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Background  Tall fescue and meadow fescue are important as temperate pasture grasses, forming mutualistic associations with asexual  Neotyphodium  endophytes. The most frequently identified endophyte of Continental allohexaploid tall fescue is  Neotyphodium coenophialum , while representatives of two other taxa ( Fa TG-2 and  Fa TG-3) have been described as colonising decaploid and Mediterranean hexaploid tall fescue, respectively. In addition, a recent study identified two other putatively novel endophyte taxa from Mediterranean hexaploid and decaploid tall fescue accessions, which were designated as uncharacterised  Neotyphodium  species (UNS) and  Fa TG-3-like respectively. In contrast, diploid meadow fescue mainly forms associations with the endophyte taxon  Neotyphodium uncinatum , although a second endophyte taxon, termed  N. siegelii , has also been described.    Results  Multiple copies of the translation elongation factor 1-a ( tefA ) and β-tubulin ( tub2 ) ‘house-keeping’ genes, as well as the endophyte-specific  perA  gene, were identified for each fescue-derived endophyte taxon from whole genome sequence data. The assembled gene sequences were used to reconstruct evolutionary relationships between the heteroploid fescue-derived endophytes and putative ancestral sub-genomes derived from known sexual  Epichloë  species. In addition to the nuclear genome-derived genes, the complete mitochondrial genome (mt genome) sequence was obtained for each of the sequenced endophyte, and phylogenetic relationships between the mt genome protein coding gene complements were also reconstructed.    Conclusions  Complex and highly reticulated evolutionary relationships between  Epichloë-Neotyphodium  endophytes have been predicted on the basis of multiple nuclear genes and entire mitochondrial protein-coding gene complements, derived from independent assembly of whole genome sequence reads. The results are consistent with previous studies while also providing novel phylogenetic insights, particularly through inclusion of data from the endophyte lineage-specific gene, as well as affording evidence for the origin of cytoplasmic genomes. In particular, the results obtained from the present study imply the possible occurrence of at least two distinct  E. typhina  progenitors for heteropoid taxa, as well the ancestral contribution of an endophyte species distinct from (although related to) contemporary  E. baconii  to the extant hybrid species .  Furthermore, the present study confirmed the distinct taxonomic status of the newly identified fescue endophyte taxa,  Fa TG-3-like and UNS, which are consequently proposed to be renamed  Fa TG4 and  Fa TG5, respectively.

Phylogenomics of fescue grass-derived fungal endophytes based on selected nuclear genes and the mitochondrial gene complement