The complete chloroplast genome sequence of the monotypic and enigmatic genus Cavea (tribe Gymnarrheneae) and a comparison with other species in Asteraceae

The family Asteraceae includes about 10% of angiosperm species. The tribe Gymnarrheneae is an excellent example of a nonmissing link tribe. It contains two monotypic genera (Cavea and Gymnarrhena) and is positioned phylogenetically to a large clade of Asteroideae + Corymbiodeae + Cichorioideae which contain more than 80% of all the Asteraceae. The genus Cavea (tribe Gymnarrheneae) is a medicinally significant genus and relatively rare in the Qinghai-Tibet Plateau (QTP) and its adjacent areas. Based on the limited evidence, resolving phylogenetic relationship of the genus Cavea has proven difficult for a long time. Despite its important medicinal value, genomic resources of Cavea are still lacking, preventing our understanding of its evolutionary history. In recent years, the plastid genomes are widely used in phylogenetic analysis. To provide more useful genetic data for resolving the systematic disputation of Cavea, here, a complete chloroplast genome of Cavea tanguensis was obtained using Illumina sequencing data for the first time. The whole circular cp genome of C. tanguensis was 150,799 bp in length, contained a large single-copy (LSC) region of 82,514 bp and a small single-copy (SSC) region of 18,471 bp. These two regions were separated by a pair of inverted repeat regions (IRa and IRb), each of them being 24,907 bp in length. A total of 135 functional genes were annotated which consisted of 89 protein-coding genes, 38 trnA genes, and eight rRNA genes. The overall GC content of the chloroplast genome sequence was 37.5%, and the GC contents of the LSC, SSC and IR regions were 35.6%, 30.9% and 37.0%, respectively. We analysed insertions/deletions, and simple-sequence repeats in the chloroplast genomes, and discovered relatively highly variable regions (trnD-GUC/rpoB, trnL-UCC/ndhK, and ycf 1) that will potentially provide plastid markers for further taxonomic, phylogenetic, and population genetic studies in Asteraceae. The phylogenetic analyses based on 22 complete chloroplast genome sequences robustly supported that C. tanguensis formed a sister group with the subfamilies Asteroideae and Carduoideae, consistent with the finding of recent studies. This study provides new insight into the plastid genome evolution and phylogenetic relationships. Moreover, it would be fundamental to formulate potential conservation and management strategies for the enigmatic species in the Himalaya.