1
|
Nanjala C, Wanga VO, Odago W, Mutinda ES, Waswa EN, Oulo MA, Mkala EM, Kuja J, Yang JX, Dong X, Hu GW, Wang QF. Plastome structure of 8 Calanthe s.l. species (Orchidaceae): comparative genomics, phylogenetic analysis. BMC Plant Biol 2022; 22:387. [PMID: 35918646 PMCID: PMC9347164 DOI: 10.1186/s12870-022-03736-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/29/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Calanthe (Epidendroideae, Orchidaceae) is a pantropical genus distributed in Asia and Africa. Its species are of great importance in terms of economic, ornamental and medicinal values. However, due to limited and confusing delimitation characters, the taxonomy of the Calanthe alliance (Calanthe, Cephalantheropsis, and Phaius) has not been sufficiently resolved. Additionally, the limited genomic information has shown incongruences in its systematics and phylogeny. In this study, we used illumina platform sequencing, performed a de novo assembly, and did a comparative analysis of 8 Calanthe group species' plastomes: 6 Calanthe and 2 Phaius species. Phylogenetic analyses were used to reconstruct the relationships of the species as well as with other species of the family Orchidaceae. RESULTS The complete plastomes of the Calanthe group species have a quadripartite structure with varied sizes ranging between 150,105bp-158,714bp, including a large single-copy region (LSC; 83,364bp- 87,450bp), a small single-copy region (SSC; 16,297bp -18,586bp), and a pair of inverted repeat regions (IRs; 25,222bp - 26,430bp). The overall GC content of these plastomes ranged between 36.6-36.9%. These plastomes encoded 131-134 differential genes, which included 85-88 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. Comparative analysis showed no significant variations in terms of their sequences, gene content, gene order, sequence repeats and the GC content hence highly conserved. However, some genes were lost in C. delavayi (P. delavayi), including ndhC, ndhF, and ndhK genes. Compared to the coding regions, the non-coding regions had more sequence repeats hence important for species DNA barcoding. Phylogenetic analysis revealed a paraphyletic relationship in the Calanthe group, and confirmed the position of Phaius delavayi in the genus Calanthe as opposed to its previous placement in Phaius. CONCLUSION This study provides a report on the complete plastomes of 6 Calanthe and 2 Phaius species and elucidates the structural characteristics of the plastomes. It also highlights the power of plastome data to resolve phylogenetic relationships and clarifies taxonomic disputes among closely related species to improve our understanding of their systematics and evolution. Furthermore, it also provides valuable genetic resources and a basis for studying evolutionary relationships and population genetics among orchid species.
Collapse
Affiliation(s)
- Consolata Nanjala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Vincent Okelo Wanga
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Wyclif Odago
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Elizabeth Syowai Mutinda
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Emmanuel Nyongesa Waswa
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Millicent Akinyi Oulo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jia-Xin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
| |
Collapse
|
2
|
Zhai JW, Zhang GQ, Li L, Wang M, Chen LJ, Chung SW, Rodríguez FJ, Francisco-Ortega J, Lan SR, Xing FW, Liu ZJ. A new phylogenetic analysis sheds new light on the relationships in the Calanthe alliance (Orchidaceae) in China. Mol Phylogenet Evol 2014; 77:216-22. [PMID: 24747128 DOI: 10.1016/j.ympev.2014.04.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 02/21/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
Abstract
The taxonomy of the Calanthe alliance (Epidendroideae, Orchidaceae), consisting of Calanthe, Cephalantheropsis, and Phaius, has been difficult for orchidologists to understand because of the presence of common morphological features. In this study, in addition to morphological and geographical analyses, maximum parsimony and Bayesian inference analyses were performed based on nucleotide sequences of the nuclear internal transcribed spacer and cpDNA genes of 88 taxa representing the major clades of the Calanthe alliance in China. The results indicated that Cephalantheropsis is monophyletic, while both Phaius and Calanthe are polyphyletic. In Phaius, a total of three species, P. flavus, P. columnaris, and P. takeoi, were segregated to form a new genus, Paraphaius. In Calanthe, subgenus Preptanthe and sect. Styloglossum were both categorized as distinct genera from Calanthe. Our results also confirm that Calanthe delavayi and C. calanthoides are members of Calanthe. Previous studies assigned C. delavayi to Phaius and C. calanthoides to Ghiesbrechtia. Five sections, namely, Alpinocalanthe, Puberula, Ghiesbrechtia, Tricarinata, and Calanthe, three of which are new taxa, were recognized in Calanthe. Therefore, we propose that the Calanthe alliance is composed of six genera: Calanthe, Cephalantheropsis, Paraphaius, Phaius, Preptanthe and Styloglossum.
Collapse
Affiliation(s)
- Jun-Wen Zhai
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; Orchid Conservation and Research Center of Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China
| | - Lin Li
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Meina Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China
| | - Li-Jun Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China
| | - Shih-Wen Chung
- Department of Botany, Taiwan Forestry Research Institute, Taipei 10066, Taiwan
| | | | - Javier Francisco-Ortega
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA; Kushlan Tropical Science Institute, Fairchild Tropical Botanical Garden, Coral Gables, Miami, FL 33156, USA
| | - Si-Ren Lan
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Orchid Conservation and Research Center of Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Fu-Wu Xing
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Zhong-Jian Liu
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China.
| |
Collapse
|