Comparative Genomics of the Ectomycorrhizal Sister Species Rhizopogon vinicolor and Rhizopogon vesiculosus (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type B Locus.
Identifieur interne : 000C94 ( Main/Corpus ); précédent : 000C93; suivant : 000C95Comparative Genomics of the Ectomycorrhizal Sister Species Rhizopogon vinicolor and Rhizopogon vesiculosus (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type B Locus.
Auteurs : Alija Bajro Mujic ; Alan Kuo ; Andrew Tritt ; Anna Lipzen ; Cindy Chen ; Jenifer Johnson ; Aditi Sharma ; Kerrie Barry ; Igor V. Grigoriev ; Joseph W. SpataforaSource :
- G3 (Bethesda, Md.) [ 2160-1836 ] ; 2017.
English descriptors
- KwdEn :
- Basidiomycota (classification), Basidiomycota (genetics), Chromosome Mapping (MeSH), Computational Biology (methods), Genes, Mating Type, Fungal (MeSH), Genome, Fungal (MeSH), Genome-Wide Association Study (MeSH), Genomics (methods), Genotype (MeSH), High-Throughput Nucleotide Sequencing (MeSH), Mutation (MeSH), Mycorrhizae (classification), Mycorrhizae (genetics), Phylogeny (MeSH), Polymorphism, Single Nucleotide (MeSH), Quantitative Trait Loci (MeSH), Quantitative Trait, Heritable (MeSH), Synteny (MeSH).
- MESH :
- classification : Basidiomycota, Mycorrhizae.
- genetics : Basidiomycota, Mycorrhizae.
- methods : Computational Biology, Genomics.
- Chromosome Mapping, Genes, Mating Type, Fungal, Genome, Fungal, Genome-Wide Association Study, Genotype, High-Throughput Nucleotide Sequencing, Mutation, Phylogeny, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Quantitative Trait, Heritable, Synteny.
Abstract
Divergence of breeding system plays an important role in fungal speciation. Ectomycorrhizal fungi, however, pose a challenge for the study of reproductive biology because most cannot be mated under laboratory conditions. To overcome this barrier, we sequenced the draft genomes of the ectomycorrhizal sister species Rhizopogon vinicolor Smith and Zeller and R. vesiculosus Smith and Zeller (Basidiomycota, Boletales)-the first genomes available for Basidiomycota truffles-and characterized gene content and organization surrounding their mating type loci. Both species possess a pair of homeodomain transcription factor homologs at the mating type A-locus as well as pheromone receptor and pheromone precursor homologs at the mating type B-locus. Comparison of Rhizopogon genomes with genomes from Boletales, Agaricales, and Polyporales revealed synteny of the A-locus region within Boletales, but several genomic rearrangements across orders. Our findings suggest correlation between gene content at the B-locus region and breeding system in Boletales with tetrapolar species possessing more diverse gene content than bipolar species. Rhizopogon vinicolor possesses a greater number of B-locus pheromone receptor and precursor genes than R. vesiculosus, as well as a pair of isoprenyl cysteine methyltransferase genes flanking the B-locus compared to a single copy in R. vesiculosus Examination of dikaryotic single nucleotide polymorphisms within genomes revealed greater heterozygosity in R. vinicolor, consistent with increased rates of outcrossing. Both species possess the components of a heterothallic breeding system with R. vinicolor possessing a B-locus region structure consistent with tetrapolar Boletales and R. vesiculosus possessing a B-locus region structure intermediate between bipolar and tetrapolar Boletales.
