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Huang G, Wu W, Chen Y, Zhi X, Zou P, Ning Z, Fan Q, Liu Y, Deng S, Zeng K, Zhou R. Balancing selection on an MYB transcription factor maintains the twig trichome color variation in Melastoma normale. BMC Biol 2023; 21:122. [PMID: 37226197 DOI: 10.1186/s12915-023-01611-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 05/03/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND The factors that maintain phenotypic and genetic variation within a population have received long-term attention in evolutionary biology. Here the genetic basis and evolution of the geographically widespread variation in twig trichome color (from red to white) in a shrub Melastoma normale was investigated using Pool-seq and evolutionary analyses. RESULTS The results show that the twig trichome coloration is under selection in different light environments and that a 6-kb region containing an R2R3 MYB transcription factor gene is the major region of divergence between the extreme red and white morphs. This gene has two highly divergent groups of alleles, one of which likely originated from introgression from another species in this genus and has risen to high frequency (> 0.6) within each of the three populations under investigation. In contrast, polymorphisms in other regions of the genome show no sign of differentiation between the two morphs, suggesting that genomic patterns of diversity have been shaped by homogenizing gene flow. Population genetics analysis reveals signals of balancing selection acting on this gene, and it is suggested that spatially varying selection is the most likely mechanism of balancing selection in this case. CONCLUSIONS This study demonstrate that polymorphisms on a single transcription factor gene largely confer the twig trichome color variation in M. normale, while also explaining how adaptive divergence can occur and be maintained in the face of gene flow.
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Affiliation(s)
- Guilian Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Wei Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yongmei Chen
- College of Chemical Engineering, Sichuan University of Science & Engineering, Zigong, Sichuan, 643000, China
| | - Xueke Zhi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Peishan Zou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zulin Ning
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, 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
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Shulin Deng
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, 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, 510275, China.
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Gong L, Ding X, Guan W, Zhang D, Zhang J, Bai J, Xu W, Huang J, Qiu X, Zheng X, Zhang D, Li S, Huang Z, Su H. Comparative chloroplast genome analyses of Amomum: insights into evolutionary history and species identification. BMC PLANT BIOLOGY 2022; 22:520. [PMID: 36352400 PMCID: PMC9644571 DOI: 10.1186/s12870-022-03898-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Species in genus Amomum always have important medicinal and economic values. Classification of Amomum using morphological characters has long been a challenge because they exhibit high similarity. The main goals of this study were to mine genetic markers from cp genomes for Amomum species identification and discover their evolutionary history through comparative analysis. RESULTS Three species Amomum villosum, Amomum maximum and Amomum longipetiolatum were sequenced and annotated for the complete chloroplast (cp) genomes, and the cp genomes of A. longipetiolatum and A. maximum were the first reported. Three cp genomes exhibited typical quadripartite structures with 163,269-163,591 bp in length. Each genome encodes 130 functional genes including 79 protein-coding, 26 tRNAs and 3 rRNAs genes. 113-152 SSRs and 99 long repeats were identified in the three cp genomes. By designing specific primers, we amplified the highly variable loci and the mined genetic marker ccsA exhibited a relatively high species identification resolution in Amomum. The nonsynonymous and synonymous substitution ratios (Ka/Ks) in Amomum and Alpinia showed that most genes were subjected to a purifying selection. Phylogenetic analysis revealed the evolutionary relationships of Amomum and Alpinia species and proved that Amomum is paraphyletic. In addition, the sequenced sample of A. villosum was found to be a hybrid, becoming the first report of natural hybridization of this genus. Meanwhile, the high-throughput sequencing-based ITS2 analysis was proved to be an efficient tool for interspecific hybrid identification and with the help of the chloroplast genome, the hybrid parents can be also be determined. CONCLUSION The comparative analysis and mined genetic markers of cp genomes were conducive to species identification and evolutionary relationships of Amomum.
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Affiliation(s)
- Lu Gong
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiaoxia Ding
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Wan Guan
- Luqiao Hospital, Taizhou Enze Medical Center (Group), Taizhou, Zhejiang, China
| | - Danchun Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
| | - Jing Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Junqi Bai
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Wen Xu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Juan Huang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiaohui Qiu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiasheng Zheng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Danyan Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Shijie Li
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhihai Huang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China.
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China.
| | - He Su
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China.
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China.
