Coevolution of Pooideae grasses and their Epichloë endophytes within a hologenome framework

Abstract

Pooideae represents a diverse subfamily of grasses with over 4000 species classified into 12 tribes and 216 genera. Over 67 million years of evolution shaped their dynamic genomes, resulting in their enormous phenotypic and ecological diversity. During this time, many members of the Pooideae have further co-evolved with fungal endophytes of Epichloë (family Clavicipitaceae). Epichloë display long-term associations with their temperate grass hosts and are naturally restricted within the Pooideae to a host genus or closely related grass genera within a tribe. Epichloë grow systemically within the above ground organs of their grass hosts and form a continuum of interactions from vertically transmitted mutualists (asexual species) to horizontally transmitted antagonists (sexual species). While sexual Epichloë species are haploid, most asexual species are alloploids, interspecific hybrids having ancestries involving two or more distinct Epichloë lineages. Comparative genomic and phylogenomic analyses of Pooideae and Epichloë species make these symbioses an excellent model for tracing coevolution through diversification within a hologenomic framework. We hypothesized that the predominant vertical transmission of these endophytes would favour a Pooideae-Epichloë coevolutionary scenario, although horizontal transmission, both sexual and asexual, of endophytes can alter this. We reconstructed the phylogeny of Pooideae host species using single-copy nuclear genes and that of Epichloë species using nuclear barcoding markers and available sequenced genomes. We also filtered and assembled Epichloë genes from host genome skimming data. Phylogenetic reconstructions were performed using maximum likelihood and coalescence-based approaches. Potential coevolutionary trends of Pooideae grasses and their Epichloë fungal endophytes were analysed statistically, based on host-parasite associations, and through concordance scores of host-endophyte topological conflicts. We performed coevolutionary analyses for the main tribal and subtribal representatives of Pooideae and described Epichloë species, and then focused on the more recently evolved Loliinae grasses (e.g., Festuca and Lolium) and their Epichloë symbionts. We found diffuse and lineage-specific coevolutionary trends for some groups of Pooideae and their endophytes, also explored through co-genomic approaches. The more detailed analysis of ~200 Loliinae species confirmed that at least 15% of them associate with Epichloë endophytes. Furthermore, we detected 20 lineage-specific relationships for temperate and tropical mountain fescues and their endophytes. Our analyses revealed significant coevolution for Loliinae and their symbionts at individual scale for two lineages, the fine-leaved F. sect. ovina clade (sheep fescues) with E. festucae strains, and the broad-leaved Schedonorus-Lolium clade (meadow and tall fescues, ryegrasses) with E. typhina, E. hybrida, E. occultans, E. siegelii, and E. uncinata strains. Interestingly, these two groups of Loliinae showed high intraclade hybridization rates, but low interclade rates. Our results highlight the impact of the narrow vs. broad hybridogenous nature of the host plant in the strong vs. weak lineage-specific coevolutionary trends with their respective Epichloë endophytes.