Evidence of non-tandemly repeated rDNAs and their intragenomic heterogeneity in Rhizophagus irregularis

Taro Maeda,Naoya Takeda,Nao Okuma,Hiromu Kameoka,Shuji Shigenobu,Katsushi Yamaguchi,Masayoshi Kawaguchi,Yuuki Kobayashi,Takahiro Bino

doi:10.1038/s42003-018-0094-7

Abstract

Arbuscular mycorrhizal fungus (AMF) species are some of the most widespread symbionts of land plants. Our much improved reference genome assembly of a model AMF, Rhizophagus irregularis DAOM-181602 (total contigs = 210), facilitated a discovery of repetitive elements with unusual characteristics. R. irregularis has only ten or 11 copies of complete 45S rDNAs, whereas the general eukaryotic genome has tens to thousands of rDNA copies. R. irregularis rDNAs are highly heterogeneous and lack a tandem repeat structure. These findings provide evidence for the hypothesis that rDNA heterogeneity depends on the lack of tandem repeat structures. RNA-Seq analysis confirmed that all rDNA variants are actively transcribed. Observed rDNA/rRNA polymorphisms may modulate translation by using different ribosomes depending on biotic and abiotic interactions. The non-tandem repeat structure and intragenomic heterogeneity of AMF rDNA/rRNA may facilitate successful adaptation to various environmental conditions, increasing host compatibility of these symbiotic fungi.

Highlights

Arbuscular mycorrhizal fungus (AMF) species are some of the most widespread symbionts of land plants
We generated a 76-fold whole-genome shotgun sequence (11.7 Gb in total) (Supplementary Table 2) from genome DNA isolated from a spore suspension of a commercial strain of R. irregularis DAOM-181602 using the PacBio SMRT sequencing platform
Nine contigs were almost identical to carrot DNA sequences deposited in the public database (Supplementary Table 3), and these were removed as contaminants derived from a host plant used by the manufacturer

Summary

Introduction

Arbuscular mycorrhizal fungus (AMF) species are some of the most widespread symbionts of land plants. Genomic data have been provided for Rhizophagus irregularis DAOM-181602 (=DOAM197198)[12,13,14], Gigaspora rosea[12], Rhizophagus clarus[15], and other isolates of R. irregularis[14,16] These studies revealed potential host-dependent biological pathways[12,17] and candidate genes for plant infection and sexual reproduction[15,16,17]. Since Sanders et al.[21], many studies have indicated intracellular polymorphisms of rDNA (ITS) in various AMF species[22,23,24], and the sequencing of isolated nuclei from Claroideoglomus etunicatum and R. irregularis DAOM-181602 suggested sequence variation among the paralogous rDNAs, i.e., intragenomic heterogeneity[13,25]. The heterogeneous rDNAs observed in AMF species implies the collapse of their concerted evolution, and suggest the unique maintenance system of rDNA copy number

Methods

Results

Conclusion