Genome comparisons suggest an association between Ceratocystis host adaptations and effector clusters in unique transposable element families.
Identifieur interne : 000154 ( Main/Exploration ); précédent : 000153; suivant : 000155Genome comparisons suggest an association between Ceratocystis host adaptations and effector clusters in unique transposable element families.
Auteurs : Arista Fourie [Afrique du Sud] ; Ronnie De Jonge [Pays-Bas] ; Magriet A. Van Der Nest [Afrique du Sud] ; Tuan A. Duong [Afrique du Sud] ; Michael J. Wingfield [Afrique du Sud] ; Brenda D. Wingfield [Afrique du Sud] ; Irene Barnes [Afrique du Sud]Source :
- Fungal genetics and biology : FG & B [ 1096-0937 ] ; 2020.
Abstract
Ceratocystis fimbriata is a host specific fungal pathogen of sweet potato (Ipomoea batatas). The closely related species, C. manginecans, is an important pathogen of trees (e.g. Acacia mangium and Mangifera indica) but has never been isolated from tuber crops. The genetic factors that determine the host range and host specificity of these species have not been determined. The aim of this study was to compare the genomes of C. fimbriata and C. manginecans in order to identify species-specific genetic differences that could be associated with host specificity. This included whole-genome alignments as well as comparisons of gene content and transposable elements (TEs). The genomes of the two species were found to be very similar, sharing similar catalogues of CAZymes, peptidases and lipases. However, the genomes of the two species also varied, harbouring species-specific genes (e.g. small secreted effectors, nutrient processing proteins and stress response proteins). A portion of the TEs identified (17%) had a unique distribution in each species. Transposable elements appeared to have played a prominent role in the divergence of the two species because they were strongly associated with chromosomal translocations and inversions as well as with unique genomic regions containing species-specific genes. Two large effector clusters, with unique TEs in each species, were identified. These effectors displayed non-synonymous mutations and deletions, conserved within a species, and could serve as mutational hot-spots for the development of host specificity in the two species.
DOI: 10.1016/j.fgb.2020.103433
PubMed: 32652232
Affiliations:
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Duong</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002</wicri:regionArea><wicri:noRegion>Pretoria 0002</wicri:noRegion></affiliation></author><author><name sortKey="Wingfield, Michael J" sort="Wingfield, Michael J" uniqKey="Wingfield M" first="Michael J" last="Wingfield">Michael J. Wingfield</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002</wicri:regionArea><wicri:noRegion>Pretoria 0002</wicri:noRegion></affiliation></author><author><name sortKey="Wingfield, Brenda D" sort="Wingfield, Brenda D" uniqKey="Wingfield B" first="Brenda D" last="Wingfield">Brenda D. Wingfield</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002</wicri:regionArea><wicri:noRegion>Pretoria 0002</wicri:noRegion></affiliation></author><author><name sortKey="Barnes, Irene" sort="Barnes, Irene" uniqKey="Barnes I" first="Irene" last="Barnes">Irene Barnes</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa. Electronic address: irene.barnes@fabi.up.ac.za.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002</wicri:regionArea><wicri:noRegion>Pretoria 0002</wicri:noRegion></affiliation></author></analytic><series><title level="j">Fungal genetics and biology : FG & B</title><idno type="eISSN">1096-0937</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">Ceratocystis fimbriata is a host specific fungal pathogen of sweet potato (Ipomoea batatas). The closely related species, C. manginecans, is an important pathogen of trees (e.g. Acacia mangium and Mangifera indica) but has never been isolated from tuber crops. The genetic factors that determine the host range and host specificity of these species have not been determined. The aim of this study was to compare the genomes of C. fimbriata and C. manginecans in order to identify species-specific genetic differences that could be associated with host specificity. This included whole-genome alignments as well as comparisons of gene content and transposable elements (TEs). The genomes of the two species were found to be very similar, sharing similar catalogues of CAZymes, peptidases and lipases. However, the genomes of the two species also varied, harbouring species-specific genes (e.g. small secreted effectors, nutrient processing proteins and stress response proteins). A portion of the TEs identified (17%) had a unique distribution in each species. Transposable elements appeared to have played a prominent role in the divergence of the two species because they were strongly associated with chromosomal translocations and inversions as well as with unique genomic regions containing species-specific genes. Two large effector clusters, with unique TEs in each species, were identified. These effectors displayed non-synonymous mutations and deletions, conserved within a species, and could serve as mutational hot-spots for the development of host specificity in the two species.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">32652232</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>08</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1096-0937</ISSN><JournalIssue CitedMedium="Internet"><Volume>143</Volume><PubDate><Year>2020</Year><Month>Oct</Month></PubDate></JournalIssue><Title>Fungal genetics and biology : FG & B</Title><ISOAbbreviation>Fungal Genet Biol</ISOAbbreviation></Journal><ArticleTitle>Genome comparisons suggest an association between Ceratocystis host adaptations and effector clusters in unique transposable element families.