Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus

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 BisselingRené Geurts, Sanwen Huang

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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.

Original languageEnglish
Article numbere1004078
JournalPLoS Genetics
Volume10
Issue number1
DOIs
Publication statusPublished - 9 Jan 2014

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