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Rosazlina R, Jacobsen N, Ørgaard M, Othman AS. Molecular evidence of the hybrid origin of Cryptocoryne ×purpurea Ridl. nothovar. purpurea (Araceae). PLoS One 2021; 16:e0239499. [PMID: 33476321 PMCID: PMC7819605 DOI: 10.1371/journal.pone.0239499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/12/2020] [Indexed: 11/18/2022] Open
Abstract
Natural hybridization has been considered a source of taxonomic complexity in Cryptocoryne. A combined study of DNA sequencing data from the internal transcribed spacer (ITS) of nuclear ribosomal DNA and the trnK-matK region of chloroplast DNA was used to identify the parents of Cryptocoryne putative hybrids from Peninsular Malaysia. Based on the intermediate morphology and sympatric distribution area, the plants were tentatively identified as the hybrid Cryptocoryne ×purpurea nothovar. purpurea. The plants were pollen sterile and had long been considered as hybrids, supposedly between two related and co-existing species, C. cordata var. cordata and C. griffithii. The status of C. ×purpurea nothovar. purpurea was independently confirmed by the presence of an additive ITS sequence pattern from these two parental species in hybrid individuals. An analysis of the chloroplast trnK-matK sequences showed that the hybridization is bidirectional with the putative hybrids sharing identical sequences from C. cordata var. cordata and C. griffithii, indicating that both putative parental species had been the maternal parent in different accessions.
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Affiliation(s)
- Rusly Rosazlina
- School of Biological Sciences, University Sains Malaysia, Minden, Penang, Malaysia
- * E-mail: (RR); (ASO)
| | - Niels Jacobsen
- Department of Plant and Environmental Sciences, Section of Organismal Biology, Faculty of Science, University of Copenhagen, Frederiksberg C, Copenhagen, Denmark
| | - Marian Ørgaard
- Department of Plant and Environmental Sciences, Section of Organismal Biology, Faculty of Science, University of Copenhagen, Frederiksberg C, Copenhagen, Denmark
| | - Ahmad Sofiman Othman
- School of Biological Sciences, University Sains Malaysia, Minden, Penang, Malaysia
- * E-mail: (RR); (ASO)
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Beirinckx L, Vanschoenwinkel B, Triest L. Hidden Hybridization and Habitat Differentiation in a Mediterranean Macrophyte, the Euryhaline Genus Ruppia. FRONTIERS IN PLANT SCIENCE 2020; 11:830. [PMID: 32754168 PMCID: PMC7366321 DOI: 10.3389/fpls.2020.00830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
In many aquatic plant taxa, classification based on morphology has always been difficult. Molecular markers revealed that the complexity in several of these aquatic taxa could be addressed to recurrent hybridization events and cryptic species diversity. The submerged macrophyte genus Ruppia is one of these aquatic genera with a complex taxonomy due to the absence of clear distinguishable traits and several hybridization events. Two species co-exist throughout Europe, R. maritima and R. spiralis (previously known as R. cirrhosa), but recent molecular studies also found several indications of hybridization, introgression and chloroplast capture between these species. However, the full extent and frequency of hybridization and introgression in this genus has not been studied so far, nor is it clear how these hybrid lineages can co-exist locally with their parental species. In this paper, we wanted to detect whether a single coastal wetland where both species co-exist can act as a Ruppia hybrid zone. As a case study, we chose the Camargue, a Mediterranean coastal wetland that harbors a wide diversity in aquatic habitats, especially in terms of salinity and hydro-regime. We sampled several Ruppia populations within this wetland. To identify each sample and reconstruct the local genetic structure of the two parental species and their hybrids, we used both chloroplast and nuclear microsatellite markers. Afterward, we tested whether different species had different habitat preferences. Our results confirmed that R. maritima and R. spiralis are two strongly divergent species with different reproductive ecologies and different habitat preferences. This prevents frequent hybridization and consequently we could not detect any trace of a recent hybridization event. However, we found several populations of later-generation hybrids, including a population of R. maritima x hybrid backcrosses. The hybrid populations occupy a different habitat and are genetically distinct from their parental species, although they tend to be morphological similar to parental R. maritima. Although local hybridization and introgression in Ruppia is less frequent than we expected, the taxonomy of Ruppia is complicated due to ancient hybridizations and several back-crossings.
