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Yuan L, Ni Y, Chen H, Li J, Lu Q, Wang L, Zhang X, Yue J, Yang H, Liu C. Comparative chloroplast genomes study of five officinal Ardisia Species: Unraveling interspecific diversity and evolutionary insights in Ardisia. Gene 2024; 912:148349. [PMID: 38460806 DOI: 10.1016/j.gene.2024.148349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/11/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Ardisia S.W. (Primulaceae), naturally distributed in tropical and subtropical regions, has edible and medicinal values and is prevalent in clinical and daily use in China. More genetic information for distinct species delineation is needed to support the development and utilization of the genus Ardisia. We sequenced, annotated, and compared the chloroplast genomes of five Ardisia species: A. brunnescens, A. pusilla, A. squamulosa, A. crenata, and A. brevicaulis in this study. We found a typical quadripartite structure in all five chloroplast genomes, with lengths ranging from 155,045 to 156,943 bp. Except for A. pusilla, which lacked the ycf15 gene, the other four Ardisia species contained 114 unique genes, including 79 protein-coding genes, 30 tRNAs, and four rRNAs. In addition, the rps19 pseudogene gene was present only in A. brunnescens. Five highly variable DNA barcodes were identified for five Ardisia species, including trnT-GGU-psbD, trnT-UGU-trnL-UAA, rps4-trnT-UGU, rpl32-trnL-UAG, and rpoB-trnC-GAA. The RNA editiing sites of protein-coding genes in the five Ardisia plastome were characterized and compared, and 274 (A. crenata)-288 (A. brevicaulis) were found. The results of the phylogenetic analysis were consistent with the morphological classification. Sequence alignment and phylogenetic analysis showed that ycf15 genes were highly divergent in Primulaceae. Reconstructions of ancestral character states indicated that leaf margin morphology is critical for classifying the genus Ardisia, with a rodent-like character being the most primitive. These results provide valuable information on the taxonomy and evolution of Ardisia plants.
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Affiliation(s)
- Lichai Yuan
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Ni
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Haimei Chen
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Jingling Li
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Qianqi Lu
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
| | - Liqiang Wang
- College of Pharmacy, Heze University, Heze, Shandong, China.
| | - Xinyi Zhang
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Jingwen Yue
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
| | - Heyu Yang
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Chang Liu
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Zhao Z, Li Y, Zhai JW, Liu ZJ, Li MH. Organelle Genomes of Epipogium roseum Provide Insight into the Evolution of Mycoheterotrophic Orchids. Int J Mol Sci 2024; 25:1578. [PMID: 38338856 PMCID: PMC10855806 DOI: 10.3390/ijms25031578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Epipogium roseum, commonly known as one of the ghost orchids due to its rarity and almost transparent color, is a non-photosynthetic and fully mycoheterotrophic plant. Given its special nutritional strategies and evolutionary significance, the mitogenome was first characterized, and three plastomes sampled from Asia were assembled. The plastomes were found to be the smallest among Orchidaceae, with lengths ranging from 18,339 to 19,047 bp, and exhibited high sequence variety. For the mitogenome, a total of 414,552 bp in length, comprising 26 circular chromosomes, were identified. A total of 54 genes, including 38 protein-coding genes, 13 tRNA genes, and 3 rRNA genes, were annotated. Multiple repeat sequences spanning a length of 203,423 bp (45.47%) were discovered. Intriguingly, six plastid regions via intracellular gene transfer and four plastid regions via horizontal gene transfer to the mitogenome were observed. The phylogenomics, incorporating 90 plastomes and 56 mitogenomes, consistently revealed the sister relationship of Epipogium and Gastrodia, with a bootstrap percentage of 100%. These findings shed light on the organelle evolution of Orchidaceae and non-photosynthetic plants.
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Affiliation(s)
| | | | | | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.); (Y.L.); (J.-W.Z.)
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.Z.); (Y.L.); (J.-W.Z.)
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