Comparative Analysis of the Complete Chloroplast Genomes of Nine Paphiopedilum Species

Abstract

Paphiopedilum is known as “lady’s or Venus” slipper orchids due to its prominent shoe-shaped labellum, with high ornamental value. Phylogenetic relationships among some species in Paphiopedilum genus cannot be effectively determined by morphological features alone or through the analysis of nuclear or chloroplast DNA fragments. In order to provide aid in understanding the evolutionary and phylogenetic relationship in Paphiopedilum at chloroplast (cp) genome-scale level, the complete cp genomes of six Paphiopedilum species were newly sequenced in this study, and three other published cp genome sequences of Paphiopedilum were included in the comparative analyses. The cp genomes of the six Paphiopedilum species ranged from 154,908 bp (P. hirsutissimum) to 161,300 bp (P. victoria-mariae) in size, all constituting four-part annular structures. Analyses of the nucleotide substitutions, insertions/deletions, and simple sequence repeats in the cp genomes were conducted. Ten highly variable regions that could serve as potential DNA barcodes or phylogenetic markers for this diverse genus were identified. Sequence variations in the non-coding regions were greater than that in the conserved protein-coding regions, as well as in the large single copy (LSC) and small single copy (SSC) regions than in the inverted repeat (IR) regions. Phylogenetic analysis revealed that all Paphiopedilum species clustered in one monophyletic clade in the Cypripedioideae subfamily and then subdivided into seven smaller branches corresponding to different subgenus or sections of the genus, with high bootstrap supports, indicate that cp genome sequencing can be an effective means in resolving the complex relationship in Paphiopedilum.

Comparative phylogenetic analysis of complete plastid genomes of Renanthera (Orchidaceae)

“…The SSRs numbers in the LSC region of plastome of R. coccinea and R. philippinensis are 53 and 47, respectively. The distribution of SSR in the four species of Renanthera was consistent with that of most angiosperms (Xu et al, 2021;Sun et al, 2022;Xia et al, 2022).…”

Comparative Chloroplast Genomes of Nicotiana Species (Solanaceae): Insights Into the Genetic Variation, Phylogenetic Relationship, and Polyploid Speciation

“…The comparative analysis of variation information in different regions indicated that the IR regions were highly conserved compared to the LSC and SSC regions, as reflected by the fact that <6.5% of the SNPs that had been identified in this study were located within the IR regions even though IR regions constituted about one-third of the chloroplast genomes ( Figures 1A , 2A ; Supplementary Table 3 ). The low level of variant sites and nucleotide diversity observed in the IR regions was very common among plant chloroplast genomes (Choi et al, 2016 ; Wang et al, 2019 , 2022 ; Sun et al, 2022 ). In addition, the intergenic regions had greater divergence than the exon and intron regions ( Figure 2C ; Supplementary Table 8 ).…”

Riboproteome remodeling during quiescence exit in Saccharomyces cerevisiae

“…In addition, it could also be that RPs that fail to assemble into ribosomes are rapidly ubiquitinated and degraded in the nucleus in a proteasome-dependent manner as previously described. 88 Nevertheless, since the populations of ribosome subunits after 60 min of stimulation have different protein composition to those seen during quiescence, it appears that another process is responsible for the diversity of ribosomes raising the possibility that RPs could be exchanged using de novo synthesized RPs produced during quiescence exit. On the other hand, 80S ribosomes from quiescent cells could be recycled to polysomes once translational activity is induced.…”