Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Melanoseris cyanea group

Melanoseris, a diverse genus in the Lactucinae subtribe, has 21 species in China, with 13 being endemic. The high diversity of this genus presents taxonomic challenges, particularly in the M. cyanea group, where overlapping distributions and transitional morphological traits complicate classification. This study aims to analyze the chloroplast genomes of Melanoseris, with a focus on the M. cyanea group, to explore structural differences and phylogenetic relationships among these closely related species. We analyzed the chloroplast genomes of 16 Melanoseris samples, including 12 new genomes from the M. cyanea group. The genome sizes ranged from 152,255 to 152,558 bp and exhibited a typical quadripartite structure, with an average GC content of 37.7%. Each genome encodes 132 genes, including 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. Repeat analysis identified 89 to 105 dispersed repeats, 24 to 28 tandem repeats, and 35 to 39 SSRs, with mononucleotide A/T repeats being the most common. Sequence alignment revealed that variable regions were mainly concentrated in the single-copy regions. Nucleotide diversity ranged from 0 to 0.00485, highlighting 10 mutation hotspot regions. Phylogenetic analysis showed a limited differentiation among species within the M. cyanea group. This research enhances our understanding of the genetic diversity of Melanoseris, laying the foundation for future taxonomic and phylogenetic studies.