of this white-rot fungus and related fungi.</AbstractText><CopyrightInformation>Copyright © 2020 Elsevier B.V. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Xu</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Song</LastName><ForeName>Andong</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Fengqin</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Mingyue</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Xiao</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Qiang</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan 610106, China. Electronic address: leeq110@126.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Na</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan 450002, China. Electronic address: naliu@henau.edu.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>06</Month><Day>18</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Int J Biol Macromol</MedlineTA><NlmUniqueID>7909578</NlmUniqueID><ISSNLinking>0141-8130</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Gene rearrangement</Keyword><Keyword MajorTopicYN="N">Mitochondrial genome</Keyword><Keyword MajorTopicYN="N">Phanerochaete carnosa</Keyword><Keyword MajorTopicYN="N">Phylogenetic analysis</Keyword><Keyword MajorTopicYN="N">Protein coding gene</Keyword><Keyword MajorTopicYN="N">Repeat sequence</Keyword></KeywordList><CoiStatement>Declaration of competing interest The authors declare that they have no conflict of interest.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>04</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>06</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>06</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>6</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>6</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>6</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32562727</ArticleId><ArticleId IdType="pii">S0141-8130(20)33586-8</ArticleId><ArticleId IdType="doi">10.1016/j.ijbiomac.2020.06.142</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Wang, Xu" sort="Wang, Xu" uniqKey="Wang X" first="Xu" last="Wang">Xu Wang</name></noRegion><name sortKey="Chen, Mingyue" sort="Chen, Mingyue" uniqKey="Chen M" first="Mingyue" last="Chen">Mingyue Chen</name><name sortKey="Li, Qiang" sort="Li, Qiang" uniqKey="Li Q" first="Qiang" last="Li">Qiang Li</name><name sortKey="Li, Xiao" sort="Li, Xiao" uniqKey="Li X" first="Xiao" last="Li">Xiao Li</name><name sortKey="Liu, Na" sort="Liu, Na" uniqKey="Liu N" first="Na" last="Liu">Na Liu</name><name sortKey="Song, Andong" sort="Song, Andong" uniqKey="Song A" first="Andong" last="Song">Andong Song</name><name sortKey="Wang, Fengqin" sort="Wang, Fengqin" uniqKey="Wang F" first="Fengqin" last="Wang">Fengqin Wang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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