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

Mengkai Li; Lu Tang; Jianping Deng; Hanqing Tang; Shicheng Shao; Zhen Xing; Yan Luo

doi:10.7717/peerj.14721

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

PeerJ. 2023 Feb 10:11:e14721. doi: 10.7717/peerj.14721. eCollection 2023.

Authors

Mengkai Li^{1

2}, Lu Tang³, Jianping Deng¹, Hanqing Tang⁴, Shicheng Shao⁵, Zhen Xing², Yan Luo¹

Affiliations

¹ Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences & Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China.
² Resources & Environment College, Tibet Agriculture & Animal Husbandry University, Nyingchi, China.
³ Center for Gardening and Horticulture, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China.
⁴ School of Resources and Environmental Science, Hubei University, Wuhan, China.
⁵ CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China.

Abstract

Background: Chloroplast (cp) genomes are useful and informative molecular markers used for species determination and phylogenetic analysis. Bulbophyllum is one of the most taxonomically complex taxa in Orchidaceae. However, the genome characteristics of Bulbophyllum are poorly understood.

Methods: Based on comparative morphological and genomic analysis, a new species Bulbophyllum pilopetalum from eastern Himalaya belonging to section Cirrhopetalum is described and illustrated. This study used chloroplast genomic sequences and ribosomal DNA (nrDNA) analysis to distinguish the new Bulbophyllum species and determine its phylogenetic position. An additional phylogenetic analysis was conducted using 74 coding sequences from 15 complete chloroplast genomes from the genus Bulbophyllum, as well as nrDNA sequences and two chloroplast DNA sequences from 33 Bulbophyllun species.

Results: The new species is morphologically similar to B. pingnanense, B. albociliatum, and B. brevipedunculatum 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 Bulbophyllum 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, B. pingnanense and B. albociliatum, this chloroplast genome exhibited great interspecific divergence and contained several Indels that were specific to the new species. The plastid tree showed that B. pilopetalum is most closely-related to B. pingnanense. The phylogenetic tree based on combined nrDNA and chloroplast DNA sequences indicated that section Cirrhopetalum was monophyletic and B. pilopetalum was a member of this section.

Discussion: 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.

Keywords: Bulbophyllum; Chloroplast genome; New species; Orchidaceae; Phylogenetic position.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chloroplasts / genetics
DNA, Chloroplast*
Genomics
Orchidaceae* / genetics
Phylogeny

Substances

DNA, Chloroplast

Grants and funding

This study was supported by the National Natural Science Foundation of China (Grant No. 31870183 and 32171655) and the West Light Talent Program of the Chinese Academy of Sciences (Grant No. E1XB011B01). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.