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Recent advances in molecular phylogenetics provide us with information of  Allium  L. taxonomy and evolution, such as the subgenus  Cyathophora , which is monophyletic and contains five species. However, previous studies detected distinct incongruence between the nrDNA and cpDNA phylogenies, and the interspecies relationships of this subgenus need to be furtherly resolved. In our study, we newly assembled the whole chloroplast genome of four species in subgenus  Cyathophora  and two allied  Allium  species. The complete cp genomes were found to possess a quadripartite structure, and the genome size ranged from 152,913 to 154,174 bp. Among these cp genomes, there were subtle differences in the gene order, gene content, and GC content. Seven hotspot regions ( infA ,  rps16 ,  rps15 ,  ndhF ,  trnG-UCC ,  trnC-GCA , and  trnK-UUU ) with nucleotide diversity greater than 0.02 were discovered. The selection analysis showed that some genes have elevated Ka/Ks ratios. Phylogenetic analysis depended on the complete chloroplast genome (CCG), and the intergenic spacer regions (IGS) and coding DNA sequences (CDS) showed same topologies with high support, which revealed that subgenus  Cyathophora  was a monophyletic group, containing four species, and  A. cyathophorum  var.  farreri  was sister to  A. spicatum  with 100% bootstrap value. Our study revealed selective pressure may exert effect on several genes of the six  Allium  species, which may be useful for them to adapt to their specific living environment. We have well resolved the phylogenetic relationship of species in the subgenus  Cyathophora , which will contribute to future evolutionary studies or phylogeographic analysis of  Allium .

biomed research international

Comparative Analysis of the Complete Chloroplast Genomes in <i>Allium</i> Subgenus <i>Cyathophora</i> (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution

Comparative Analysis of the Complete Chloroplast Genomes in Allium Subgenus Cyathophora (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution