Comparative chloroplast genomics of three species of Bulbophyllum section Cirrhopetalum (Orchidaceae), with an emphasis on the description of a new species from Eastern Himalaya

• Published in: PeerJ (San Francisco, CA) CA), 2023-02, Vol.11, p.e14721-e14721, Article e14721
• Main Authors: Li, Mengkai, Tang, Lu, Deng, Jianping, Tang, Hanqing, Shao, Shicheng, Xing, Zhen, Luo, Yan
• Format: Article
• Language: English
• Subjects: Biodiversity; Bulbophyllum; Chloroplast DNA; Chloroplast genome; Chloroplasts; Chloroplasts - genetics; Comparative analysis; Conservation Biology; Discovery and exploration; Divergence; DNA; DNA sequencing; DNA, Chloroplast; Flowers & plants; Genes; Genetic research; Genomes; Genomic analysis; Genomics; Morphology; New species; Nucleotide sequence; Nucleotide sequencing; Orchidaceae; Orchidaceae - genetics; Phylogenetic position; Phylogenetics; Phylogeny; Physical characteristics; Plant Science; Taxonomy
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.14721

Chloroplast (cp) genomes are useful and informative molecular markers used for species determination and phylogenetic analysis. is one of the most taxonomically complex taxa in Orchidaceae. However, the genome characteristics of are poorly understood. Based on comparative morphological and genomic analysis, a new species from eastern Himalaya belonging to section is described and illustrated. This study used chloroplast genomic sequences and ribosomal DNA (nrDNA) analysis to distinguish the new species and determine its phylogenetic position. An additional phylogenetic analysis was conducted using 74 coding sequences from 15 complete chloroplast genomes from the genus , as well as nrDNA sequences and two chloroplast DNA sequences from 33 species. The new species is morphologically similar to , , and in vegetative and floral morphology, but it can be distinguished by its ovate-triangle dorsal sepal without a marginal ciliate. The chloroplast genome of the new species is 151,148 bp in length, and includes a pair of inverted repeats (IRs) of 25,833 bp, a large single-copy region (LSC) of 86,138 bp, and a small single-copy region (SSC) of 13,300 bp. The chloroplast genome includes 108 unique genes encoding 75 proteins, 30 tRNAs, and four rRNAs. Compared with the cp genomes of its two most closely-related species, and , this chloroplast genome exhibited great interspecific divergence and contained several Indels that were specific to the new species. The plastid tree showed that is most closely-related to . The phylogenetic tree based on combined nrDNA and chloroplast DNA sequences indicated that section was monophyletic and was a member of this section. The taxonomic status of the new species is strongly supported by cp genome data. Our study highlights the importance of using the complete cp genome to identify species, elucidate the taxonomy, and reconstruct the phylogeny of plant groups with complicated taxonomic problems.