Genome size analyses of Pucciniales reveal the largest fungal genomes.
Identifieur interne : 000571 ( Main/Exploration ); précédent : 000570; suivant : 000572Genome size analyses of Pucciniales reveal the largest fungal genomes.
Auteurs : Sílvia Tavares [Portugal] ; Ana Paula Ramos [Portugal] ; Ana Sofia Pires [Portugal] ; Helena G. Azinheira [Portugal] ; Patrícia Caldeirinha [Portugal] ; Tobias Link [Allemagne] ; Rita Abranches [Portugal] ; Maria Do Céu Silva [Portugal] ; Ralf T. Voegele [Allemagne] ; João Loureiro [Portugal] ; Pedro Talhinhas [Portugal]Source :
- Frontiers in plant science [ 1664-462X ] ; 2014.
Abstract
Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.
DOI: 10.3389/fpls.2014.00422
PubMed: 25206357
PubMed Central: PMC4143883
Affiliations:
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Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal.</nlm:affiliation><country xml:lang="fr">Portugal</country><wicri:regionArea>Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras</wicri:regionArea><wicri:noRegion>Universidade Nova de Lisboa Oeiras</wicri:noRegion></affiliation></author><author><name sortKey="Ramos, Ana Paula" sort="Ramos, Ana Paula" uniqKey="Ramos A" first="Ana Paula" last="Ramos">Ana Paula Ramos</name><affiliation wicri:level="1"><nlm:affiliation>CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de Lisboa Lisbon, Portugal.</nlm:affiliation><country xml:lang="fr">Portugal</country><wicri:regionArea>CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de Lisboa Lisbon</wicri:regionArea><wicri:noRegion>Universidade de Lisboa Lisbon</wicri:noRegion></affiliation></author><author><name sortKey="Pires, Ana Sofia" sort="Pires, Ana Sofia" uniqKey="Pires A" first="Ana Sofia" last="Pires">Ana Sofia Pires</name><affiliation wicri:level="1"><nlm:affiliation>Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal.</nlm:affiliation><country xml:lang="fr">Portugal</country><wicri:regionArea>Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras</wicri:regionArea><wicri:noRegion>Universidade Nova de Lisboa Oeiras</wicri:noRegion></affiliation></author><author><name sortKey="Azinheira, Helena G" sort="Azinheira, Helena G" uniqKey="Azinheira H" first="Helena G" last="Azinheira">Helena G. Azinheira</name><affiliation wicri:level="1"><nlm:affiliation>Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de Lisboa Lisbon, Portugal.</nlm:affiliation><country xml:lang="fr">Portugal</country><wicri:regionArea>Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de Lisboa Lisbon</wicri:regionArea><wicri:noRegion>Universidade de Lisboa Lisbon</wicri:noRegion></affiliation></author><author><name sortKey="Caldeirinha, Patricia" sort="Caldeirinha, Patricia" uniqKey="Caldeirinha P" first="Patrícia" last="Caldeirinha">Patrícia Caldeirinha</name><affiliation wicri:level="1"><nlm:affiliation>Department of Life Sciences, Centre for Functional Ecology, University of Coimbra Coimbra, Portugal.</nlm:affiliation><country xml:lang="fr">Portugal</country><wicri:regionArea>Department of Life Sciences, Centre for Functional Ecology, University of Coimbra Coimbra</wicri:regionArea><wicri:noRegion>University of Coimbra Coimbra</wicri:noRegion></affiliation></author><author><name sortKey="Link, Tobias" sort="Link, Tobias" uniqKey="Link T" first="Tobias" last="Link">Tobias Link</name><affiliation wicri:level="1"><nlm:affiliation>Institut für Phytomedizin, Universität Hohenheim Stuttgart, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institut für Phytomedizin, Universität Hohenheim Stuttgart</wicri:regionArea><wicri:noRegion>Universität Hohenheim Stuttgart</wicri:noRegion><wicri:noRegion>Universität Hohenheim Stuttgart</wicri:noRegion><wicri:noRegion>Universität Hohenheim Stuttgart</wicri:noRegion></affiliation></author><author><name sortKey="Abranches, Rita" sort="Abranches, Rita" uniqKey="Abranches R" first="Rita" last="Abranches">Rita Abranches</name><affiliation wicri:level="1"><nlm:affiliation>Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal.</nlm:affiliation><country xml:lang="fr">Portugal</country><wicri:regionArea>Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras</wicri:regionArea><wicri:noRegion>Universidade Nova de Lisboa Oeiras</wicri:noRegion></affiliation></author><author><name sortKey="Silva, Maria Do Ceu" sort="Silva, Maria Do Ceu" uniqKey="Silva M" first="Maria Do Céu" last="Silva">Maria Do Céu Silva</name><affiliation wicri:level="1"><nlm:affiliation>Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de Lisboa Lisbon, Portugal.</nlm:affiliation><country xml:lang="fr">Portugal</country><wicri:regionArea>Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de Lisboa Lisbon</wicri:regionArea><wicri:noRegion>Universidade de Lisboa Lisbon</wicri:noRegion></affiliation></author><author><name sortKey="Voegele, Ralf T" sort="Voegele, Ralf T" uniqKey="Voegele R" first="Ralf T" last="Voegele">Ralf T. Voegele</name><affiliation wicri:level="1"><nlm:affiliation>Institut für Phytomedizin, Universität Hohenheim Stuttgart, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institut für Phytomedizin, Universität Hohenheim Stuttgart</wicri:regionArea><wicri:noRegion>Universität Hohenheim Stuttgart</wicri:noRegion><wicri:noRegion>Universität Hohenheim Stuttgart</wicri:noRegion><wicri:noRegion>Universität Hohenheim Stuttgart</wicri:noRegion></affiliation></author><author><name sortKey="Loureiro, Joao" sort="Loureiro, Joao" uniqKey="Loureiro J" first="João" last="Loureiro">João Loureiro</name><affiliation wicri:level="1"><nlm:affiliation>Department of Life Sciences, Centre for Functional Ecology, University of Coimbra Coimbra, Portugal.