Population genomics unravels the genetic diversity and evolutionary history of Hedyotis taishanensis: An endemic Chinese plant with a limited population size

Hedyotis taishanensis , an erect perennial herb in the Rubiaceae family, is endemic to Gudoushan Nature Reserve (China). It has extremely narrow distribution necessitates investigations into genetic diversity and population evolutionary history to assess extinction risks and formulate evidence-based conservation strategies. Here, we reported the first de novo assembly of the H. taishanensis chloroplast genome and employed double-digest RAD sequencing (ddRADseq) to investigate population genetic structure and genomic diversity across its natural distribution. The chloroplast genome of Hedyotis taishanensis exhibits a quadripartite structure, spanning 153,986 bp (HT2) to 154,128 bp (HT1). Whole-genome alignments revealed substantial sequence divergence in three protein-coding loci ( accD , rpoC2 , ycf1 ) and six intergenic spacer regions. Analysis of nucleotide polymorphism reveals numerous hypervariable regions that can serve as potential molecular markers for population genetic studies. Population genetic structure analyses indicates that the four extant populations of H. taishanensis are derived from a common ancestor without lineage divergence. H. taishanensis exhibits lower genetic diversity than other species within the genus and shows evidence of inbreeding. The effective population size of this species has been continuously declining since 0.07 million years ago. To prevent population decline and further inbreeding depression in H. taishanensis , certain conservation measures should be implemented immediately.