Evolution within the fungal genusVerticilliumis characterized by chromosomal rearrangement and gene loss

Abstract

SUMMARYThe fungal genus Verticillium contains ten species, some of which are notorious plant pathogens causing vascular wilt diseases in host plants, while others are known as saprophytes and opportunistic plant pathogens. Whereas the genome of V. dahliae, the most notorious plan pathogen of the genus, has been well characterized, evolution and speciation of other members of the genus received little attention thus far. Here, we sequenced the genomes of the nine haploid Verticillium spp. to study evolutionary trajectories of their divergence from a last common ancestor. Frequent occurrence of chromosomal rearrangement and gene family loss was identified. In addition to ~11,000 core genes that are shared among all species, only 200-600 species-specific genes occur. Intriguingly, these species-specific genes show different features than core genes.

Extensive chromosomal rearrangements and rapid evolution of novel effector superfamilies contribute to host adaptation and speciation in the basal ascomycetous fungi

“…Understanding the genomic basis that leads to the evolution of plant-pathogen species can greatly advance our knowledge of the emergence of new pathogens and new diseases (Restrepo et al, 2014 Faino et al, 2016;Shi-Kunne et al, 2018).…”

Dynamic virulence‐related regions of the plant pathogenic fungus Verticillium dahliae display enhanced sequence conservation

“…Genomes of Verticillium albo-atrum PD747, Verticillium alfalfae PD683, V. dahliae JR2 and VdLs17, Verticillium isaacii PD618, Verticillium klebahnii PD401, Verticillium nubilum PD621, Verticillium tricorpus PD593 and MUCL9792, Verticillium zaregamsianum PD739 were previously assembled Klosterman et al, 2011;Seidl et al, 2015;Shi-Kunne, Faino, Berg, Thomma, & Seidl, 2018) and sequence reads of Verticillium nonalfalfae isolates TAB2 and Rec are publicly available (Bioproject PRJNA283258; Jelen, Jonge, Peer, Javornik, & Jakse, 2016). Verticillium strains CQ2, 85S, PD670, PD660, PD659 and PD736 were newly sequenced.…”

“…After obtaining final assemblies, we used quast (Gurevich, Saveliev, Vyahhi, & Tesler, 2013) to calculate genome statistics. Gene annotations for V. dahliae strain JR2 and other Verticillium species were obtained from previous studies (Faino et al, 2016;Shi-Kunne et al, 2018), except for V. isaacii strain PD660 that was annotated with the Maker2 pipeline in this study according to Shi-Kunne et al (2018) and Holt and Yandell (2011).…”

“…The phylogenetic trees of the Verticillium genus were previously generated using 5,228 single-copy orthologs that are conserved among all of the genomes (Shi-Kunne et al, 2018). The phylogenetic tree of V. dahliae strains JR2, CQ2, VdLs17 and 85S with V. alfalfae as outgroup was constructed using realphy (default settings; Bertels, Silander, Pachkov, Rainey, & Van Nimwegen, 2014).…”

“…Considering that horizontal transfer is unlikely, the high sequence identity between Verticillium LS sequences indicates that their origin is ancestral and predates speciation, and that lower numbers of DNA substitutions seem to occur in the LS regions. To determine the distribution of conserved LS sequences across the Verticillium genus, we constructed a pan-LS-genome by combining regions with high interspecific sequence identity of the four Verticillium species V. dahliae strain JR2, V. alfalfae strain PD683, V. tricorpus strain PD593, and V. klebahnii strain PD401 that were selected because of their high assembly contiguity and spread over the Verticillium genus (Inderbitzin et al, 2011;Shi-Kunne et al, 2018). After removal of repetitive and duplicated sequences, we obtained a pan-LS-genome of ~2 Mb, of which 60% occurs in clade Flavexudans and 72% in clade Flavnonexudans ( Figure 6).…”