Combined analysis of population genetic structures in a living-fossil grass Brachyelytrum erectum, and its endophyte Epichloë brachyelytri.

Abstract

Brachyelytrum is the earliest diverging genus known relative to other genera of grass subfamily Poöideae. Brachyelytrum erectum inhabits forest understory in temperate eastern North America and possesses the endophyte Epichloë brachyelytri. A genome sequence of E. brachyelytri included genes for biosynthesis of peramine, the loline alkaloid precursor exo-1-acetamidopyrrolizidine (AcAP), and the ergot alkaloid precursor chanoclavine. In a survey of 24 B. erectum populations in Kentucky and southern Indiana, endophytes were genotyped by PCR for alkaloid genes and mating types. All had ppzA1 for peramine whereas genes for AcAP and chanoclavine exhibited presence/absence polymorphism. Approximate alkaloid levels in leaves were, per g dw, 4–15 µg peramine, 2000–5000 µg AcAP and 175–300 µg chanoclavine when the corresponding gene clusters were present. The sexual state of E. brachyelytri was observed on few plants in only two populations, and the overall ratio of mating types A and B was 1.0:4.3, indicating very limited sexual reproduction for this endophyte. We obtained RNA-seq data from 4–12 symbiotic (E+) plants and 2–7 asymbiotic (E–) plants each in seven populations separated by distances of 10–321 km (average = 171 km), then applied our recently described rna-clique method to infer pairwise genetic distance matrices comparing plants in different populations, plants with different endophyte genotypes, and endophytes with different genotypes. Results indicated geographical structure of B. erectum that distinguished even the closest populations. Within populations we observed partial structure of plant subpopulations based on symbiotic status (E+ vs. E–) or endophyte genotype. The relationship of endophyte genetic structure to endophyte genotypes was consistent with infrequent sexual recombination. Overall, the results indicate local adaptation of B. erectum populations for which its functionally and genetically diverse endophyte species plays a role.