Telomere-to-Telomere Genome Sequences across a Single Genus Reveal Highly Variable Chromosome Rearrangement Rates but Absolute Stasis of Chromosome Number

Abstract

Genome rearrangements in filamentous fungi are prevalent but little is known about the modalities of their evolution, in part because few complete genomes are available within a single genus. To address this, we have generated and compared 15 complete telomere-to-telomere genomes across the phylogeny of a single genus of filamentous fungi, Epichloë. We find that the striking distinction between gene-rich and repeat-rich regions previously reported for isolated species is ubiquitous across the Epichloë genus. We built a species phylogeny from single-copy gene orthologs to provide a comparative framing to study chromosome composition and structural change through evolutionary time. All Epichloë genomes have exactly seven nuclear chromosomes, but despite this conserved ploidy, analyses reveal low synteny and substantial rearrangement of gene content across the genus. These rearrangements are highly lineage-dependent, with most occurring over short evolutionary distances, with long periods of structural stasis. Quantification of chromosomal rearrangements shows they are uncorrelated with numbers of substitutions and evolutionary distances, suggesting that different modes of evolution are acting to create nucleotide and chromosome-scale changes.

Keywords: Epichloë; chromosome evolution; genome structure; structural variation.

Figure 1

(A) Genome sizes for 15 Epichloë strains. The color of points indicates the repeat element content (%) of each genome. (B) Genome-wide rearrangements between four Epichloë species, inferred from gene-based syntenic analysis. Chromosomes are numbered relative to their size within each species, as the extensive rearrangements prevent homology-based numbering. (C) Evolutionary restructuring of a representative chromosome across the genus Epichloë. Sequences homologous in gene content to chromosome 2 in E. clarkii are highlighted in orange. Stars indicate positions in the phylogeny where major inter-chromosomal rearrangements have occurred. The chromosome numbers for each species are indicated.

Figure 2

(A) Phylogenetic relationships between the 15 Epichloë species/strains inferred using maximum likelihood from 1,489 single copy gene orthologs. Blue dots indicate the positions of extant genomes; yellow dots indicate inferred ancestral genomes; mutations inferred by Progressive Cactus were counted on the red branches. All branches have support values of 1. (B) Heatmap highlighting the relative numbers of eight mutation classes accumulated on the terminal branches of the phylogeny between the closest ancestral genome and extant taxa. All rates are scaled from zero to one, with zero corresponding to the lowest number of mutations in the dataset and one to the highest. (C) Violin plots showing the absolute numbers of the eight mutation classes accumulated on terminal branches, with a log-scaled y axis. (D) Proportion of gene and repeat regions impacted by structural variation in each Epichloë strain, relative to the ancestral genomes inferred using Progressive Cactus. For each genome, the proportion of affected nucleotides was calculated by looking at the coverage of sequences duplicated, inverted, transposed and inserted relative to the closest ancestral genome.