A brief overview of the size and composition of the myrtle rust genome and its taxonomic status.
Identifieur interne : 000079 ( Main/Exploration ); précédent : 000078; suivant : 000080A brief overview of the size and composition of the myrtle rust genome and its taxonomic status.
Auteurs : Mui-Keng Tan [Australie] ; Damian Collins [Australie] ; Zhiliang Chen [Australie] ; Anna Englezou [Australie] ; Marc R. Wilkins [Australie]Source :
- Mycology [ 2150-1203 ] ; 2014.
Abstract
Using de novo assembly of 46 million paired end sequence reads of length 250 bp for a myrtle rust isolate, we have estimated its genome size to be between 103 and 145 Mb and the number of proteins as >19,000. Annotation of the contigs found a very large percentage of proteins are associated with molecular functions of DNA binding or binding in biological processes for DNA integration and RNA-dependent DNA replication. A large proportion of these activities are attributed to the transposable elements (TEs). These elements are estimated to comprise 27% of the genome with 22% retrotransposons and 5% DNA transposons. The exon and intron boundaries of 46 genes occurring on contigs >20,000 bp have been determined. The number of introns range from 2 to 20 with a mean of 7. Phylogenetic analyses using partial COXI, 18S rRNA and 28S rRNA genes have placed myrtle rust in the Pucciniaceae lineage on a separate taxonomic branch from the families of Pucciniaceae, Phragmidiaceae, Sphaerophragmiaceae, Phragmidiaceae, Uropyxidaceae, Chaconiaceae and Phakopsoraceae. Further work is thus required to determine the family placement of myrtle rust in the Pucciniaceae of Pucciniales.
DOI: 10.1080/21501203.2014.919967
PubMed: 24999437
PubMed Central: PMC4066913
Affiliations:
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Wilkins</name><affiliation wicri:level="1"><nlm:affiliation>Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Kensington, NSW 2052, Australia ; Ramaciotti Centre for Genomics, The University of New South Wales, Kensington, NSW 2052, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Kensington, NSW 2052, Australia ; Ramaciotti Centre for Genomics, The University of New South Wales, Kensington, NSW 2052</wicri:regionArea><wicri:noRegion>NSW 2052</wicri:noRegion></affiliation></author></analytic><series><title level="j">Mycology</title><idno type="ISSN">2150-1203</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Using <i>de novo</i> assembly of 46 million paired end sequence reads of length 250 bp for a myrtle rust isolate, we have estimated its genome size to be between 103 and 145 Mb and the number of proteins as >19,000. Annotation of the contigs found a very large percentage of proteins are associated with molecular functions of DNA binding or binding in biological processes for DNA integration and RNA-dependent DNA replication. A large proportion of these activities are attributed to the transposable elements (TEs). These elements are estimated to comprise 27% of the genome with 22% retrotransposons and 5% DNA transposons. The exon and intron boundaries of 46 genes occurring on contigs >20,000 bp have been determined. The number of introns range from 2 to 20 with a mean of 7. Phylogenetic analyses using partial <i>COXI, 18S rRNA</i> and <i>28S rRNA</i> genes have placed myrtle rust in the Pucciniaceae lineage on a separate taxonomic branch from the families of Pucciniaceae, Phragmidiaceae, Sphaerophragmiaceae, Phragmidiaceae, Uropyxidaceae, Chaconiaceae and Phakopsoraceae. Further work is thus required to determine the family placement of myrtle rust in the Pucciniaceae of Pucciniales.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">24999437</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>01</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">2150-1203</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><Issue>2</Issue><PubDate><Year>2014</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Mycology</Title><ISOAbbreviation>Mycology</ISOAbbreviation></Journal><ArticleTitle>A brief overview of the size and composition of the myrtle rust genome and its taxonomic status.</ArticleTitle><Pagination><MedlinePgn>52-63</MedlinePgn></Pagination><Abstract><AbstractText>Using <i>de novo</i> assembly of 46 million paired end sequence reads of length 250 bp for a myrtle rust isolate, we have estimated its genome size to be between 103 and 145 Mb and the number of proteins as >19,000. Annotation of the contigs found a very large percentage of proteins are associated with molecular functions of DNA binding or binding in biological processes for DNA integration and RNA-dependent DNA replication. A large proportion of these activities are attributed to the transposable elements (TEs). These elements are estimated to comprise 27% of the genome with 22% retrotransposons and 5% DNA transposons. The exon and intron boundaries of 46 genes occurring on contigs >20,000 bp have been determined. The number of introns range from 2 to 20 with a mean of 7. Phylogenetic analyses using partial <i>COXI, 18S rRNA</i> and <i>28S rRNA</i> genes have placed myrtle rust in the Pucciniaceae lineage on a separate taxonomic branch from the families of Pucciniaceae, Phragmidiaceae, Sphaerophragmiaceae, Phragmidiaceae, Uropyxidaceae, Chaconiaceae and Phakopsoraceae. Further work is thus required to determine the family placement of myrtle rust in the Pucciniaceae of Pucciniales.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tan</LastName><ForeName>Mui-Keng</ForeName><Initials>MK</Initials><AffiliationInfo><Affiliation>NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Private Bag 4008, Narellan, NSW 2567, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Collins</LastName><ForeName>Damian</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Private Bag 4008, Narellan, NSW 2567, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Zhiliang</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Kensington, NSW 2052, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Englezou</LastName><ForeName>Anna</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Private Bag 4008, Narellan, NSW 2567, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wilkins</LastName><ForeName>Marc R</ForeName><Initials>MR</Initials><AffiliationInfo><Affiliation>Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Kensington, NSW 2052, Australia ; Ramaciotti Centre for Genomics, The University of New South Wales, Kensington, NSW 2052, Australia.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>05</Month><Day>29</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mycology</MedlineTA><NlmUniqueID>101523848</NlmUniqueID><ISSNLinking>2150-1203</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">DNA repeats</Keyword><Keyword MajorTopicYN="N">Melampsora</Keyword><Keyword MajorTopicYN="N">Phakopsora</Keyword><Keyword MajorTopicYN="N">Puccinia</Keyword><Keyword MajorTopicYN="N">phylogeny</Keyword><Keyword MajorTopicYN="N">transposons</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>02</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2014</Year><Month>04</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>7</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>7</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>7</Month><Day>8</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24999437</ArticleId><ArticleId IdType="doi">10.1080/21501203.2014.919967</ArticleId><ArticleId IdType="pmc">PMC4066913</ArticleId></ArticleIdList><pmc-dir>pmcsd</pmc-dir>
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