Chromosomal rearrangements with stable repertoires of genes and transposable elements in an invasive forest-pathogenic fungus

Abstract

Dutech (2022) Chromosomal rearrangements with stable repertoires of genes and transposable elements in aninvasive forest-pathogenic fungus, Peer Community Journal, 2: e28.

Applying molecular and genetic methods to trees and their fungal communities

“…However, the overall TE content (ca. 10% of the genomes; mostly Gypsy family TEs) and RIP frequency in a North American C. parasitica reference strain and a native Japanese strain are comparable (Demené et al 2022). Moreover, there is only poor association in this species between TEs and genes with possible functions in pathogenesis (Demené et al 2022;Stauber et al 2021).…”

“…10% of the genomes; mostly Gypsy family TEs) and RIP frequency in a North American C. parasitica reference strain and a native Japanese strain are comparable (Demené et al 2022). Moreover, there is only poor association in this species between TEs and genes with possible functions in pathogenesis (Demené et al 2022;Stauber et al 2021). However, kingdom-wide inventories observed higher TEinsertions in genes of plant pathogens and of animal-related fungi than in species of other fungal lifestyles, implying that TE-interlinked rapidly evolving genomic compartments may shape key adaptations in pathogen evolution, e.g.…”

“…With regards to trees, sequenced genomes were mostly of basidiomycetous wood decay fungi (e.g., Fernandez-Fueyo et al 2012;Floudas et al 2012;Hori et al 2014;Levasseur et al 2014;Martinez et al 2004Martinez et al , 2009, including some root and stem rotting pathogens (Akulova et al 2020;Kües et al 2015;Ohm et al 2010;Olson et al 2012). Genomes of some other types of ascoand basidiomycetous pathogens, such as some on leaves (Dhillon et al 2015;Duplessis et al 2011a;Zhu et al 2012) and of wilt-, blight-and cancer-pathogens in bark and xylem are available, including those of several insect-associated fungal species (Alamouti et al 2011;Comeau et al 2015;Crouch et al 2020;Demené et al 2022;Dhillon et al 2015;Ibarra Caballero et al 2019;Sbaraini et al 2017;Schuelke et al 2017;Stauber et al 2020;Stenlid et al 2017;Yin et al 2015). There is also a growing collection of genomes of symbiotic ECM species (e.g., Kohler et al 2015;Lofgren et al 2021;Looney et al 2022;Martin et al 2008Martin et al , 2010Martino et al 2018;Miyauchi et al 2020b;Peter et al 2016;Wagner et al 2015), some ericoid mycorrhizal ascomycetous fungi (Kohler et al 2015;Martino et al 2018;Perotto et al 2018), an arbuscular mycorrhizal fungus from the conifer Cryptomeria japonica …”

Million years old recombination suppression and balancing selection in a region partially linked to the mating-type locus in the invasive chestnut blight fungal pathogenCryphonectria parasitica

“…The LD between the two high-LD blocks was lower (r 2 = 0.59) than within blocks but was still higher than elsewhere along the genome (orange rectangle at the right border of the red triangle; We found no other regions of the genomes with r 2 >0.9 between SNPs across such a large genomic distance in any population. On scaffold_6 in the CL1 cluster, two smaller SNP blocks had a r 2 >0.9 between each other despite being distant (Fig S2A ; between SNPs blocks at 3-20 kb and 2.151-2.278 kb), which is likely due to the major intra-scaffold translocation described in this region between the EP155 and ESM15 strains (33). The maximum size of the blocks with r²>0.9 on other scaffolds ranged from 135 to 540 kb in the CL1 cluster, as previously described (31).…”

“…Assemblies were manually curated as previously described (33) and scaffolds were cut when an evidence of a chimeric connection was detected (i.e. mis-paired short reads).…”