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Affiliation(s)
- Lise Beirinckx
- Ecology and Biodiversity Research Group, Plant Biology and Nature Management, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Bram Vanschoenwinkel
- Community Ecology Laboratory, Department of Biology, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Centre for Environmental Management, University of the Free State, Bloemfontein, South Africa
| | - Ludwig Triest
- Ecology and Biodiversity Research Group, Plant Biology and Nature Management, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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Dai JH, Zhou QJ, Zhou RC, Liu Y. A new species of Bredia (Sonerileae, Melastomataceae) from Sichuan, China. PHYTOKEYS 2020; 152:1-14. [PMID: 32714011 PMCID: PMC7351796 DOI: 10.3897/phytokeys.152.53512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Bredia hispida (Sonerileae, Melastomataceae), a species occurring in southeastern Sichuan, China, is newly described based on morphological and molecular data. The generic placement of B. hispida is well supported by phylogenetic analysis and morphological characters, including basally cordate, hairy leaf blade, cymose inflorescence, basally gibbous anthers and enlarged ovary crown enclosing an inverted frustum-shaped depression. Both molecular and morphological divergence showed that B. hispida is well separated from its close relatives, justifying its recognition as a distinct species. The new species resembles B. repens, B. changii and B. guidongensis in the prostrate habit and isomorphic stamens but differs markedly in the unequal opposed leaves, the 2-4 mm long, stout bristles on the adaxial surface of leaf blade and acuminate leaf apex. Bredia hispida co-occurs with B. esquirolii in the wild. No morphologically putative hybrids between them were observed despite their overlap in flowering season. The isolating mechanism remains unclear, pending further investigation.
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Affiliation(s)
- Jin-Hong Dai
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, No. 135, Xin-Gang-Xi Road, Guangzhou 510275, ChinaSun Yat-sen UniversityGuangzhouChina
| | - Qiu-Jie Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, No. 135, Xin-Gang-Xi Road, Guangzhou 510275, ChinaSun Yat-sen UniversityGuangzhouChina
| | - Ren-Chao Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, No. 135, Xin-Gang-Xi Road, Guangzhou 510275, ChinaSun Yat-sen UniversityGuangzhouChina
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, No. 135, Xin-Gang-Xi Road, Guangzhou 510275, ChinaSun Yat-sen UniversityGuangzhouChina
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Zhou Q, Lin CW, Ng WL, Dai J, Denda T, Zhou R, Liu Y. Analyses of Plastome Sequences Improve Phylogenetic Resolution and Provide New Insight Into the Evolutionary History of Asian Sonerileae/Dissochaeteae. FRONTIERS IN PLANT SCIENCE 2019; 10:1477. [PMID: 31824528 PMCID: PMC6881482 DOI: 10.3389/fpls.2019.01477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/24/2019] [Indexed: 05/31/2023]
Abstract
Sonerileae/Dissochaeteae (Melastomataceae) comprises ca. 50 genera, two thirds of which occur in Southeast Asia. Phylogenetic relationships within this clade remain largely unclear, which hampers our understanding of its origin, evolution, and biogeography. Here, we explored the use of chloroplast genomes in phylogenetic reconstruction of Sonerileae/Dissochaeteae, by sampling 138 species and 23 genera in this clade. A total of 151 complete plastid genomes were assembled for this study. Plastid genomic data provided better support for the backbone of the Sonerileae/Dissochaeteae phylogeny, and also for relationships among most closely related species, but failed to resolve the short internodes likely resulted from rapid radiation. Trees inferred from plastid genome and nrITS sequences were largely congruent regarding the major lineages of Sonerileae/Dissochaeteae. The present analyses recovered 15 major lineages well recognized in both nrITS and plastid phylogeny. Molecular dating and biogeographical analyses indicated a South American origin for Sonerileae/Dissochaeteae during late Eocene (stem age: 34.78 Mya). Two dispersal events from South America to the Old World were detected in late Eocene (33.96 Mya) and Mid Oligocene (28.33 Mya) respectively. The core Asian clade began to diversify around early Miocene in Indo-Burma and dispersed subsequently to Malesia and Sino-Japanese regions, possibly promoted by global temperature changes and East Asian monsoon activity. Our analyses supported previous hypothesis that Medinilla reached Madagascar by transoceanic dispersal in Miocene. In addition, generic limits of some genera concerned were discussed.
