Phylogeny of Brachypodium distachyon complex based on chloroplast genomes assembled from whole genome sequence reads. Brachypodium distachyon complex chloroplast genomes

Assembly, annotation, alignment and phylogenomic analyses were conducted with 57 chloroplast genomes of accessions belonging to the three annual species of the Brachypodium distachyon complex (B. distachyon, B. stacei and B. hybridum). Genomic rearrangements were detected between the B. distachyon and B. stacei genomes, with a 1,161 bp insert in LSC and deletion of one copy of rps19 gene in IRb of the B. stacei and B. hybridum genomes, respectively. The three studied B. hybridum plastid genomes were inherited from B. stacei-type maternal parents.