</ArticleTitle><Pagination><MedlinePgn>103433</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S1087-1845(20)30124-9</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.fgb.2020.103433</ELocationID><Abstract><AbstractText>Ceratocystis fimbriata is a host specific fungal pathogen of sweet potato (Ipomoea batatas). The closely related species, C. manginecans, is an important pathogen of trees (e.g. Acacia mangium and Mangifera indica) but has never been isolated from tuber crops. The genetic factors that determine the host range and host specificity of these species have not been determined. The aim of this study was to compare the genomes of C. fimbriata and C. manginecans in order to identify species-specific genetic differences that could be associated with host specificity. This included whole-genome alignments as well as comparisons of gene content and transposable elements (TEs). The genomes of the two species were found to be very similar, sharing similar catalogues of CAZymes, peptidases and lipases. However, the genomes of the two species also varied, harbouring species-specific genes (e.g. small secreted effectors, nutrient processing proteins and stress response proteins). A portion of the TEs identified (17%) had a unique distribution in each species. Transposable elements appeared to have played a prominent role in the divergence of the two species because they were strongly associated with chromosomal translocations and inversions as well as with unique genomic regions containing species-specific genes. Two large effector clusters, with unique TEs in each species, were identified. These effectors displayed non-synonymous mutations and deletions, conserved within a species, and could serve as mutational hot-spots for the development of host specificity in the two species.</AbstractText><CopyrightInformation>Copyright © 2020 Elsevier Inc. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Fourie</LastName><ForeName>Arista</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>de Jonge</LastName><ForeName>Ronnie</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht 3584 CH, the Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>van der Nest</LastName><ForeName>Magriet A</ForeName><Initials>MA</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; Biotechnology Platform, Agricultural Research Council, Private Bag X05, Onderstepoort 0110, 0002, South Africa.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Duong</LastName><ForeName>Tuan A</ForeName><Initials>TA</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wingfield</LastName><ForeName>Michael J</ForeName><Initials>MJ</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wingfield</LastName><ForeName>Brenda D</ForeName><Initials>BD</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Barnes</LastName><ForeName>Irene</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa. Electronic address: irene.barnes@fabi.up.ac.za.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>07</Month><Day>08</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Fungal Genet Biol</MedlineTA><NlmUniqueID>9607601</NlmUniqueID><ISSNLinking>1087-1845</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Ceratocystidaceae</Keyword><Keyword MajorTopicYN="N">Chromosomal rearrangement</Keyword><Keyword MajorTopicYN="N">Effectors</Keyword><Keyword MajorTopicYN="N">Fungi</Keyword><Keyword MajorTopicYN="N">Genome comparison</Keyword><Keyword MajorTopicYN="N">RIP</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>01</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>06</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>06</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>7</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>7</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>7</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32652232</ArticleId><ArticleId IdType="pii">S1087-1845(20)30124-9</ArticleId><ArticleId IdType="doi">10.1016/j.fgb.2020.103433</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Afrique du Sud</li><li>Pays-Bas</li></country><region><li>Utrecht (province)</li></region><settlement><li>Utrecht</li></settlement><orgName><li>Université d'Utrecht</li></orgName></list><tree><country name="Afrique du Sud"><noRegion><name sortKey="Fourie, Arista" sort="Fourie, Arista" uniqKey="Fourie A" first="Arista" last="Fourie">Arista Fourie</name></noRegion><name sortKey="Barnes, Irene" sort="Barnes, Irene" uniqKey="Barnes I" first="Irene" last="Barnes">Irene Barnes</name><name sortKey="Duong, Tuan A" sort="Duong, Tuan A" uniqKey="Duong T" first="Tuan A" last="Duong">Tuan A. Duong</name><name sortKey="Van Der Nest, Magriet A" sort="Van Der Nest, Magriet A" uniqKey="Van Der Nest M" first="Magriet A" last="Van Der Nest">Magriet A. Van Der Nest</name><name sortKey="Wingfield, Brenda D" sort="Wingfield, Brenda D" uniqKey="Wingfield B" first="Brenda D" last="Wingfield">Brenda D. Wingfield</name><name sortKey="Wingfield, Michael J" sort="Wingfield, Michael J" uniqKey="Wingfield M" first="Michael J" last="Wingfield">Michael J. Wingfield</name></country><country name="Pays-Bas"><region name="Utrecht (province)"><name sortKey="De Jonge, Ronnie" sort="De Jonge, Ronnie" uniqKey="De Jonge R" first="Ronnie" last="De Jonge">Ronnie De Jonge</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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