title: Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus.
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.
authors.affiliation: Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China.
authors.forename: Kui
authors.initials: K
authors.lastname: Lin
authors.affiliation: Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands.
authors.forename: Erik
authors.initials: E
authors.lastname: Limpens
authors.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.
authors.forename: Zhonghua
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands.
authors.forename: Sergey
authors.initials: S
authors.lastname: Ivanov
authors.affiliation: The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom.
authors.forename: Diane G O
authors.initials: DG
authors.lastname: Saunders
authors.affiliation: Novome Biotech Inc., Zhongguancun Life Science Park, Beijing, China.
authors.forename: Desheng
authors.initials: D
authors.lastname: Mu
authors.affiliation: Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China.
authors.forename: Erli
authors.initials: E
authors.lastname: Pang
authors.affiliation: Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China.
authors.forename: Huifen
authors.initials: H
authors.lastname: Cao
authors.affiliation: Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China.
authors.forename: Hwangho
authors.initials: H
authors.lastname: Cha
authors.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.
authors.forename: Tao
authors.initials: T
authors.lastname: Lin
authors.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.
authors.forename: Qian
authors.initials: Q
authors.lastname: Zhou
authors.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.
authors.forename: Yi
authors.initials: Y
authors.lastname: Shang
authors.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.
authors.forename: Ying
authors.initials: Y
authors.lastname: Li
authors.affiliation: Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands.
authors.forename: Trupti
authors.initials: T
authors.lastname: Sharma
authors.affiliation: Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands.
authors.forename: Robin
authors.initials: R
authors.lastname: van Velzen
authors.affiliation: Laboratory of Cell Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands.
authors.forename: Norbert
authors.initials: N
authors.lastname: de Ruijter
authors.affiliation: Laboratory of Genetics, Department of Plant Science, Wageningen University, Wageningen, The Netherlands.
authors.forename: Duur K
authors.initials: DK
authors.lastname: Aanen
authors.affiliation: The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom.
authors.forename: Joe
authors.initials: J
authors.lastname: Win
authors.affiliation: The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom.
authors.forename: Sophien
authors.initials: S
authors.lastname: Kamoun
authors.affiliation: Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands ; College of Science, King Saud University, Riyadh, Saudi Arabia.
authors.forename: Ton
authors.initials: T
authors.lastname: Bisseling
authors.affiliation: Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands.
authors.forename: René
authors.initials: R
authors.lastname: Geurts
authors.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.
authors.forename: Sanwen
authors.initials: S
authors.lastname: Huang
mesh_terms: D001483:Base Sequence; D002467:Cell Nucleus / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics*; D016681:Genome, Fungal; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D038821:Mycorrhizae / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D013172:Spores, Fungal / Q000235:genetics
chemical_list: D004275:DNA, Ribosomal