Decoding horizontal gene transfer mechanisms in Epichloë–grass symbiosis

Abstract

Epichloë endophytes establish mutualistic symbioses with host grasses, significantly enhancing host resistance to diverse biotic and abiotic stresses. Understanding molecular mechanisms of symbiosis and stress response regulatory in Epichloë-host symbionts could provide us effective strategies to overcome the challenges posed by global climate change. Horizontal gene transfer (HGT) is a critical evolutionary mechanism for both fungi and plants to improve their survival, propagation and environmental stress adaptation. A glucanase gene in perennial ryegrass and a disease resistance gene (Fhb7) in wheat are speculated to have originally arrived from Epichloë endophytes based on the nucleotide sequence identity, suggesting that HGT may be a widespread events presented in Epichloë–plant symbionts. However, there is no conclusive evidence for the occurrence of HGT in Epichloë–plant symbionts, and the mechanism by which it occurs as well as its functional implications in symbionts remain unclear. Achnatherum inebrians belongs to the grass tribe Triticeae and is genetically close to the model grass Brachypodium distachyon, the symbiont of A. inebrians with which Epichloë exhibits remarkable stress tolerance. To obtain more definite evidence and reveal the mechanisms of HGT events in Epichloë-plant symbionts, we performed chromosome-level de novo genome assemblies of A. inebrians and E. gansuensis isolated from the symbiont through a combined strategy integrating Illumina HiSeq sequencing, PacBio sequencing and Hi-C technology. The analysis results showed that the genome of A. inebrians is relatively small (~1.47 Gb) with low heterozygosity, which is conductive to the analysis of HGT events. Whole-genome resequencing of the A. inebrians-E. gansuensis symbiont generated over 50 Gb of sequencing data. Through the comparative genome analysis, three possible E. gansuensis-derived HGT reads were detected in the symbiotic A. inebrians genome, with the evidence of each read clearly flanked by definitive A. inebrians genome sequences. This finding strongly support the occurrence of HGT events during the symbiotic interaction of E. gansuensis with A. inebrians. However, only three HGT-derived reads were identified in a quite massive sequencing data, suggesting that these HGT events may not heritable. Intriguingly, functional annotation based on homology comparison revealed that the genes in HGT reads were enriched in biological processes related to DNA recombination and repair, transposon integration, and transcriptional regulation. Our results provide valuable genomic resources and a robust foundation for further dissection of symbiotic regulatory mechanisms mediated by HGT events between Epichloë endophytes and host grasses.