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Feng XX, Huang XF, Huang YN, Liu ZX, Li RK, Zhou JY, Guo W, Chen XY, Tian DK. Begoniaparvibracteata, a new species in Begonia sect. Platycentrum (Begoniaceae) from Guangxi of China, based on morphological and molecular evidence. PHYTOKEYS 2022; 214:27-38. [PMID: 36760548 PMCID: PMC9836518 DOI: 10.3897/phytokeys.214.90004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/11/2022] [Indexed: 06/18/2023]
Abstract
The previously reported begonias in a limestone forest of Guangxi mainly belong to Begoniasect.Coelocentrum Irmscher. In this article, we described and illustrated a new species in sect. Platycentrum (Klotzsch) A.DC., Begoniaparvibracteata X.X.Feng, R.K.Li & Z.X.Liu, which was discovered in a karst forest of south-western Guangxi. The begonia shows high morphological similarity to B.subhowii S.H. Huang and B.psilophylla Irmscher, but differs from the latter two in its narrower oblique-ovate asymmetric leaf blade, 4 (occasionally 6) tepals of pistillate flower and smaller membranous inflorescence bracts. Molecular phylogenetic analysis, based on ITS sequence data, supports the new species as monophyletic and distinct from B.subhowii and B.psilophylla. Considering its narrow distribution and the disturbance of human activities, the conservation status of new taxon is evaluated as "Vulnerable" (VU B1, B2 ab (i, iv, v), D2) according to the IUCN Red List Categories and Criteria.
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Affiliation(s)
- Xin-Xin Feng
- Dongguan Botanical Garden, Dongguan 523086, ChinaDongguan Botanical GardenDongguanChina
| | - Xiao-Feng Huang
- Dongguan Botanical Garden, Dongguan 523086, ChinaDongguan Botanical GardenDongguanChina
| | - Yu-Ni Huang
- Dongguan Botanical Garden, Dongguan 523086, ChinaDongguan Botanical GardenDongguanChina
| | - Zhi-Xian Liu
- Dongguan Botanical Garden, Dongguan 523086, ChinaDongguan Botanical GardenDongguanChina
| | - Ren-Kun Li
- Enshi Dongsheng Plant Development Co. Ltd., Enshi 445000, ChinaEnshi Dongsheng Plant Development Co. Ltd.EnshiChina
| | - Jin-Ye Zhou
- Flower Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, ChinaFlower Research Institute, Guangxi Academy of Agricultural SciencesNanningChina
| | - Wei Guo
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, ChinaZhongkai University of Agriculture and EngineeringGuangzhouChina
| | - Xiao-Yan Chen
- Guangdong Joco Eco-Environment Co., Ltd, Dongguan 523012, Guangdong, ChinaGuangdong Joco Eco-Environment Co., LtdDongguanChina
| | - Dai-Ke Tian
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 3888 Chenhua Road, Songjiang, Shanghai 201602, ChinaShanghai Chenshan Plant Science Research Center, Chinese Academy of SciencesShanghaiChina
- Shanghai Key Laboratory for Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai 201602, ChinaShanghai Key Laboratory for Plant Functional Genomics and Resources, Shanghai Chenshan Botanical GardenShanghaiChina
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Molecular evidence for natural hybridization between Rumex crispus and R. obtusifolius (Polygonaceae) in Korea. Sci Rep 2022; 12:5423. [PMID: 35361815 PMCID: PMC8971494 DOI: 10.1038/s41598-022-09292-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/21/2022] [Indexed: 11/09/2022] Open
Abstract
Interspecific hybridization has been suggested to occur frequently in Rumex (Polygonaceae). Several hypothesized combinations of parental species of hybrids based on their intermediate morphology have been suggested in the genus, but few of them have been phylogenetically tested. We analyzed nuclear and chloroplast DNA sequence data of a putative natural hybrid between Rumex crispus and Rumex obtusifolius from Korea to confirm its hybrid status and to determine the maternal parent. Analysis of the nuclear DNA pgiC region revealed that R. crispus and R. obtusifolius have contributed to the nuclear genome of the putative hybrids. The haplotype distribution pattern inferred from the combined sequence data set of five chloroplast DNA regions (matK, rbcL-accD IGS, trnK-rps16 IGS, ycf6-psbM IGS and psbA-trnH IGS) indicated bidirectional hybridization events between R. crispus and R. obtusifolius. This paper provides the first molecular evidence for interspecific hybridization between R. crispus and R. obtusifolius. In addition, our findings strongly suggested that Korean populations of Rumex japonicus have a hybrid origin, and R. crispus may represent one of the parental taxa.
