Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus.
Identifieur interne : 001983 ( Main/Corpus ); précédent : 001982; suivant : 001984Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus.
Auteurs : Kui Lin ; Erik Limpens ; Zhonghua Zhang ; Sergey Ivanov ; Diane G O. Saunders ; Desheng Mu ; Erli Pang ; Huifen Cao ; Hwangho Cha ; Tao Lin ; Qian Zhou ; Yi Shang ; Ying Li ; Trupti Sharma ; Robin Van Velzen ; Norbert De Ruijter ; Duur K. Aanen ; Joe Win ; Sophien Kamoun ; Ton Bisseling ; René Geurts ; Sanwen HuangSource :
- PLoS genetics [ 1553-7404 ] ; 2014.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Ribosomal.
- genetics : Cell Nucleus, Mycorrhizae, Open Reading Frames, Spores, Fungal.
- Base Sequence, Genome, Fungal, High-Throughput Nucleotide Sequencing, Molecular Sequence Data, Phylogeny.
Abstract
Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.
DOI: 10.1371/journal.pgen.1004078
PubMed: 24415955
PubMed Central: PMC3886924
Links to Exploration step
pubmed:24415955Le document en format XML
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<author><name sortKey="Mu, Desheng" sort="Mu, Desheng" uniqKey="Mu D" first="Desheng" last="Mu">Desheng Mu</name>
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<author><name sortKey="Zhou, Qian" sort="Zhou, Qian" uniqKey="Zhou Q" first="Qian" last="Zhou">Qian Zhou</name>
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<author><name sortKey="Shang, Yi" sort="Shang, Yi" uniqKey="Shang Y" first="Yi" last="Shang">Yi Shang</name>
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<author><name sortKey="Sharma, Trupti" sort="Sharma, Trupti" uniqKey="Sharma T" first="Trupti" last="Sharma">Trupti Sharma</name>
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<author><name sortKey="Van Velzen, Robin" sort="Van Velzen, Robin" uniqKey="Van Velzen R" first="Robin" last="Van Velzen">Robin Van Velzen</name>
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</affiliation>
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<author><name sortKey="De Ruijter, Norbert" sort="De Ruijter, Norbert" uniqKey="De Ruijter N" first="Norbert" last="De Ruijter">Norbert De Ruijter</name>
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<author><name sortKey="Aanen, Duur K" sort="Aanen, Duur K" uniqKey="Aanen D" first="Duur K" last="Aanen">Duur K. Aanen</name>
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<author><name sortKey="Win, Joe" sort="Win, Joe" uniqKey="Win J" first="Joe" last="Win">Joe Win</name>
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<author><name sortKey="Kamoun, Sophien" sort="Kamoun, Sophien" uniqKey="Kamoun S" first="Sophien" last="Kamoun">Sophien Kamoun</name>
<affiliation><nlm:affiliation>The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom.</nlm:affiliation>
</affiliation>
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<author><name sortKey="Bisseling, Ton" sort="Bisseling, Ton" uniqKey="Bisseling T" first="Ton" last="Bisseling">Ton Bisseling</name>
<affiliation><nlm:affiliation>Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands ; College of Science, King Saud University, Riyadh, Saudi Arabia.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Geurts, Rene" sort="Geurts, Rene" uniqKey="Geurts R" first="René" last="Geurts">René Geurts</name>
<affiliation><nlm:affiliation>Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Huang, Sanwen" sort="Huang, Sanwen" uniqKey="Huang S" first="Sanwen" last="Huang">Sanwen Huang</name>
<affiliation><nlm:affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China ; Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.</nlm:affiliation>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus.</title>
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<affiliation><nlm:affiliation>Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China.</nlm:affiliation>
</affiliation>
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<author><name sortKey="Limpens, Erik" sort="Limpens, Erik" uniqKey="Limpens E" first="Erik" last="Limpens">Erik Limpens</name>
<affiliation><nlm:affiliation>Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Zhang, Zhonghua" sort="Zhang, Zhonghua" uniqKey="Zhang Z" first="Zhonghua" last="Zhang">Zhonghua Zhang</name>
<affiliation><nlm:affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China.</nlm:affiliation>
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<author><name sortKey="Ivanov, Sergey" sort="Ivanov, Sergey" uniqKey="Ivanov S" first="Sergey" last="Ivanov">Sergey Ivanov</name>
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</affiliation>
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<author><name sortKey="Saunders, Diane G O" sort="Saunders, Diane G O" uniqKey="Saunders D" first="Diane G O" last="Saunders">Diane G O. Saunders</name>
<affiliation><nlm:affiliation>The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Mu, Desheng" sort="Mu, Desheng" uniqKey="Mu D" first="Desheng" last="Mu">Desheng Mu</name>
<affiliation><nlm:affiliation>Novome Biotech Inc., Zhongguancun Life Science Park, Beijing, China.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Pang, Erli" sort="Pang, Erli" uniqKey="Pang E" first="Erli" last="Pang">Erli Pang</name>
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<author><name sortKey="Cao, Huifen" sort="Cao, Huifen" uniqKey="Cao H" first="Huifen" last="Cao">Huifen Cao</name>
