Comparative analysis of chloroplast genomes of two rare Pecteilis species (Orchidaceae)

Abstract

Pecteilis susannae and P. hawkesiana are rare and endangered species with important medicine and ornament value. However, little is known about the genetic information of these two species. In order to understand the basic characteristics of the chloroplast genome of these two Pecteilis species, and to develop molecular markers for species identification, conservation genetic and phylogenetic analysis, the genome skimming approach using next-generation sequencing methods was used to generate chloroplast DNA sequences in this study. The chloroplast genomes were assembled and annotated by bioinformatics analysis. Simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs), and insertions and deletions (InDels) were identified. Furthermore, comparative chloroplast genomic and phylogenetic analyses were conducted with closely related species. The results were as follows: (1) The newly sequenced chloroplast genomes of P. susannae and P. hawkesiana were 154 407 bp and 153 891 bp in size. They comprised a pair of 26 550 bp and 26 523 bp inverted repeats (IR) that separated a large 84 204 bp and 83 756 bp single copy region (LSC) and a small 17 103 bp and 17 089 bp single copy region (SSC), respectively. Both chloroplast genomes contained 111 unique genes, including 77 protein-coding genes, 30 tRNA and 4 rRNA genes. (2) Ninety-four simple sequence repeats (SSRs) were identified in the P. susannae chloroplast genome and 92 in that of P. hawkesiana. (3) Comparisons of two chloroplast genomes revealed that there were nucleotide variations including 706 single-nucleotide polymorphism sites and 152 InDels between the two Pecteilis species, of which several markers (cpInDel 067) could discriminate the two Pecteilis species. (4) The one most divergent gene (accD) and the nine most divergent intergenic regions (rps19-psbA, matK-trnQ-UUG, psbM-psbD, trnT-UGU-ndhJ, accD-psaI, ycf4-cemA, clpP-psbB, ndhF-trnL-UAG, rps15-ycf1) among genomes were detected. (5) The phylogenetic analysis based on the chloroplast genome sequences revealed that P. susannae, P. hawkesiana and Habenaria dentata are closely related. The molecular markers (SSRs, InDels and hotspots) developed from the chloroplast genomes of two Pecteilis species in the present study can be used to identify related species and provide valuable genetic resources in utilizing and conserving natural resources.

Keywords

• pecteilis susannae
• p. hawkesiana
• chloroplast genome
• molecular markers
• phylogeny