Intraspecific genetic variation within chloroplast genome of a rare and endangered species Paphiopedilum parishii (Orchidaceae)

Paphiopedilum parishii is a rare and endangered species with few localities and fragmented populations found in China, Myanmar, Thailand and Laos. Environmental changes and over-harvesting have led to a decrease in its wild populations. It is important to protect endangered species genetic diversity since it provides the species with the ability to adapt and survive. However, little is known about the genetic information of this species. This study aims to detect intraspecific variation and develop polymorphic genetic markers of P. parishii. The complete chloroplast genome of four individuals of wild P. parishii was obtained by sequencing, assembling and annotating, then compared with the existing genomic data of two individuals available from GenBank to detect the intraspecific variation. Further, simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs), and insertions and deletions (InDels) were identified. The results were as follows: (1) The four new sequencing chloroplast genomes were quadr