<affiliation><nlm:affiliation>Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China.</nlm:affiliation>
</affiliation>
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<author><name sortKey="Cha, Hwangho" sort="Cha, Hwangho" uniqKey="Cha H" first="Hwangho" last="Cha">Hwangho Cha</name>
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<author><name sortKey="Lin, Tao" sort="Lin, Tao" uniqKey="Lin T" first="Tao" last="Lin">Tao Lin</name>
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<author><name sortKey="Zhou, Qian" sort="Zhou, Qian" uniqKey="Zhou Q" first="Qian" last="Zhou">Qian Zhou</name>
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</affiliation>
</author>
<author><name sortKey="Shang, Yi" sort="Shang, Yi" uniqKey="Shang Y" first="Yi" last="Shang">Yi Shang</name>
<affiliation><nlm:affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Li, Ying" sort="Li, Ying" uniqKey="Li Y" first="Ying" last="Li">Ying Li</name>
<affiliation><nlm:affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Sharma, Trupti" sort="Sharma, Trupti" uniqKey="Sharma T" first="Trupti" last="Sharma">Trupti Sharma</name>
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</affiliation>
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<author><name sortKey="De Ruijter, Norbert" sort="De Ruijter, Norbert" uniqKey="De Ruijter N" first="Norbert" last="De Ruijter">Norbert De Ruijter</name>
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</affiliation>
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<author><name sortKey="Aanen, Duur K" sort="Aanen, Duur K" uniqKey="Aanen D" first="Duur K" last="Aanen">Duur K. Aanen</name>
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<author><name sortKey="Win, Joe" sort="Win, Joe" uniqKey="Win J" first="Joe" last="Win">Joe Win</name>
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</affiliation>
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</affiliation>
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</affiliation>
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<term>Cell Nucleus (genetics)</term>
<term>DNA, Ribosomal (genetics)</term>
<term>Genome, Fungal (MeSH)</term>
<term>High-Throughput Nucleotide Sequencing (MeSH)</term>
<term>Molecular Sequence Data (MeSH)</term>
<term>Mycorrhizae (genetics)</term>
<term>Open Reading Frames (genetics)</term>
<term>Phylogeny (MeSH)</term>
<term>Spores, Fungal (genetics)</term>
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<term>Mycorrhizae</term>
<term>Open Reading Frames</term>
<term>Spores, Fungal</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term>
<term>Genome, Fungal</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Molecular Sequence Data</term>
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<front><div type="abstract" xml:lang="en">Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya. </div>
</front>
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<DateCompleted><Year>2014</Year>
<Month>06</Month>
<Day>17</Day>
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<Month>03</Month>
<Day>05</Day>
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<Title>PLoS genetics</Title>
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<ArticleTitle>Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus.</ArticleTitle>
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<Abstract><AbstractText>Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya. </AbstractText>
</Abstract>
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<ForeName>Kui</ForeName>
<Initials>K</Initials>
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</AffiliationInfo>
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<ForeName>Erik</ForeName>
<Initials>E</Initials>
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</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Zhang</LastName>
<ForeName>Zhonghua</ForeName>
<Initials>Z</Initials>
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</AffiliationInfo>
</Author>
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<ForeName>Sergey</ForeName>
<Initials>S</Initials>
<AffiliationInfo><Affiliation>Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands.</Affiliation>
</AffiliationInfo>
</Author>
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<ForeName>Diane G O</ForeName>
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<ForeName>Desheng</ForeName>
<Initials>D</Initials>
<AffiliationInfo><Affiliation>Novome Biotech Inc., Zhongguancun Life Science Park, Beijing, China.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Pang</LastName>
<ForeName>Erli</ForeName>
<Initials>E</Initials>
<AffiliationInfo><Affiliation>Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China.</Affiliation>
</AffiliationInfo>
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</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Cha</LastName>
<ForeName>Hwangho</ForeName>
<Initials>H</Initials>
<AffiliationInfo><Affiliation>Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Lin</LastName>
<ForeName>Tao</ForeName>
<Initials>T</Initials>
<AffiliationInfo><Affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Zhou</LastName>
<ForeName>Qian</ForeName>
<Initials>Q</Initials>
<AffiliationInfo><Affiliation>Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Shang</LastName>
<ForeName>Yi</ForeName>
<Initials>Y</Initials>
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