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Affiliation(s)
- Qiujie Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Che-Wei Lin
- Division of Botanical Garden, Herbarium of Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Malaysia
| | - Jinhong Dai
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tetsuo Denda
- Laboratory of Ecology and Systematics, Faculty of Science, University of the Ryukyus, Nishihara, Japan
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Zheng X, Ren C, Huang S, Li J, Zhao Y. Structure and features of the complete chloroplast genome of Melastoma dodecandrum. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:1043-1054. [PMID: 31404219 PMCID: PMC6656900 DOI: 10.1007/s12298-019-00651-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/27/2018] [Accepted: 02/19/2019] [Indexed: 05/29/2023]
Abstract
Melastoma dodecandrum, the only creeping species in the Melastoma genus, serves as a medicinal herb in southeast China. It belongs to the huge family Melastomataceae, which contains over 5000 species worldwide. In this study, we used next-generation sequencing to determine the complete chloroplast genome sequences of M. dodecandrum, which is a circular molecule of 156,611 bp in length. After annotation, we identified 131 putative genes in total, comprised of 85 protein-coding genes, 38 transfer RNA genes and 8 ribosomal RNA genes. Genome structure, GC content, repeat sequences and codon usage were investigated to gain a comprehensive understanding of this genome. Furthermore, we conducted comparative genome analyses between the M. dodecandrum genome and that of four other Melastomataceae species. Additionally, a phylogenetic analysis was performed based on available chloroplast genomes of Melastomataceae species and several Myrtaceae species, revealing the taxonomic relationships between M. dodecandrum and related species. In conclusion, our study represents the first look into the complete chloroplast genome of M. dodecandrum, providing abundant information for further studies such as species identification, taxonomy and phylogenetic resolution of Melastomataceae species.
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Affiliation(s)
- Xiasheng Zheng
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Changwei Ren
- Department of Cardiovascular Surgery Center, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029 China
| | - Song Huang
- DNA Barcoding Laboratory for TCM Authentication, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Jing Li
- Traditional Chinese Medicine Gynecology Laboratory in Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
| | - Ying Zhao
- Traditional Chinese Medicine Gynecology Laboratory in Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510006 China
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Wu R, Zou P, Tan G, Hu Z, Wang Y, Ning Z, Wu W, Liu Y, He S, Zhou R. Molecular identification of natural hybridization between Melastoma malabathricum and Melastoama beccarianum in Sarawak, Malaysia. Ecol Evol 2019; 9:5766-5776. [PMID: 31160997 PMCID: PMC6540941 DOI: 10.1002/ece3.5160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 03/16/2019] [Accepted: 03/18/2019] [Indexed: 12/27/2022] Open
Abstract
Hybridization is very common in flowering plants and it plays a significant role in plant evolution and adaptation. Melastoma L. (Melastomataceae) comprises about 80-90 species in tropical Asia and Oceania, among which 41 species occur in Borneo. Natural hybridization is frequently reported in Melastoma in China, but so far there have been no confirmed cases of hybridization in Southeast Asia (including Borneo), where most species occur. Here, we identified a case of natural hybridization between Melastoma malabathricum L. and Melastoma beccarianum Cogn. in Sarawak, Malaysia, by using sequence data of three nuclear genes and one chloroplast intergenic spacer. Melastoma malabathricum is the most widespread species of this genus, occurring in almost the whole range of this genus, while M. beccarianum is a local species endemic to northern Borneo. Our results showed that natural hybridization and introgression occur between M. malabathricum and M. beccarianum, and the introgression was asymmetrical, mainly from M. malabathricum to M. beccarianum. As adaptive traits can be transferred by introgression, our study suggests that natural hybridization should be a significant mechanism for the evolution and adaptation of Melastoma in Southeast Asia. However, introgression from the common species M. malabathricum to the relatively rare species M. beccarianum may cause the decline of M. beccarianum, incurring conservation concern. With a large number of species of Melastoma and almost year-around flowering in Southeast Asia, more cases of natural hybridization are expected to be found and identified in near future.
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Affiliation(s)
- Renzhi Wu
- College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
| | - Peishan Zou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Guangwen Tan
- Pubang Landscape Architecture Co., LtdGuangzhouChina
| | - Zhenyang Hu
- Pubang Landscape Architecture Co., LtdGuangzhouChina
| | - Yongqi Wang
- Pubang Landscape Architecture Co., LtdGuangzhouChina
| | - Zulin Ning
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Wei Wu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Shaoyun He
- College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
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Ng WL, Wu W, Zou P, Zhou R. Comparative transcriptomics sheds light on differential adaptation and species diversification between two Melastoma species and their F 1 hybrid. AOB PLANTS 2019; 11:plz019. [PMID: 31037213 PMCID: PMC6481908 DOI: 10.1093/aobpla/plz019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 03/27/2019] [Indexed: 06/09/2023]
Abstract
Variation in gene expression has been shown to promote adaptive divergence, and can lead to speciation. The plant genus Melastoma, thought to have diversified through adaptive radiation, provides an excellent model for the study of gene expressional changes during adaptive differentiation and following interspecific hybridization. In this study, we performed RNA-seq on M. candidum, M. sanguineum and their F1 hybrid, to investigate the role of gene expression in species diversification within the genus. Reference transcriptomes were assembled using combined data from both parental species, resulting in 50 519 and 48 120 transcripts for the leaf and flower petal, after removing redundancy. Differential expression analysis uncovered 3793 and 2116 differentially expressed (DE) transcripts, most of which are between M. candidum and M. sanguineum. Differential expression was observed for genes related to light responses, as well as genes that regulate the development of leaf trichomes, a trait that among others is thought to protect plants against sunlight, suggesting the differential adaptation of the species to sunlight intensity. The analysis of positively selected genes between the two species also revealed possible differential adaptation to other abiotic stresses such as drought and temperature. In the hybrid, almost all possible modes of expression were observed at the DE transcripts, although at most transcripts, the expression levels were similar to that of either parent instead of being intermediate. A small number of transgressively expressed transcripts that matched genes known to promote plant growth and adaptation to stresses in new environments were also found, possibly explaining the vigour observed in the hybrid. The findings in this study provided insights into the role of gene expression in the diversification of Melastoma, which we believe is an important example for more cross-taxa comparisons in the future.
