Nielsen, K. N. | bioRxiv Science

bioRxiv2021

A NEW CASE OF DIPLOIDY WITHIN A HAPLOID GENUS OF ENTOMOPATHOGENIC FUNGI

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 Metarhizium 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 under the name Green Guard, 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 consisting of 20.8% repetitive elements, which is the highest proportion described of any Metarhizium species. The genome assembly and the inferred diploid state, can shed light on past research on this strain and could fuel future investigation into the fitness landscape of aberrant ploidy levels, not least in the contest of biocontrol agents.

genomics↗

bioRxiv2021

The pangenome of the fungal pathogen Neonectria neomacrospora

The fungal plant pathogen Neonectria neomacrospora (C. Booth & Samuels) Mantiri & Samuels (Ascomycota, Hypocreales) is a bark parasite causing twig blight, canker, and in severe cases, dieback in fir (Abies spp.). Although often described as a mild pathogen, foresty and phytosanitary agencies have expressed their concern for potential economic impact. Two epidemics caused by this species are known: one from eastern Canada and one current within Northern Europe. We present key genome features of N. neomacrospora, to facilitate the research into the biology of this pathogen. We present the first genome assembly of N. neomacrospora as well as the first pangenome within this genus. The reference genome for N. neomacrospora is a long-read sequenced Danish isolate, while the pangenome is pieced together using additional 60 short-read sequenced strains covering the known geographical distribution of the species, including Europe, North America, and China. The gapless reference genome consist of twelve chromosomes sequenced telomere to telomere to a total length of 37.1 Mb. The mitochondrial genome was assembled and circularised with a length of 22 Kb. The gapless nuclear genome contains a total of 11,291 annotated genes, where 642 only have a hypothetical function, and a 4.3 % repeat content. Two minor chromosomes are enriched in transposable elements, AT content, and effector candidates. Chromosome 12 segregates within the population, indicating an accessory nature. The pangenome compile 15,101 genes, 34% more genes than present in the single isolate reference genome of N. neomacrospora. These genes organise into 13,069 homologous clusters, of which 8,316 clusters are present in all analysed strains, 985 are private to single strains. The British Columbian population branched out before the other populations and are characterized by comparatively larger genomes. The increased genome size can be explained by an expansion of repetitive elements. The comparative analysis finds a higher number of genes with a signal peptide within N. neomacrospora and species within the genus compared to the closely related genera. A species-specific pattern is observed in the carbohydrate-active enzyme repertoire, with a reduced number of polysaccharide lyases, compared to other species within the genus. The CAZymes battery responsible for plant cell wall degradation is similar to that observed in necrotrophic and hemibiotrophic plant pathogenic fungi. The genome size of N. neomacrospora is close to the median size for Ascomycota but is the smallest genome within the Neonectria genus. Comparative analysis revealed significant intraspecies genome size differences between populations explained by a difference in repeat content. Isolates with the smallest genomes formed a monophyletic group consisting of all strains from Europe and Quebec. Based on the field observations, we assume that N. neomacrospora is a hemibiotroph. Our analysis revealed a secretome consistent with a hemibiotrophic lifestyle.

genomics↗

bioRxiv2020

Population genomics of the emerging forest pathogen Neonectria neomacrospora

The fungal pathogen Neonectria neomacrospora is of increasing concern in Europe where, within the last decade, it has caused substantial damage to forest stands and ornamental trees of the genus Abies (Mill.). Using whole-genome sequencing of a comprehensive collection of isolates, we show the extent of three major clades within N. neomacrospora, which most likely diverged around the end of the last Ice Age. We find it likely that the current European epidemic of N. neomacrospora was founded from a population belonging to the east North American clade. All European isolates (1957-2019) had a common evolutionary history, but substantial and asymmetrical gene flow from the larger American source population could be detected. The European population shows multiple signs of having gone through a bottleneck and subsequent population expansion.

genomics↗