Insight into sequence variation and phylogenetic relationships of Dactylis subspecies inferred from complete chloroplast genome

Orchardgrass (Dactylis glomerata L) is a species in the Gramineae family that is highly important economically and valued for its role in ecology. However, the phylogeny and taxonomy of D. glomerata are still controversial based on current morphological and molecular evidence. The study of chloroplast (cp) genomes has developed into a powerful tool to develop molecular markers for related species and reveal the relationships between plant evolution and phylogenetics. In this study, we sequenced and assembled 14 cp genomes of D. glomerata subspecies. In addition, comparative genomic analysis and phylogenetic inference of all 14 cp genomes were conducted. The length of 14 cp genomes ranged from 134375 bp (D. glomerata subsp. lobata) to 134993 bp (D. glomerata subsp. lusitanica) and exhibited synteny of gene organization and order. A total of 129 unique genes were identified in the cp genome of D. glomerata, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The cp sequences were highly conserved, and key sequence variations were detected at the junctions of inverted repeats (IRs) / small single-copy (SSC) regions. Nine highly variable regions were identified among the subspecies, including rps19-psbA, psbM-petN, trnG-UCC-trnT-GGU, psaA-ycf3, rbcL-psal, psbE-petL, rps12-trnV-GAC, trnV-GAC-rps12, rpl2-rpl23, based on a sequence divergence analysis. We subsequently observed that the expansion of IRs may cause an increase in the size of genome. A total of 285 RNA editing sites were detected that were relevant to 52 genes in the subspecies of D. glomerata, where rpoB exhibited the most abundant RNA editing sites. Estimations of the divergence time showed that D. glomerata and wheat (Triticum) diverged during the early Oligocene. The cp genome sequences of these subspecies of D. glomerata will provide useful insights for further studies on phylogeny, the identification of subspecies and the development of hypotheses of the evolutionary history of the genus Dactylis and even the Gramineae family.