Greater genetic and regulatory plasticity of retained duplicates in Epichloë endophytic fungi

Abstract

Gene duplicates can act as a source of genetic material from which new functions arise. Most duplicated genes revert to single copy genes and only a small proportion are retained. However, it remains unclear why some duplicate genes persist in the genome for an extended time. We investigate this question by analysing retained gene duplicates in the fungal genus Epichloë, ascomycete fungi that form close endophytic symbioses with their host grasses. Retained duplicates within this genus have two independent origins, but both long pre‐date the origin and diversification of the genus Epichloë. We find that loss of retained duplicates within the genus is frequent and often associated with speciation. Retained duplicates have faster evolutionary rates (Ka) and show relaxed selection (Ka/Ks) compared to single copy genes. Both features are time‐dependent. Through comparison of conspecific strains, we find greater evolutionary rates in coding regions and sequence divergence in regulatory regions of retained duplicates than single copy genes, with this pattern more pronounced for strains adapted to different grass host species. Consistent with this sequence divergence in regulatory regions, transcriptome analyses show greater expression variation of retained duplicates than single copy genes. This suggest that cis‐regulatory changes make important contributions to the expression patterns of retained duplicates. Coupled with supporting observations from the model yeast Saccharomyces cerevisiae, these data suggest that genetic robustness and regulatory plasticity are common drivers behind the retention of duplicated genes in fungi.

Plant genome evolution in the genusEucalyptusdriven by structural rearrangements that promote sequence divergence

“…These hypotheses rely upon the genic properties of duplications, i.e. if duplications don't gain novel function or retain ancestral function, purifying selection will likely result in their removal (Wu and Cox, 2019). While duplications were the least genic of all rearrangement types, a significant number (45.71%) were found to contain genes, likely contributing to their preservation.…”

“…The observed pattern of duplication loss as time since divergence increased was unsurprising, as duplications, while highly important to adaptation and evolution, are rarely conserved (Inoue et al ., 2015; Naseeb et al ., 2017). Why some duplications are preserved while the majority are lost is speculative; however, theory centres on neofunctionalisation, subfunctionalisation, and novel function evolution (Freeling, Scanlon and Fowler, 2015; Braasch et al ., 2016; Lien et al ., 2016; Wu and Cox, 2019). These hypotheses rely upon the genic properties of duplications, i.e.…”

Interspecific comparison of gene expression profiles using machine learning

“…A common approach for estimation of expression similarity in groups of duplicated genes is the calculation of Euclidean distance [19,30,[42][43][44]. Thus we compared our results described above with that of a classifier based on Euclidean distance.…”

Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence

“…Translocations, while less studied than other rearrangements (Robberecht et al, 2013), may have similar genomic effects as inversions (Ortiz-Barrientos et al, 2016). Duplications, highly common and also likely to be selected against (Flagel & Wendel, 2009; Wu & Cox, 2019), could be preserved due to their ability to acquire new function (neofunctionalisation) or by retaining a subset of original function (subfunctionalisation) (Braasch et al, 2016; Freeling et al, 2015; Lien et al, 2016; Wu & Cox, 2019). Large (> 50 bp) insertions and deletions, which are often genotyped as presence/absence variants (PAVs), copy number variations (CNV), or gene duplications, are also very common within genomes (Conrad & Hurles, 2007; Pokrovac & Pezer, 2022).…”