Fig 1.
(a) Genomic region containing the B10 SSR in Epichloë festucae Fl1. The position of primers B10.1 and B10.2 used to amplify the B10 SSR (green) are shown in grey. The SSR is within an exon of a putative bZIP transcription factor (EfM3.072790) (red). (b) Repeat sequence of (CAG)n(CAT)n(CAA)n between Epichloë strains is colored by tri-nucleotide repeats, CAG (yellow), CAT (violet), CAA (pink). Single nucleotide polymorphisms resulting in changes in tri-nucleotide repeats (CCG and CCA) are not colored. (c) Consensus sequences for each Epichloë strain identifying variety in repeat units.
Fig 2.
Consequences of B10 repeat changes on peptide sequence.
Comparison of the B10 repeats of Epichloë glyceriae and Epichloë amarillans and the amino acid each tri-nucleotide encodes. Repeats are colored CAG (yellow), CAT (violet) and CAA (pink). Amino acids encoded are colored for the repeat sequence from which they are derived.
Fig 3.
Amino acid sequence alignment of putative bZIP transcription factors.
CLUSTALW alignment of amino acid sequences showing the B10 SSR region (green box). The SSR is seen as repeated glutamine (Q) and histidine (H) residues. Gene IDs with associated GenBank protein accession numbers or gene models of protein homologues are: Epichloë bromicola EfP3.072790; Epichloë typhina EfP3.072790; Epichloë festucae EfM3.072790; Epichloë brachyelytri EfP3.072790; Epichloë amarillans EfP3.072790; Epichloë glyceriae EfP3.072790; Claviceps paspali EfP3.072790; Claviceps fusiformis EfP3.072790; Periglandula ipomoeae EfP3.072790; Magnaporthe oryzae MGG_08118.6 (XP_003715075); Neurospora crassa NCU03847.7 (XP_955781); Fusarium oxysporum FOXB_15670.1 (EGU73820).
Fig 4.
The B10 SSR from Epichloë uncinata strains.
(a) Sequences of the small B10 repeats contained within each E. uncinata strain. Strains are grouped and aligned for the different ecotypes. (b) Sequences of the large B10 repeats within E. uncinata strains. (c) B10 repeats of the proposed ancestors of E. uncinata, Epichloë typhina and Epichloë bromicola. (d) Schematic representation of the B10 repeat structures from E. uncinata and its proposed ancestors. A single B10 allele is found within E. typhina and E. bromicola, while two alleles are contained within E. uncinata. Repeat structure of E. typhina and E. bromicola are similar to that of E. uncinata. Repeat structure is colored to represent repeated units CAG (yellow), CAT (violet) and CAA (pink).
Table 1.
SSR alleles of Epichloë uncinata and proposed ancestors.
Fig 5.
Maximum-likelihood phylogenetic tree of Epichloë spp. B10 alleles.
The appropriate likelihood ratio test support values are indicated over the branches.
Fig 6.
Amino acid sequence alignment of putative copper sensing transcription factors.
CLUSTALW alignment of amino acid sequences showing the B12 SSR region (green box). The SSR is seen as repeated glutamine (Q) and histidine (H) residues. Gene IDs with associated GenBank protein accession numbers or gene models of protein homologues are: Epichloë typhina EfP3.020790; Epichloë festucae EfM3.020790; Epichloë brachyelytri EfP3.020790; Epichloë amarillans EfP3.020790; Epichloë glyceriae EfP3.020790; Claviceps paspali EfP3.020790; Periglandula ipomoeae EfP3.020790; Fusarium graminearum FGSG_08431.3 (XP_011320343); Neurospora crassa NCU04773.7 (XP_960222); Magnaporthe oryzae MGG_08875.6 (XP_003713900).
Fig 7.
Amino acid sequence alignment of putative G-protein coupled receptors.
CLUSTALW alignment of amino acid sequences showing the B13 SSR region (green box). The SSR is seen as repeated glutamine (Q) and histidine (H) residues. Gene IDs with associated GenBank protein accession numbers or gene models of protein homologues are: Epichloë festucae EfM3.080640; Epichloë typhina EfP3.080640; Epichloë amarillans EfP3.080640; Epichloë brachyelytri EfP3.080640; Epichloë glyceriae EfP3.080640; Periglandula ipomoeae EfP3.080640; Aciculosporium take EfP3.080640; Claviceps fusiformis EfP3.080640; Claviceps paspali EfP3.080640; Fusarium graminearum FGSG_05239.3 (XP_011323750).
Table 2.
B10-like repeats in Sordariomycetes fungi.