Comparative Complete Chloroplast Genome Analyses and Contribution to the Understanding of Chloroplast Phylogeny and Adaptive Evolution in Subgenus Anguinum

The subgenus Anguinum (G. Don. ex W.D.J. Koch) N. Friesen disjunctly distributes in the high mountains from south-western Europe to eastern Asia and in northeastern North America. Due to interspecies hybridization, introgression and incomplete lineage sorting, the detection of interspecies differences within Anguinum is notoriously challenging. Here we report the complete chloroplast (cp) genome sequences of A. nanodes Airy-Shaw, A. ovalifolium Hand.-Mazz., A. ovalifolium var. leuconeurum J.M. Xu and A. victorialis L. from Anguinum and A. cyathophorum Bur. & Franch from subgenus Cyathophora (R.M. Fritsch) R.M. Fritsch as outgroup, four of which were first reported. We compared them with cp genomes of A. cepa L., A. obliquum L., A. prattii C.H. Wright. The Anguinum cp genomes ranged from 153,674 to 155,055 bp in length. Each cp genome contained 131 unigenes, consisting of 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The eight Allium L. cp genomes exhibited significant differences at the SC/IR junction regions. Fourteen cpDNA markers with most variable sites were identified as mutational hotspots, and simple sequence repeats (SSRs) and long repeats were also identified. Three single-copy genes (accD, rps14, rpl33) may be under a great selection pressure indicated by positive selection analysis. The plastome-based phylogeny indicated a monophyletic position of the subgenus Anguinum, which was consistent with previous phylogenetic studies. Overall, the availability of these complete cp genomes provides valuable information for further studies of population genetics and investigation of the evolution in the genus Allium.