3
|
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. [DOI: https:/doi.org/10.1186/s12870-022-03736-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/29/2022] [Indexed: 06/21/2023]
Abstract
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
|
4
|
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
|