DOI: 10.1534/g3.117.039396
PubMed: 28450370
PubMed Central: PMC5473757
Links to Exploration step
pubmed:28450370Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Comparative Genomics of the Ectomycorrhizal Sister Species <i>Rhizopogon vinicolor</i> and <i>Rhizopogon vesiculosus</i> (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type <i>B</i> Locus.</title><author><name sortKey="Mujic, Alija Bajro" sort="Mujic, Alija Bajro" uniqKey="Mujic A" first="Alija Bajro" last="Mujic">Alija Bajro Mujic</name><affiliation><nlm:affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 amujic@gmail.com.</nlm:affiliation></affiliation></author><author><name sortKey="Kuo, Alan" sort="Kuo, Alan" uniqKey="Kuo A" first="Alan" last="Kuo">Alan Kuo</name><affiliation><nlm:affiliation>Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458.</nlm:affiliation></affiliation></author><author><name sortKey="Tritt, Andrew" sort="Tritt, Andrew" uniqKey="Tritt A" first="Andrew" last="Tritt">Andrew Tritt</name><affiliation><nlm:affiliation>Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458.</nlm:affiliation></affiliation></author><author><name sortKey="Lipzen, Anna" sort="Lipzen, Anna" uniqKey="Lipzen A" first="Anna" last="Lipzen">Anna Lipzen</name><affiliation><nlm:affiliation>Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Cindy" sort="Chen, Cindy" uniqKey="Chen C" first="Cindy" last="Chen">Cindy Chen</name><affiliation><nlm:affiliation>Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458.</nlm:affiliation></affiliation></author><author><name sortKey="Johnson, Jenifer" sort="Johnson, Jenifer" uniqKey="Johnson J" first="Jenifer" last="Johnson">Jenifer Johnson</name><affiliation><nlm:affiliation>Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458.</nlm:affiliation></affiliation></author><author><name sortKey="Sharma, Aditi" sort="Sharma, Aditi" uniqKey="Sharma A" first="Aditi" last="Sharma">Aditi Sharma</name><affiliation><nlm:affiliation>Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458.</nlm:affiliation></affiliation></author><author><name sortKey="Barry, Kerrie" sort="Barry, Kerrie" uniqKey="Barry K" first="Kerrie" last="Barry">Kerrie Barry</name><affiliation><nlm:affiliation>Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458.</nlm:affiliation></affiliation></author><author><name sortKey="Grigoriev, Igor V" sort="Grigoriev, Igor V" uniqKey="Grigoriev I" first="Igor V" last="Grigoriev">Igor V. 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Grigoriev</name><affiliation><nlm:affiliation>Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458.</nlm:affiliation></affiliation></author><author><name sortKey="Spatafora, Joseph W" sort="Spatafora, Joseph W" uniqKey="Spatafora J" first="Joseph W" last="Spatafora">Joseph W. Spatafora</name><affiliation><nlm:affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331.</nlm:affiliation></affiliation></author></analytic><series><title level="j">G3 (Bethesda, Md.)</title><idno type="eISSN">2160-1836</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Basidiomycota (classification)</term><term>Basidiomycota (genetics)</term><term>Chromosome Mapping (MeSH)</term><term>Computational Biology (methods)</term><term>Genes, Mating Type, Fungal (MeSH)</term><term>Genome, Fungal (MeSH)</term><term>Genome-Wide Association Study (MeSH)</term><term>Genomics (methods)</term><term>Genotype (MeSH)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Mutation (MeSH)</term><term>Mycorrhizae (classification)</term><term>Mycorrhizae (genetics)</term><term>Phylogeny (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Quantitative Trait Loci (MeSH)</term><term>Quantitative Trait, Heritable (MeSH)</term><term>Synteny (MeSH)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Basidiomycota</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Basidiomycota</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term><term>Genomics</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term><term>Genes, Mating Type, Fungal</term><term>Genome, Fungal</term><term>Genome-Wide Association Study</term><term>Genotype</term><term>High-Throughput Nucleotide Sequencing</term><term>Mutation</term><term>Phylogeny</term><term>Polymorphism, Single Nucleotide</term><term>Quantitative Trait Loci</term><term>Quantitative Trait, Heritable</term><term>Synteny</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Divergence of breeding system plays an important role in fungal speciation. Ectomycorrhizal fungi, however, pose a challenge for the study of reproductive biology because most cannot be mated under laboratory conditions. To overcome this barrier, we sequenced the draft genomes of the ectomycorrhizal sister species <i>Rhizopogon vinicolor</i> Smith and Zeller and <i>R. vesiculosus</i> Smith and Zeller (Basidiomycota, Boletales)-the first genomes available for Basidiomycota truffles-and characterized gene content and organization surrounding their mating type loci. Both species possess a pair of homeodomain transcription factor homologs at the mating type <i>A</i>-locus as well as pheromone receptor and pheromone precursor homologs at the mating type <i>B</i>-locus. Comparison of <i>Rhizopogon</i> genomes with genomes from Boletales, Agaricales, and Polyporales revealed synteny of the <i>A</i>-locus region within Boletales, but several genomic rearrangements across orders. Our findings suggest correlation between gene content at the <i>B</i>-locus region and breeding system in Boletales with tetrapolar species possessing more diverse gene content than bipolar species. <i>Rhizopogon vinicolor</i> possesses a greater number of <i>B</i>-locus pheromone receptor and precursor genes than <i>R. vesiculosus</i>, as well as a pair of isoprenyl cysteine methyltransferase genes flanking the <i>B</i>-locus compared to a single copy in <i>R. vesiculosus</i> Examination of dikaryotic single nucleotide polymorphisms within genomes revealed greater heterozygosity in <i>R. vinicolor</i>, consistent with increased rates of outcrossing. Both species possess the components of a heterothallic breeding system with <i>R. vinicolor</i> possessing a <i>B</i>-locus region structure consistent with tetrapolar Boletales and <i>R. vesiculosus</i> possessing a <i>B</i>-locus region structure intermediate between bipolar and tetrapolar Boletales.