Diploidy within a Haploid Genus of Entomopathogenic Fungi

Abstract

Fungi in the genus Metarhizium are soil-borne plant-root endophytes and rhizosphere colonisers, but also potent insect pathogens with highly variable host ranges. These ascomycete fungi are predominantly asexually reproducing and ancestrally haploid, but two independent origins of persistent diploidy within the Coleoptera-infecting M. majus species complex are known and has been attributed to incomplete chromosomal segregation following meiosis during the sexual cycle. There is also evidence for infrequent sexual cycles in the locust-specific pathogenic fungus M. acridum (Hypocreales: Clavicipitaceae), which is an important entomopathogenic biocontrol agent used for the control of grasshoppers in agricultural systems as an alternative to chemical control. Here, we show that the genome of the M. acridum isolate ARSEF 324, which is formulated and commercially utilised is functionally diploid. We used single-molecule real-time (SMRT) sequencing technology to complete a high-quality assembly of ARSEF 324. Kmer frequencies, intragenomic collinearity between contigs and single nucleotide variant read depths across the genome revealed the first incidence of diploidy described within the species M. acridum. The haploid assembly of 44.7 Mb consisted of 20.8% repetitive elements, which is the highest proportion described of any Metarhizium species. The long-read diploid genome assembly sheds light on past research on this strain, such as unusual high UVB tolerance. The data presented here could fuel future investigation into the fitness landscape of fungi with infrequent sexual reproduction and aberrant ploidy levels, not least in the context of biocontrol agents.

Phenotypic variation and genomic variation in insect virulence traits reveal patterns of intraspecific diversity in a locust-specific fungal pathogen

“…Reads were filtered using fastq‐mcf v1.04.636 set with default parameters to trim low‐quality terminal ends (≤Q10), discard short sequences (<50 bp), and quality filter for mean Phred scores (Q < 20). Filtered reads were then mapped to haplotype 1 of the M. acridum reference genome for isolate ARSEF 324 (Nielsen et al, 2021), using BWA v0.7.15 (aln algorithm), under default settings. PCR duplicates were subsequently removed from mapped reads using samtools v1.10 (markdup ‐r; Li et al, 2009), and the average coverage of all reads to the reference assessed using samtools.…”

“…Using the gene annotation for the reference genome ARSEF 324 (Nielsen et al, 2021), genomic regions of interest were used as coordinates in BEDTOOLS v2.30.0 (Quinlan & Hall, 2010). Gene ontology (GO) enrichment analyses were performed using the R package GOstats v.2.62.0 (Falcon & Gentleman, 2007).…”

“…Current knowledge of M. acridum specialization is mostly based on studies of two reference isolates, either CQMa 102 (China) or ARSEF 324 (Australia; Gao et al, 2011; Wang & St. Leger, 2005). The focus on these two isolates has had notable benefits for pest management, considering that both are mass produced for large‐scale locust control (Douthwaite et al, 2001; Peng et al, 2008) and have been whole‐genome sequenced (Gao et al, 2011; Nielsen et al, 2021). Within the genus Metarhizium , intraspecific diversity has mostly been analysed with multiple fungal barcode loci and amplified fragment length polymorphism (AFLP) data, which has shown non‐clonal diversity within isolates of the broad‐host‐range species Metarhizium flavoviride W. Gams & Rozsypal found in Denmark (Keyser et al, 2015), as well as phylogenetically distinct clades of both Metarhizium brunneum Petch (Steinwender et al, 2014) and Metarhizium robertsii J.F.…”

Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned?

“…One of the greatest debates in early-diverging fungal evolution was the ploidy of the dominant life form given the predominantly haploid nature seen in the Dikarya . One outcome of the analysis of genome sequences of zygomycetes species is that diploids are more common than expected [ 9 , 55 , 56 , 57 ].…”