Pan-plastome and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes
● Few pan-genomic studies have been conducted in plants, and none of them have focused on the intra-specific diversity and evolution of their plastid genomes.
● We address this issue in Brachypodium distachyon, a model system for monocots, and its close relatives B. stacei and B. hybridum, for which a large genomic data set has been compiled. We analyze inter- and intra-specific plastid comparative genomics and phylogenomic relationships within a family-wide framework.
● Major indel differences were detected between B. distachyon and B. stacei/B. hybridum plastomes. Within B. distachyon, we detected two main lineages, an Extremely Delayed Flowering (EDF+) clade and a Spanish Turkish (S+T+) clade, plus nine chloroplast capture and two ptDNA introgression and micro-recombination events. Early Oligocene (30.9 Mya) and Late Miocene (10.1 Mya) divergence times were inferred for the respective stem and crown nodes of Brachypodium and a very recent Mid-Pleistocene (0.9 Mya) time for the B. distachyon split.
● Flowering time variation is a main factor driving rapid intra-specific divergence in B. distachyon, though it is counterbalanced by repeated introgression between previously isolated lineages. Swapping of plastomes between the three different genomic groups (EDF+, S+, T+) likely resulted from random backcrossing followed by stabilization through selection pressure.