Plastomes of Bletilla (Orchidaceae) and Phylogenetic Implications

Abstract

The genus Bletilla is a small genus of only five species distributed across Asia, including B. chartacea, B. foliosa, B. formosana, B. ochracea and B. striata, which is of great medicinal importance. Furthermore, this genus is a member of the key tribe Arethuseae (Orchidaceae), harboring an extremely complicated taxonomic history. Recently, the monophyletic status of Bletilla has been challenged, and the phylogenetic relationships within this genus are still unclear. The plastome, which is rich in both sequence and structural variation, has emerged as a powerful tool for understanding plant evolution. Along with four new plastomes, this work is committed to exploring plastomic markers to elucidate the phylogeny of Bletilla. Our results reveal considerable plastomic differences between B. sinensis and the other three taxa in many aspects. Most importantly, the specific features of the IR junction patterns, novel pttRNA structures and codon aversion motifs can serve as useful molecular markers for Bletilla phylogeny. Moreover, based on maximum likelihood and Bayesian inference methods, our phylogenetic analyses based on two datasets of Arethuseae strongly imply that Bletilla is non-monophyletic. Accordingly, our findings from this study provide novel potential markers for species identification, and shed light on the evolution of Bletilla and Arethuseae.

Ten Plastomes of Crassula (Crassulaceae) and Phylogenetic Implications

“…Specifically, the codon aversion motifs in orthologous genes are generally conserved in specific lineages [ 29 , 30 , 31 ]. To date, these analyses have only been performed in a few plant plastomes [ 17 , 26 ]. For example, the specific codon aversion motifs of rpoA gene could distinguish not only the two genera ( Aeonium and Monanthes ), but also the three subclades of Aeonium in our recent report [ 17 ].…”

“…Codon usage bias (CUB), indicating the preferential utilization of synonymous codons in protein-coding genes (PCGs), has evolved via combined effects of genetic drift, mutation, and natural selection [ 17 , 25 , 26 , 27 , 28 ]. Owing to different species having diverse codon usage patterns, investigations of CUB can reveal phylogenetic relationships between species [ 17 , 25 , 26 , 27 , 28 ]. Codon aversion is defined as the codon which is not used in a certain gene [ 29 , 30 , 31 ].…”

“…species (Orchidaceae Juss.) have suggested that plastid CUB and codon aversion patterns might harbor phylogenetic signals [ 17 , 26 ]. Therefore, the analyses of plastid genes in codon-usage aspects might broaden our understanding of the phylogeny of both Crassula and Crassulaceae.…”

The Complete Chloroplast Genomes of Blepharoglossum elegans and B. grossum and Comparative Analysis with Related Species (Orchidaceae, Malaxideae)

“…In Orchidaceae, for instance, some genera exhibit unresolved phylogenetic relationships and uncertain monophyletic status with traditional sequences from a single or few markers, such as nrDNA-ITS and matK. However, the cp genome data have demonstrated remarkable advantages in resolving the developmental relationships and systematic positions of complex taxa, resulting in significant improvements in accuracy and reliability [10,11]. Moreover, a comparative analysis of cp genomes presents a promising avenue for investigating sequence variations and identifying mutation hotspots.…”

The characteristics of the complete chloroplast genome of Staurogyne concinnula (Hance) O. Kuntze (Acanthaceae)

“… 2018 ; Han et al. 2022 ), it may provide a greater resolution toward phylogenetic analysis of Staurogynei ; thus, provides aid to the understanding of the evolution pattern and phylogenomics of Acanthaceae.…”