Stochastic nuclear organization and host-dependent allele contribution in Rhizophagus irregularis

BMC Genomics

Research Article

Claudia Bergin¹  Anna Rosling²  Zhiyong Pan³  Raúl Y. Wijfjes⁴  Ben Auxier⁵  Erik Limpens⁶  Jelle van Creij⁶  Jianyong An⁷  Ton Bisseling⁷ 

[1] Department of Cell and Molecular Biology, Uppsala University, and Microbial Single Cell Genomics Facility, Science for Life Laboratory, Uppsala, Sweden;Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden;Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, People’s Republic of China;Laboratory of Bioinformatics, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands;Current affiliation: Faculty of Biology, Ludwig Maximilian University of Munich, Munich, Germany;Laboratory of Genetics, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands;Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands;Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, The Netherlands;Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, 102206, Beijing, China;

关键词: Arbuscular mycorrhiza;    Heterokaryote;    Recombination;    Parasexual;    Single nucleus sequencing;    Symbiosis;    Rhizophagus irregularis;    PacBio SMRT sequencing;   

DOI  :  10.1186/s12864-023-09126-6

 received in 2021-11-24, accepted in 2023-01-10,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundArbuscular mycorrhizal (AM) fungi are arguably the most important symbionts of plants, offering a range of benefits to their hosts. However, the provisioning of these benefits does not appear to be uniform among AM fungal individuals, with genetic variation between fungal symbionts having a substantial impact on plant performance. Interestingly, genetic variation has also been reported within fungal individuals, which contain millions of haploid nuclei sharing a common cytoplasm. In the model AM fungus, Rhizophagus irregularis, several isolates have been reported to be dikaryotes, containing two genetically distinct types of nuclei recognized based on their mating-type (MAT) locus identity. However, their extremely coenocytic nature and lack of a known single nucleus stage has raised questions on the origin, distribution and dynamics of this genetic variation.ResultsHere we performed DNA and RNA sequencing at the mycelial individual, single spore and single nucleus levels to gain insight into the dynamic genetic make-up of the dikaryote-like R. irregularis C3 isolate and the effect of different host plants on its genetic variation. Our analyses reveal that parallel spore and root culture batches can have widely variable ratios of two main genotypes in C3. Additionally, numerous polymorphisms were found with frequencies that deviated significantly from the general genotype ratio, indicating a diverse population of slightly different nucleotypes. Changing host plants did not show consistent host effects on nucleotype ratio’s after multiple rounds of subculturing. Instead, we found a major effect of host plant-identity on allele-specific expression in C3.ConclusionOur analyses indicate a highly dynamic/variable genetic organization in different isolates of R. irregularis. Seemingly random fluctuations in nucleotype ratio’s upon spore formation, recombination events, high variability of non-tandemly repeated rDNA sequences and host-dependent allele expression all add levels of variation that may contribute to the evolutionary success of these widespread symbionts.

【 授权许可】

CC BY   
© The Author(s) 2023

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