Complete chloroplast genome structural characterization of two Phalaenopsis (Orchidaceae) species and comparative analysis with their alliance.

BACKGROUND: The taxonomy and infrageneric delimitation of Phalaenopsis Blume has been significantly disputed due to some overlapping morphological features between species related, which needed further evidence for clarification. The structural characterization of complete chloroplast genomes of P. storbatiana and P. wilsonii were analyzed and compared with those of related taxa to provide a better understanding of their genomic information on taxonomy and phylogeny. RESULTS: It was shown that chloroplast genomes of Phalaenopsis storbatiana and P. wilsonii had a typical quadripartite structure with conserved genome arrangements and moderate divergence. The chloroplast genomes of P. storbatiana and P. wilsonii were 145,885 bp and 145,445 bp in length, respectively, and shared a similar GC content of 36.8%. Gene annotations of two species revealed 109 single-copy genes consistently. In addition, 20 genes duplicated in the inverted regions, 16 genes each possessed one or more introns, and five ndh (NA (D)H dehydrogenase) genes were observed in both. Comparative analysis of the total cp genomes of P. storbatiana and P. wilsonii with those of other six related Phalaenopsis species confirmed the stable sequence identity for coding and non-coding regions and higher sequence variation in SC regions than IR regions. Most of their protein-coding genes had a high degree of codon preference. Moreover, 45 genes were discovered with significantly positive selection. However, different amplifications in IR regions were observed in these eight species. Phylogenetic analysis based on CDS from 60 species representing main clades in Orchidaceae indicated that Phalaenopsis species including P. stobartiana and P. wilsonii formed a monophyletic clade with high bootstrap nested in tribe Vandeae of Epidendroideae, which was consistent with those from previous studies. CONCLUSIONS: The results could provide insight into understanding the plastome evolution and phylogenetic relationships of Phalaenopsis.

The complete chloroplast genome sequence of Phalaenopsis wilsonii Rolfe, a vulnerable wild moth orchid species (Orchidaceae).

Phalaenopsis wilsonii Rolfe is a vulnerable wild moth orchid species with important horticultural value. The complete chloroplast genome sequence of P. wilsonii was generated by de novo assembly using whole genome next-generation sequencing to provide genomic data for further conservation genetics, phylogeny and molecular breeding in Phalaenopsis. The complete plastome of P. wilsonii is 145,096 bp in length, containing two inverted repeats (IR) regions (24,787 bp), a large single-copy (LSC) region (84,688 bp), and a small single-copy (SSC) region (10,834 bp). The chloroplast genome encoded 119 unique genes, including 73 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC content of the whole genome is 36.9%. Phylogenetic analysis indicated P. wilsonii was closely related to P. lowii.