</nlm:affiliation><country xml:lang="fr">Portugal</country><wicri:regionArea>Department of Life Sciences, Centre for Functional Ecology, University of Coimbra Coimbra</wicri:regionArea><wicri:noRegion>University of Coimbra Coimbra</wicri:noRegion></affiliation></author><author><name sortKey="Talhinhas, Pedro" sort="Talhinhas, Pedro" uniqKey="Talhinhas P" first="Pedro" last="Talhinhas">Pedro Talhinhas</name><affiliation wicri:level="1"><nlm:affiliation>Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal ; CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de Lisboa Lisbon, Portugal.</nlm:affiliation><country xml:lang="fr">Portugal</country><wicri:regionArea>Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal ; CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de Lisboa Lisbon</wicri:regionArea><wicri:noRegion>Universidade de Lisboa Lisbon</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</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">Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research. </div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">25206357</PMID><DateCompleted><Year>2014</Year><Month>09</Month><Day>10</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Genome size analyses of Pucciniales reveal the largest fungal genomes.</ArticleTitle><Pagination><MedlinePgn>422</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fpls.2014.00422</ELocationID><Abstract><AbstractText>Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tavares</LastName><ForeName>Sílvia</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ramos</LastName><ForeName>Ana Paula</ForeName><Initials>AP</Initials><AffiliationInfo><Affiliation>CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de Lisboa Lisbon, Portugal.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pires</LastName><ForeName>Ana Sofia</ForeName><Initials>AS</Initials><AffiliationInfo><Affiliation>Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Azinheira</LastName><ForeName>Helena G</ForeName><Initials>HG</Initials><AffiliationInfo><Affiliation>Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de Lisboa Lisbon, Portugal.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Caldeirinha</LastName><ForeName>Patrícia</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Life Sciences, Centre for Functional Ecology, University of Coimbra Coimbra, Portugal.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Link</LastName><ForeName>Tobias</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Institut für Phytomedizin, Universität Hohenheim Stuttgart, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Abranches</LastName><ForeName>Rita</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Silva</LastName><ForeName>Maria do Céu</ForeName><Initials>Mdo C</Initials><AffiliationInfo><Affiliation>Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de Lisboa Lisbon, Portugal.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Voegele</LastName><ForeName>Ralf T</ForeName><Initials>RT</Initials><AffiliationInfo><Affiliation>Institut für Phytomedizin, Universität Hohenheim Stuttgart, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Loureiro</LastName><ForeName>João</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Life Sciences, Centre for Functional Ecology, University of Coimbra Coimbra, Portugal.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Talhinhas</LastName><ForeName>Pedro</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Centro de Investigação das Ferrugens do Cafeeiro, BioTrop, Instituto de Investigação Científica Tropical Oeiras, Portugal ; Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal ; CEER-Biosystems Engeneering, Instituto Superior de Agronomia, Universidade de Lisboa Lisbon, Portugal.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>08</Month><Day>26</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Plant Sci</MedlineTA><NlmUniqueID>101568200</NlmUniqueID><ISSNLinking>1664-462X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Gymnosporangium confusum</Keyword><Keyword MajorTopicYN="N">flow cytometry</Keyword><Keyword MajorTopicYN="N">mycological cytogenomics</Keyword><Keyword MajorTopicYN="N">nuclear DNA content</Keyword><Keyword MajorTopicYN="N">rust fungi</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>05</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>08</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>9</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>9</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>9</Month><Day>11</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25206357</ArticleId><ArticleId IdType="doi">10.3389/fpls.2014.00422</ArticleId><ArticleId IdType="pmc">PMC4143883</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Ann Bot. 2006 Sep;98(3):515-27</Citation><ArticleIdList><ArticleId IdType="pubmed">16820406</ArticleId></ArticleIdList></Reference><Reference><Citation>Mycology. 2014 Jun;5(2):52-63</Citation><ArticleIdList><ArticleId 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sortKey="Abranches, Rita" sort="Abranches, Rita" uniqKey="Abranches R" first="Rita" last="Abranches">Rita Abranches</name><name sortKey="Azinheira, Helena G" sort="Azinheira, Helena G" uniqKey="Azinheira H" first="Helena G" last="Azinheira">Helena G. 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