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Chen S, Milne R, Zhou R, Meng K, Yin Q, Guo W, Ma Y, Mao K, Xu K, Kim YD, Do TV, Liao W, Fan Q. When tropical and subtropical congeners met: Multiple ancient hybridization events within Eriobotrya in the Yunnan-Guizhou Plateau, a tropical-subtropical transition area in China. Mol Ecol 2021; 31:1543-1561. [PMID: 34910340 DOI: 10.1111/mec.16325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 01/09/2023]
Abstract
Global climate changes during the Miocene may have created ample opportunities for hybridization between members of tropical and subtropical biomes at the boundary between these zones. Yet, very few studies have explored this possibility. The Yunnan-Guizhou Plateau (YGP) in Southwest China is a biodiversity hotspot for vascular plants, located in a transitional area between the floristic regions of tropical Southeast Asia and subtropical East Asia. The genus Eriobotrya (Rosaceae) comprises both tropical and subtropical taxa, with 12 species recorded in the YGP, making it a suitable basis for testing the hypothesis of between-biome hybridization. Therefore, we surveyed the evolutionary history of Eriobotrya by examining three chloroplast regions and five nuclear genes for 817 individuals (47 populations) of 23 Eriobotrya species (including 19 populations of 12 species in the YGP), plus genome re-sequencing of 33 representative samples. We concluded that: (1) phylogenetic positions for 16 species exhibited strong cytonuclear conflicts, most probably due to ancient hybridization; (2) the YGP is a hotspot for hybridization, with 11 species showing clear evidence of chloroplast capture; and (3) Eriobotrya probably originated in tropical Asia during the Eocene. From the Miocene onwards, the intensification of the Eastern Asia monsoon and global cooling may have shifted the tropical-subtropical boundary and caused secondary contact between species, thus providing ample opportunity for hybridization and diversification of Eriobotrya, especially in the YGP. Our study highlights the significant role that paleoclimate changes probably played in driving hybridization and generating rich species diversity in climate transition zones.
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Affiliation(s)
- Sufang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Richard Milne
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, UK
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Kaikai Meng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Qianyi Yin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wei Guo
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongpeng Ma
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Kewang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Young-Dong Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon City, South Korea
| | - Truong Van Do
- Vietnam National Museum of Nature, Vietnam Academy of Science & Technology, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science & Technology, Hanoi, Vietnam
| | - Wenbo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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Chen S, Guo W, Chen Z, Liao W, Fan Q. Strong Genetic Structure Observed in Primulina danxiaensis, a Small Herb Endemic to Mount Danxia With Extremely Small Populations. Front Genet 2021; 12:722149. [PMID: 34691147 PMCID: PMC8526925 DOI: 10.3389/fgene.2021.722149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
Danxia landform occurring sporadically in southern China is a unique type of petrographic geomorphology. It has nurtured about 400 rare or threatened plant and animal species, whose diversity, endemism, and conservation have called increasing scientific and public attentions. Among them, Primulina danxiaensis (W. B. Liao, S. S. Lin, and R. J. Shen) W. B. Liao and K. F. Chung is a tiny perennial grass species recorded only in Mount Danxia, a natural World Heritage Site as part of China’s Danxia. In this study, restriction site-associated DNA sequencing (RAD-seq) was performed to investigate genetic diversity among these 12 populations of P. danxiaensis. A total of 432,041 variant sites were detected in 84,779 loci across 94 samples. The expected heterozygosity (HE) ranged from 0.017 to 0.139. Bottleneck signals were detected in most populations, Tajima’s D tests showed that most loci could be under recent positive selection, and one of the six positively selected loci identified by BayeScan was annotated as tRNAGlu, which may contribute to the species’ adaptation to shady environment. STRUCTURE analysis and phylogenetic tree showed that the 12 populations of P. danxiaensis could be divided into four gene pools (clades) corresponding to their geographic locations, and significant correlation was observed between genetic and geographic distances. Our study demonstrated that P. danxiaensis maintained a middle level of genetic diversity and strong population structure; geographic distance could be an important factor limiting gene flow among populations of P. danxiaensis, which were only sporadically recorded in Mount Danxia.
