Dynamic virulence-related regions of the fungal plant pathogen Verticillium dahliae display remarkably enhanced sequence conservation

Abstract

Selection pressure impacts genomes unevenly, as different genes adapt with differential speed to establish an organism’s optimal fitness. Plant pathogens co-evolve with their hosts, which implies continuously adaption to evade host immunity. Effectors are secreted proteins that mediate immunity evasion, but may also typically become recognized by host immune receptors. To facilitate effector repertoire alterations, in many pathogens, effector genes reside in dynamic genomic regions that are thought to display accelerated evolution, a phenomenon that is captured by the two-speed genome hypothesis. The genome of the vascular wilt pathogen Verticillium dahliae has been proposed to obey to a similar two-speed regime with dynamic, lineage-specific regions that are characterized by genomic rearrangements, increased transposable element activity and enrichment in in planta-induced effector genes. However, little is known of the origin of, and sequence diversification within, these lineage-specific regions. Based on comparative genomics among Verticillium spp. we now show differential sequence divergence between core and lineage-specific genomic regions of V. dahliae. Surprisingly, we observed that lineage-specific regions display markedly increased sequence conservation. Since single nucleotide diversity is reduced in these regions, host adaptation seems to be merely achieved through presence/absence polymorphisms. Increased sequence conservation of genomic regions important for pathogenicity is an unprecedented finding for filamentous plant pathogens and signifies the diversity of genomic dynamics in host-pathogen co-evolution.

Target the core: durable plant resistance against filamentous plant pathogens through effector recognition

“…Genes specifically expressed during plant infection were over‐represented in those genome regions that were located near telomeres and within other discrete chromosomal segments. This is in striking contrast with the evolution of the four V. dahliae accessory genome regions that are important for pathogenicity and where lower levels of single nucleotide polymorphisms have been observed . Adaptation within V. dahliae accessory genome regions is merely achieved through absence/presence gene polymorphisms.…”

In silicoprediction and characterisation of secondary metabolite clusters in the plant pathogenic fungusVerticillium dahliae

“…2017; Depotter et al . 2018). Among these 22 strains is the gapless genome assembly of strain VdLs17 (Klosterman et al .…”

“…2015) and the nearly complete genome assemblies of strains CQ2 and 85S (Depotter et al . 2018). The remaining genome assemblies are considerably fragmented, with over 500 contigs for each of the assemblies.…”

The Genome of the Fungal PathogenVerticillium dahliaeReveals Extensive Bacterial to Fungal Gene Transfer

“…In order to assess whether the other HGT candidates are LS and associated with repeats as well, we plotted genomic repeat densities and the genomic location of all HGT candidates. Although only Ave1 is located at a genuine LS region ( Depotter et al. 2018 ), most of the HGT candidates (34 out of 44) reside in proximity (within 1 kb) to a repetitive sequence ( fig.…”