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28450370</PMID><DateCompleted><Year>2018</Year><Month>03</Month><Day>26</Day></DateCompleted><DateRevised><Year>2019</Year><Month>01</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2160-1836</ISSN><JournalIssue CitedMedium="Internet"><Volume>7</Volume><Issue>6</Issue><PubDate><Year>2017</Year><Month>06</Month><Day>07</Day></PubDate></JournalIssue><Title>G3 (Bethesda, Md.)</Title><ISOAbbreviation>G3 (Bethesda)</ISOAbbreviation></Journal><ArticleTitle>Comparative Genomics of the Ectomycorrhizal Sister Species <i>Rhizopogon vinicolor</i> and <i>Rhizopogon vesiculosus</i> (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type <i>B</i> Locus.</ArticleTitle><Pagination><MedlinePgn>1775-1789</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1534/g3.117.039396</ELocationID><Abstract><AbstractText>Divergence of breeding system plays an important role in fungal speciation. Ectomycorrhizal fungi, however, pose a challenge for the study of reproductive biology because most cannot be mated under laboratory conditions. To overcome this barrier, we sequenced the draft genomes of the ectomycorrhizal sister species <i>Rhizopogon vinicolor</i> Smith and Zeller and <i>R. vesiculosus</i> Smith and Zeller (Basidiomycota, Boletales)-the first genomes available for Basidiomycota truffles-and characterized gene content and organization surrounding their mating type loci. Both species possess a pair of homeodomain transcription factor homologs at the mating type <i>A</i>-locus as well as pheromone receptor and pheromone precursor homologs at the mating type <i>B</i>-locus. Comparison of <i>Rhizopogon</i> genomes with genomes from Boletales, Agaricales, and Polyporales revealed synteny of the <i>A</i>-locus region within Boletales, but several genomic rearrangements across orders. Our findings suggest correlation between gene content at the <i>B</i>-locus region and breeding system in Boletales with tetrapolar species possessing more diverse gene content than bipolar species. <i>Rhizopogon vinicolor</i> possesses a greater number of <i>B</i>-locus pheromone receptor and precursor genes than <i>R. vesiculosus</i>, as well as a pair of isoprenyl cysteine methyltransferase genes flanking the <i>B</i>-locus compared to a single copy in <i>R. vesiculosus</i> Examination of dikaryotic single nucleotide polymorphisms within genomes revealed greater heterozygosity in <i>R. vinicolor</i>, consistent with increased rates of outcrossing. Both species possess the components of a heterothallic breeding system with <i>R. vinicolor</i> possessing a <i>B</i>-locus region structure consistent with tetrapolar Boletales and <i>R. vesiculosus</i> possessing a <i>B</i>-locus region structure intermediate between bipolar and tetrapolar Boletales.</AbstractText><CopyrightInformation>Copyright © 2017 Mujic et al.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Mujic</LastName><ForeName>Alija Bajro</ForeName><Initials>AB</Initials><AffiliationInfo><Affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 amujic@gmail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kuo</LastName><ForeName>Alan</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tritt</LastName><ForeName>Andrew</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lipzen</LastName><ForeName>Anna</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Cindy</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Johnson</LastName><ForeName>Jenifer</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sharma</LastName><ForeName>Aditi</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Barry</LastName><ForeName>Kerrie</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grigoriev</LastName><ForeName>Igor V</ForeName><Initials>IV</Initials><AffiliationInfo><Affiliation>Joint Genome Institute, United States Department of Energy, Walnut Creek, California 95458.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Spatafora</LastName><ForeName>Joseph W</ForeName><Initials>JW</Initials><AffiliationInfo><Affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>06</Month><Day>07</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>G3 (Bethesda)</MedlineTA><NlmUniqueID>101566598</NlmUniqueID><ISSNLinking>2160-1836</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001487" MajorTopicYN="N">Basidiomycota</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D049770" MajorTopicYN="Y">Genes, Mating Type, Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016681" MajorTopicYN="Y">Genome, Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055106" MajorTopicYN="N">Genome-Wide Association Study</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="Y">Genomics</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009154" MajorTopicYN="N">Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D040641" MajorTopicYN="N">Quantitative Trait Loci</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019655" MajorTopicYN="N">Quantitative Trait, Heritable</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D026801" MajorTopicYN="N">Synteny</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Boletales</Keyword><Keyword MajorTopicYN="Y">Genetics of Sex</Keyword><Keyword MajorTopicYN="Y">ectomycorrhizae</Keyword><Keyword MajorTopicYN="Y">fungal mating pheromone</Keyword><Keyword MajorTopicYN="Y">isoprenylcysteine carboxyl methyltransferase</Keyword><Keyword MajorTopicYN="Y">truffle</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>4</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>3</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>4</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28450370</ArticleId><ArticleId IdType="pii">g3.117.039396</ArticleId><ArticleId IdType="doi">10.1534/g3.117.039396</ArticleId><ArticleId IdType="pmc">PMC5473757</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Proc Natl Acad 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