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Affiliation(s)
- Sufang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wei Guo
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Zaixiong Chen
- Administrative Commission of Danxiashan National Park, Shaoguan, China
| | - Wenbo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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Meng KK, Chen SF, Xu KW, Zhou RC, Li MW, Dhamala MK, Liao WB, Fan Q. Phylogenomic analyses based on genome-skimming data reveal cyto-nuclear discordance in the evolutionary history of Cotoneaster (Rosaceae). Mol Phylogenet Evol 2021; 158:107083. [PMID: 33516804 DOI: 10.1016/j.ympev.2021.107083] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 12/16/2020] [Accepted: 01/12/2021] [Indexed: 11/19/2022]
Abstract
As a consequence of hybridization, polyploidization, and apomixis, the genus Cotoneaster (Rosaceae) represents one of the most complicated and controversial lineages in Rosaceae, with ca. 370 species which have been classified into two subgenera and several sections, and is notorious for its taxonomic difficulty. The infrageneric relationships and taxonomy of Cotoneaster have remained poorly understood. Previous studies have focused mainly on natural hybridization involving only several species, and phylogeny based on very limited markers. In the present study, the sequences of complete chloroplast genomes and 204 low-copy nuclear genes of 72 accessions, representing 69 species as ingroups, were used to conduct the most comprehensive phylogenetic analysis so far for Cotoneaster. Based on the sequences of complete chloroplast genomes and many nuclear genes, our analyses yield two robust phylogenetic trees respectively. Chloroplast genome and nuclear data confidently resolved relationships of this genus into two major clades which largely supported current classification based on morphological evidence. However, conflicts between the chloroplast genome and low-copy nuclear phylogenies were observed in both the species level and clade level. Cyto-nuclear discordance in the phylogeny could be caused by frequent hybridization events and incomplete sorting lineage (ILS). In addition, our divergence-time analysis revealed an evolutionary radiation of the genus from late Miocene to date.
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Affiliation(s)
- Kai-Kai Meng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Su-Fang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ke-Wang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Ren-Chao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ming-Wan Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Man Kumar Dhamala
- Central Department of Environmental Science, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Wen-Bo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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Zhang NN, Yu JJ, Wang YH, Gong X. Molecular evidence for asymmetric hybridization in three closely related sympatric species. AOB PLANTS 2018; 10:ply011. [PMID: 29492242 PMCID: PMC5824843 DOI: 10.1093/aobpla/ply011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 02/07/2018] [Indexed: 05/14/2023]
Abstract
Natural hybridization is common in plants and results in different evolutionary consequences to hybridizing species. Pre- and post-zygotic reproductive isolating barriers can impede hybridization between closely related species to maintain their species integrity. In Northwest Yunnan, three Ligularia species (Ligularia cyathiceps, L. duciformis and L. yunnanensis) and four types of morphologically intermediate individuals were discovered growing together in an area subject to human disturbance. In this study, we used three low-copy nuclear loci to test the natural hybridization hypothesis and the hybridization direction was ascertained by three chloroplast DNA fragments. The results indicated there were two hybridization groups at the study site, L. cyathiceps × L. duciformis and L. duciformis × L. yunnanensis, and two types of morphologically intermediate individuals were produced by L. cyathiceps and L. duciformis, and another two types were produced by L. duciformis and L. yunnanensis, while no hybrids between L. cyathiceps and L. yunnanensis were observed. Both hybridizing groups showed bidirectional but asymmetric hybridization and the factors influencing the symmetry are discussed. Most hybrids produced by the two hybridization groups seemed to be F1 generation. Hybrids with different morphologies within the same hybridization group showed similar genetic components. The results suggest that although human disturbance may promote natural hybridization among the three Ligularia species bringing them together, hybrids are limited to F1s and therefore species boundaries might be maintained.
