Comparative analyses and phylogenetic relationships of thirteen Pholidota species (Orchidaceae) inferred from complete chloroplast genomes

Abstract

Background The orchid genus Pholidota Lindl. ex Hook. is economically important as some species has long been used in traditional medicine. However, the systematic status of the genus and intergeneric relationships inferred from previous molecular studies are unclear due to insufficient sampling and lack of informative sites. So far, only limited genomic information has been available. The taxonomy of Pholidota remains unresolved and somewhat controversial. In this study, the complete chloroplast (cp.) genomes of thirteen Pholidota species were sequenced and analyzed to gain insight into the phylogeny of Pholidota and mutation patterns in their cp. genomes. Results All examined thirteen Pholidota cp. genomes exhibited typical quadripartite circular structures, with the size ranging from 158,786 to 159,781 bp. The annotation contained a total of 135 genes in each cp. genome, i.e., 89 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The codon usage analysis indicated the preference of A/U-ending codons. Repeat sequence analysis identified 444 tandem repeats, 322 palindromic repeats and 189 dispersed repeats. A total of 525 SSRs, 13,834 SNPs and 8,630 InDels were detected. Six mutational hotspots were identified as potential molecular markers. These molecular markers and highly variable regions are expected to facilitate future genetic and genomic studies. Our phylogenetic analyses confirmed the polyphyletic status of the genus Pholidota, with species grouped into four main clades: Pholidota s.s. was resolved as the sister to a clade containing species of Coelogyne; the other two clades clustered together with species of Bulleyia and Panisea, respectively; species P. ventricosa was placed at the basal position, deviated from all other species. Conclusion This is the first study to comprehensively examine the genetic variations and systematically analyze the phylogeny and evolution of Pholidota based on plastid genomic data. These findings contribute to a better understanding of plastid genome evolution of Pholidota and provide new insights into the phylogeny of Pholidota and its closely related genera within the subtribe Coelogyninae. Our research has laid the foundation for future studies on the evolutionary mechanisms and classification of this economically and medicinally important genus.

Structure, gene composition, divergence time and phylogeny analysis of the woody desert species Neltuma alba, Neltuma chilensis and Strombocarpa strombulifera

“…These GC values fall within the limit of variation registered in others studies 24,60 . Furthermore, a study about several orchid species, showed that the species with a smallest chloroplast size (Pholidota cantonensis, 158,786 bp), had a highest GC content (37.47%) 61 , similar to our observations. The plastid genome tends to reduce its size during evolution 62 , and gene length might be affected by selection during the evolution of spermatophytes 63 .…”

Comparative Phylogenetic Analysis for Aerides (Aeridinae, Orchidaceae) Based on Six Complete Plastid Genomes

“…For example, the 3 end of the rpl22 gene of all six species of Aerides, which should be intact in the LSC region, extended into the IRb region for 30-31 bp, which was found in Renanthera [22]. In addition, the ycf1 gene in the SSC region of other orchids (such as Pholidota [23] and Thuniopsis [24]) was observed crossing over JSA, extending into the IRa region. However, the ycf1 of Aerides was intact in the SSC region.…”

Comparative Analysis of Six Chloroplast Genomes in Chenopodium and Its Related Genera (Amaranthaceae): New Insights into Phylogenetic Relationships and the Development of Species-Specific Molecular Markers

“…Some researchers have used the cp genome to mine mutation sites to distinguish closely related species (especially some weed relatives), or have used the cp genome to elaborate new perspectives on plant phylogenetic relationships and taxonomy. The importance and efficiency of chloroplast genomes in related research have been confirmed by more and more studies [40,41].…”