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Wang W, Xu T, Lu H, Li G, Gao L, Liu D, Han B, Yi S. Chloroplast genome of Justicia procumbens: genomic features, comparative analysis, and phylogenetic relationships among Justicieae species. J Appl Genet 2024; 65:31-46. [PMID: 38133708 DOI: 10.1007/s13353-023-00812-5] [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: 08/04/2023] [Revised: 11/10/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Justicia procumbens L. is a traditional medicinal plant that is widely distributed in China. However, little is known about the genetic diversity and evolution of this genus, and no genomic studies have been carried out on J. procumbens previously. In this study, we aimed to assemble and annotate the first complete chloroplast genome (cpDNA) of J. procumbens and compare it with all previously published cpDNAs within the tribe Justicieae. Genome structure and comparative and phylogenetic analyses were performed. The 150,454 bp-long J. procumbens cpDNA has a circular and quadripartite structure consisting of a large single copy, a small single copy, and two inverted repeat regions. It contains 133 genes, of which 88 are protein-coding genes, 37 are tRNA genes, and eight are rRNA genes. Twenty-four simple sequence repeats (SSRs) and 81 repeat sequences were identified. Comparative analyses with other Justicieae species revealed that the non-coding regions of J. procumbens cpDNA showed greater variation than did the coding regions. Moreover, phylogenetic analysis based on 14 cpDNA sequences from Justicieae species showed that J. procumbens and J. flava were most closely related. This study provides valuable genetic information to support further research on the genetic diversity and evolutionary development of the tribe Justicieae.
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Affiliation(s)
- Wei Wang
- Traditional Chinese Medicine Institute of Anhui Dabie Mountain, West Anhui University, Lu'an, Anhui, China
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, West Anhui University, Lu'an, Anhui, China
| | - Tao Xu
- Traditional Chinese Medicine Institute of Anhui Dabie Mountain, West Anhui University, Lu'an, Anhui, China
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, West Anhui University, Lu'an, Anhui, China
| | - Haibo Lu
- Traditional Chinese Medicine Institute of Anhui Dabie Mountain, West Anhui University, Lu'an, Anhui, China
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, West Anhui University, Lu'an, Anhui, China
| | - Guosi Li
- Traditional Chinese Medicine Institute of Anhui Dabie Mountain, West Anhui University, Lu'an, Anhui, China
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, West Anhui University, Lu'an, Anhui, China
| | - Leilei Gao
- Traditional Chinese Medicine Institute of Anhui Dabie Mountain, West Anhui University, Lu'an, Anhui, China
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, West Anhui University, Lu'an, Anhui, China
| | - Dong Liu
- Traditional Chinese Medicine Institute of Anhui Dabie Mountain, West Anhui University, Lu'an, Anhui, China
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, West Anhui University, Lu'an, Anhui, China
| | - Bangxing Han
- Traditional Chinese Medicine Institute of Anhui Dabie Mountain, West Anhui University, Lu'an, Anhui, China.
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, West Anhui University, Lu'an, Anhui, China.
| | - Shanyong Yi
- Traditional Chinese Medicine Institute of Anhui Dabie Mountain, West Anhui University, Lu'an, Anhui, China.
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, West Anhui University, Lu'an, Anhui, China.
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Cao Z, Yang L, Xin Y, Xu W, Li Q, Zhang H, Tu Y, Song Y, Xin P. Comparative and phylogenetic analysis of complete chloroplast genomes from seven Neocinnamomum taxa (Lauraceae). FRONTIERS IN PLANT SCIENCE 2023; 14:1205051. [PMID: 37484476 PMCID: PMC10362447 DOI: 10.3389/fpls.2023.1205051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/29/2023] [Indexed: 07/25/2023]
Abstract
The genus Neocinnamomum is considered to be one of the most enigmatic groups in Lauraceae, mainly distributed in tropical and subtropical regions of Southeast Asia. The genus contains valuable oilseed and medicinal tree species. However, there are few studies on the genus Neocinnamomum at present, and its interspecific relationship is still unclear. In order to explore the genetic structure and evolutionary characteristics of the Neocinnamomum chloroplast genome and to resolve the species relationships within the genus, comparative genomic and phylogenetic analyses were performed on the whole chloroplast genome sequences of 51 samples representing seven Neocinnamomum taxa. The whole Neocinnamomum chloroplast genome size ranged from 150,753-150,956 bp, with a GC content of 38.8%-38.9%. A total of 128 genes were annotated within the Neocinnamomum chloroplast genome, including 84 protein coding genes, 8 rRNA genes, and 36 tRNA genes. Between 71-82 SSRs were detected, among which A/T base repeats were the most common. The chloroplast genome contained a total of 31 preferred codons. Three highly variable regions, trnN-GUU-ndhF, petA-psbJ, and ccsA-ndhD, were identified with Pi values > 0.004. Based on the whole chloroplast genome phylogenetic tree, the phylogenetic relationships among the seven Neocinnamomum taxa were determined. N. delavayi and N. fargesii were the most closely related species, and N. lecomtei was identified as the most basal taxon. In this study, the characteristics and sequence variation of the chloroplast genomes of seven Neocinnamomum taxa were revealed, and the genetic relationship among the species was clarified. The results of this study will provide a reference for subsequent molecular marker development and phylogenetic research of Neocinnamomum.
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Affiliation(s)
- Zhengying Cao
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Linyi Yang
- Yunnan Forestry Vocational and Technical College, Kunming, Yunnan, China
| | - Yaxuan Xin
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Wenbin Xu
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qishao Li
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Haorong Zhang
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Yuxiang Tu
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, Guangxi, China
| | - Peiyao Xin
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
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