Evolutionary Comparison of the Chloroplast Genome in the Woody Sonchus Alliance (Asteraceae) on the Canary Islands

The woody Sonchus alliance consists primarily of woody species of the genus Sonchus (subgenus Dendrosonchus; family Asteraceae). Most members of the alliance are endemic to the oceanic archipelagos in the phytogeographic region of Macaronesia. They display extensive morphological, ecological, and anatomical diversity, likely caused by the diverse habitats on islands and rapid adaptive radiation. As a premier example of adaptive radiation and insular woodiness of species endemic to oceanic islands, the alliance has been the subject of intensive evolutionary studies. While phylogenetic studies suggested that it is monophyletic and its major lineages radiated rapidly early in the evolutionary history of this group, genetic mechanisms of speciation and genomic evolution within the alliance remain to be investigated. We first attempted to address chloroplast (cp) genome evolution by conducting comparative genomic analysis of three representative endemic species (Sonchus acaulis, Sonchus canariensis, and Sonchus webbii) from the Canary Islands. Despite extensive morphological, anatomical, and ecological differences among them, their cp genomes were highly conserved in gene order and content, ranging from 152,071 to 152,194 bp in total length. The number of repeat variations and six highly variable regions were identified as valuable molecular markers. Phylogenetic analysis of 32 species in the family Asteraceae revealed the phylogenetic position of the woody Sonchus alliance within the tribe Cichorieae and the sister relationship between the weedy Sonchus oleraceus and the alliance