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Chen X, Feng Y, Chen S, Yang K, Wen X, Sun Y. Species Delimitation and Genetic Relationship of Castanopsis hainanensis and Castanopsis wenchangensis (Fagaceae). PLANTS (BASEL, SWITZERLAND) 2023; 12:3544. [PMID: 37896008 PMCID: PMC10609670 DOI: 10.3390/plants12203544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 09/30/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Castanopsis is one of the most common genus of trees in subtropical evergreen broad-leaved forests and tropical monsoon rainforests in China. Castanopsis hainanensis and Castanopsis wenchangensis are endemic to Hainan Island, but they were once confused as the same species due to very similar morphologies. In this study, nuclear microsatellite markers and chloroplast genomes were used to delimit C. hainanensis and C. wenchangensis. The allelic variations of nuclear microsatellites revealed that C. hainanensis and C. wenchangensis were highly genetically differentiated with very limited gene admixture. Both showed higher genetic diversity within populations and lower genetic diversity among populations, and neither had further population genetic structure. Furthermore, C. wenchangensis and C. hainanensis had very different chloroplast genomes. The independent genetic units, very limited gene admixture, different distribution ranges, and distinct habitats all suggest that C. wenchangensis and C. hainanensis are independent species, thus they should be treated as distinct conservation units.
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Affiliation(s)
- Xing Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
| | - Yi Feng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
| | - Shuang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
| | - Kai Yang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
| | - Xiangying Wen
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ye Sun
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
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Zhang X, Zhao Y, Kou Y, Chen X, Yang J, Zhang H, Zhao Z, Zhao Y, Zhao G, Li Z. Diploid chromosome-level reference genome and population genomic analyses provide insights into Gypenoside biosynthesis and demographic evolution of Gynostemma pentaphyllum (Cucurbitaceae). HORTICULTURE RESEARCH 2022; 10:uhac231. [PMID: 36643751 PMCID: PMC9832869 DOI: 10.1093/hr/uhac231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/01/2022] [Indexed: 06/17/2023]
Abstract
Gynostemma pentaphyllum (Thunb.) Makino is a perennial creeping herbaceous plant in the family Cucurbitaceae, which has great medicinal value and commercial potential, but urgent conservation efforts are needed due to the gradual decreases and fragmented distribution of its wild populations. Here, we report the high-quality diploid chromosome-level genome of G. pentaphyllum obtained using a combination of next-generation sequencing short reads, Nanopore long reads, and Hi-C sequencing technologies. The genome is anchored to 11 pseudo-chromosomes with a total size of 608.95 Mb and 26 588 predicted genes. Comparative genomic analyses indicate that G. pentaphyllum is estimated to have diverged from Momordica charantia 60.7 million years ago, with no recent whole-genome duplication event. Genomic population analyses based on genotyping-by-sequencing and ecological niche analyses indicated low genetic diversity but a strong population structure within the species, which could classify 32 G. pentaphyllum populations into three geographical groups shaped jointly by geographic and climate factors. Furthermore, comparative transcriptome analyses showed that the genes encoding enzyme involved in gypenoside biosynthesis had higher expression levels in the leaves and tendrils. Overall, the findings obtained in this study provide an effective molecular basis for further studies of demographic genetics, ecological adaption, and systematic evolution in Cucurbitaceae species, as well as contributing to molecular breeding, and the biosynthesis and biotransformation of gypenoside.
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Affiliation(s)
- Xiao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
| | - Yuhe Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
| | - Yixuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaodan Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
- College of Life Sciences, Shanxi Normal University, Taiyuan, Shanxi, 030012, China
| | - Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
| | - Hao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
- College of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China
| | - Zhe Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, Shaanxi, 710069, China
| | - Yuemei Zhao
- School of Biological Sciences, Guizhou Education University, Guiyang, Guizhou, 550018, China
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Li Y, Wang L, Zhang X, Kang H, Liu C, Mao L, Fang Y. Extensive sharing of chloroplast haplotypes among East Asian Cerris oaks: The imprints of shared ancestral polymorphism and introgression. Ecol Evol 2022; 12:e9142. [PMID: 35923946 PMCID: PMC9339761 DOI: 10.1002/ece3.9142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/27/2022] [Accepted: 07/01/2022] [Indexed: 11/08/2022] Open
Abstract
Shared ancestral polymorphism and introgression are two main causes of chloroplast DNA (cpDNA) haplotype sharing among closely related angiosperms. In this study, we explored the roles of these two processes in shaping the phylogeographic patterns of East Asian Cerris oaks by examining the geographic distributions of randomly and locally distributed shared haplotypes, which coincide with the expectations of shared ancestry and introgression, respectively. We sequenced 1340 bp of non-coding cpDNA from Quercus acutissima (n = 418) and Q. chenii (n = 183) and compiled previously published sequence data of Q. variabilis (n = 439). The phylogenetic relationships among haplotypes were examined using a median-joining network. The geographic patterns of interspecifically shared haplotypes were assessed to test whether nearby populations have a higher degree of interspecific cpDNA sharing than distant ones. We identified a total of 27 haplotypes that were grouped into three non-species-specific lineages with overlapping distributions. Ancestral haplotypes were extensively shared and randomly distributed across populations of the three species. Some young haplotypes were locally shared in mountainous areas that may have been shared refugia. The local exchange of cpDNA resulted in an excess of similar haplotypes between nearby populations. Our study demonstrated that the haplotype sharing pattern among East Asian Cerris oaks reflected the imprints of both shared ancestral polymorphism and introgression. This pattern was also associated with the relatively stable climates and complex landscapes in East Asia, which not only allowed the long-term persistence of ancestral lineages but also connected the survived populations across refugia.
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Affiliation(s)
- Yao Li
- Co‐Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the Environment, Nanjing Forestry UniversityNanjingChina
| | - Lu Wang
- Co‐Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the Environment, Nanjing Forestry UniversityNanjingChina
| | - Xingwang Zhang
- School of Life SciencesHuaibei Normal UniversityHuaibeiChina
| | - Hongzhang Kang
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Chunjiang Liu
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Lingfeng Mao
- Co‐Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the Environment, Nanjing Forestry UniversityNanjingChina
| | - Yanming Fang
- Co‐Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the Environment, Nanjing Forestry UniversityNanjingChina
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