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PLoS Genet. 2014 Jan;10(1):e1004078. doi: 10.1371/journal.pgen.1004078. Epub 2014 Jan 9.

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

Author information

1
Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China.
2
Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands.
3
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.
4
The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom.
5
Novome Biotech Inc., Zhongguancun Life Science Park, Beijing, China.
6
Laboratory of Cell Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands.
7
Laboratory of Genetics, Department of Plant Science, Wageningen University, Wageningen, The Netherlands.
8
Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands ; College of Science, King Saud University, Riyadh, Saudi Arabia.
9
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.

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.

PMID:
24415955
PMCID:
PMC3886924
DOI:
10.1371/journal.pgen.1004078
[Indexed for MEDLINE]
Free PMC Article

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