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

Abstract

Arbuscular mycorrhizal fungi (AMF) are one of the most widespread symbionts of land plants. Our substantially improved reference genome assembly of a model AMF, Rhizophagus irregularis DAOM-181602 (total contigs = 210, contig N50 = 2.3Mbp) facilitated discovery of repetitive elements with unusual characteristics. R. irregularis has only ten to eleven copies of the complete 45S rDNA, 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 of concerted evolution that rDNA homogeneity depends on its tandem repeat structure. RNA-seq analysis confirmed that all rDNA variants are actively transcribed. Observed rDNA/rRNA polymorphism may modulate translation by using different ribosomes depending on biotic and abiotic interactions. The non-tandem repeat structure and intragenomic heterogeneity of AMF rDNA may facilitate adaptation to a broad host range despite lacking a sexual life cycle.All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina

“…(), Maeda et al . () and Sun et al . (), have expanded and refined our understanding of the genomic heritage of AM symbionts.…”

“…To date, only three species of Glomeromycotina have published genomes, namely Rhizophagus irregularis (Schenck & Sm.) Walker & Schüßler (Tisserant et al ., ; Lin et al ., ; Chen et al ., ,; Maeda et al ., ), Rhizophagus clarus (Nicolson & Schenck) Walker & Schüßler (Kobayashi et al ., ) and Diversispora epigaea (Daniels & Trappe) Walker & Schüßler (formerly Glomus versiforme ; Sun et al ., ), meaning that the gene repertoires of most species of Glomeromycotina have yet to be sequenced, analysed and compared.…”

How do arbuscular mycorrhizal fungi handle phosphate? New insight into fine‐tuning of phosphate metabolism

“…This molecule could activate, for example, VTC‐catalyzed polyP synthesis in isolated yeast vacuoles even at 100 n m (Wild et al ., ), suggesting that intracellular concentration of 5PP‐InsP 5 is tightly regulated. Through resurveys of the published sequence data (Kikuchi et al ., ; Maeda et al ., ), a set of genes encoding the enzymes involved in InsPs biosynthesis/hydrolysis is found both in the R. irregularis genome and the R. clarus transcriptome (Fig. c,d).…”

“…The SPX domain has been found in the proteins involved in Pi homeostasis in a wide range of multicellular eukaryotes, including fungi, plants, and animals. In the published genome of R. irregularis (Maeda et al ., ), 10 genes encoding SPX‐domain‐containing proteins are found: VTC2, VTC4, PHO91, GDE1‐1/GDE1‐2 (glycerophosphocholine phosphodiesterases), SER2 (phosphoserine phosphatase), SYG1‐1/SYG1‐2 (suppressor of yeast gpα1 ), SPX1 (SPX‐domain‐containing protein), and NLA‐like protein (Fig. a).…”

“…(a) Architecture of SPX‐domain‐containing proteins found in the Rhizophagus irregularis genome. The protein sequences in the R. irregularis genome database (Maeda et al ., ) were scanned for the Pfam domains SPX (pfam03105) using H mmer ( http://hmmer.org/). Sequence data are deposited in DDBJ (LC339943–LC339952).…”