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Affiliation(s)
- Ning-Ning Zhang
- Plant Science Institute, School of Life Sciences, Yunnan University, 650201 Kunming, Yunnan, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201 Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Jiao-Jun Yu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201 Kunming, Yunnan, China
| | - Yue-Hua Wang
- Plant Science Institute, School of Life Sciences, Yunnan University, 650201 Kunming, Yunnan, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201 Kunming, Yunnan, China
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Molecular phylogenetics and historical biogeography of Sorbus sensu stricto (Rosaceae). Mol Phylogenet Evol 2017; 111:76-86. [DOI: 10.1016/j.ympev.2017.03.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 03/15/2017] [Accepted: 03/21/2017] [Indexed: 11/24/2022]
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Li M, Chen S, Zhou R, Fan Q, Li F, Liao W. Molecular Evidence for Natural Hybridization between Cotoneaster dielsianus and C. glaucophyllus. FRONTIERS IN PLANT SCIENCE 2017; 8:704. [PMID: 28536587 PMCID: PMC5422516 DOI: 10.3389/fpls.2017.00704] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/18/2017] [Indexed: 05/06/2023]
Abstract
Hybridization accompanied by polyploidization and apomixis has been demonstrated as a driving force in the evolution and speciation of many plants. A good example to study the evolutionary process of hybridization associated with polyploidy and apomixis is the genus Cotoneaster (Rosaceae), which includes approximately 150 species, most of which are polyploid apomicts. In this study, we investigated all Cotoneaster taxa distributed in a small region of Malipo, Yunnan, China. Based on the morphological characteristics, four Cotoneaster taxa were identified and sampled: C. dielsianus, C. glaucophyllus, C. franchetii, and a putative hybrid. Flow cytometry analyses showed that C. glaucophyllus was diploid, while the other three taxa were tetraploid. A total of five low-copy nuclear genes and six chloroplast regions were sequenced to validate the status of the putative hybrid. Sequence analyses showed that C. dielsianus and C. glaucophyllus are distantly related and they could be well separated using totally 50 fixed nucleotide substitutions and four fixed indels at the 11 investigated genes. All individuals of the putative hybrid harbored identical sequences: they showed chromatogram additivity for all fixed differences between C. dielsianus and C. glaucophyllus at the five nuclear genes, and were identical with C. glaucophyllus at the six chloroplast regions. Haplotype analysis revealed that C. dielsianus possessed nine haplotypes for the 11 genes, while C. glaucophyllus had ten, and there were no shared haplotypes between the two species. The putative hybrid harbored two haplotypes for each nuclear gene: one shared with C. dielsianus and the other with C. glaucophyllus. They possessed the same chloroplast haplotype with C. glaucophyllus. Our study provided convincing evidence for natural hybridization between C. dielsianus and C. glaucophyllus, and revealed that all hybrid individuals were derivatives of one initial F1 via apomixes. C. glaucophyllus served as the maternal parent at the initial hybridization event. We proposed that anthropological disturbance provided an opportunity for hybridization between C. dielsianus and C. glaucophyllus, and a tetraploid F1 successfully bred many identical progenies via apomixis. Under this situation, species integrity could be maintained for these Cotoneaster species, but attentions should be kept for this new-born hybrid.
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Affiliation(s)
- Mingwan Li
- Guangdong Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics, Conservation of Guangdong Higher Education Institutes, Sun Yat-sen UniversityGuangzhou, China
| | - Sufang Chen
- Guangdong Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics, Conservation of Guangdong Higher Education Institutes, Sun Yat-sen UniversityGuangzhou, China
- *Correspondence: Sufang Chen
| | - Renchao Zhou
- Guangdong Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics, Conservation of Guangdong Higher Education Institutes, Sun Yat-sen UniversityGuangzhou, China
| | - Qiang Fan
- Guangdong Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics, Conservation of Guangdong Higher Education Institutes, Sun Yat-sen UniversityGuangzhou, China
| | - Feifei Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental SciencesBeijing, China
- College of Life and Environmental Sciences, Minzu University of ChinaBeijing, China
- Feifei Li
| | - Wenbo Liao
- Guangdong Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics, Conservation of Guangdong Higher Education Institutes, Sun Yat-sen UniversityGuangzhou, China
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