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Affiliation(s)
- Wei Lun Ng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Selangor, Malaysia
| | - Wei Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Peishan Zou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
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Dai JH, Lin CW, Zhou QJ, Li CM, Zhou RC, Liu Y. The specific status of Melastoma kudoi (Melastomataceae, Melastomeae). BOTANICAL STUDIES 2019; 60:5. [PMID: 30923953 PMCID: PMC6439000 DOI: 10.1186/s40529-019-0253-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/16/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND Melastoma has undergone rapid species radiation during the last one million years, and circumscription of some species in the genus has remained controversial. Melastoma kudoi, an erect species narrowly endemic to central Taiwan was previously treated as a synonym of M. intermedium, a semicreeping hybrid between the erect species M. candidum and the creeping M. dodecandrum, making its identity questionable. We addressed this question based on molecular and morphological data. RESULTS Phylogenetic analyses based on nrITS sequence data revealed that M. kudoi is most closely related to M. dodecandrum. Further analyses of six nuclear genes (cam, chi, gapC, gbss, tpi and vr) and two chloroplast markers (trnL-trnF and psbA) showed that M. kudoi is well diverged from its close relatives. Morphologically, it is also easily distinguished from related species by its erect habit, center-positioned stigma, and spreading, basally enlarged hairs on the hypanthium. CONCLUSIONS Both molecular phylogenetic and morphological data suggest that M. kudoi is well separated from M. intermedium, M. dodecandrum, and O. scaberrima, and should be treated as a distinct species. Taxonomic treatment and detailed description of M. kudoi are provided.
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Affiliation(s)
- Jin-Hong Dai
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Che-Wei Lin
- Herbarium of Taiwan Forestry Research Institute, No. 53, Nan-Hai Road, Taipei, 100 Taiwan
| | - Qiu-Jie Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Chun-Mei Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Ren-Chao Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
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Dai JH, Zhou QJ, Yu ZY, Zhou RC, Liu Y. A new species of Fordiophyton (Sonerileae, Melastomataceae) from Yunnan, China. PHYTOKEYS 2019; 122:15-28. [PMID: 31182906 PMCID: PMC6548766 DOI: 10.3897/phytokeys.122.35260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 04/25/2019] [Indexed: 05/12/2023]
Abstract
Fordiophytonjinpingense (Melastomataceae; Sonerileae), a species occurring in south-eastern Yunnan, China, is described as new, based on morphological and molecular data. Phylogenetic analyses, based on nrITS sequence data, showed that, except F.breviscapum, all species sampled in Fordiophyton formed a strongly supported clade in which two geographical lineages were recovered. The generic placement of F.jinpingense is well supported by phylogenetic analyses and a character combination of 4-merous flowers, distinctly dimorphic stamens and the connectives basally not calcarate. Molecular divergence and morphological evidence indicate that F.jinpingense is well separated from other members of the genus, thus justifying its recognition as a distinct species. Fordiophytonjinpingense is phylogenetically closest to F.repens, but differs markedly from the latter in stem morphology (short, obtusely 4-sided vs. long, 4-angular), habit (erect vs. creeping), leaf size (6-16.5 × 4.5-13 cm vs. 4-7.5 × 4-6.5 cm) and flower number per inflorescence (5-13 vs. 3-6).
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Affiliation(s)
- Jin-Hong Dai
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, No. 135, Xin-Gang-Xi Road, Guangzhou 510275, ChinaSun Yat-sen UniversityGuangzhouChina
| | - Qiu-Jie Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, No. 135, Xin-Gang-Xi Road, Guangzhou 510275, ChinaSun Yat-sen UniversityGuangzhouChina
| | - Zhi-Yong Yu
- Management Bureau of Fenshuiling National Nature Reserve, Jinping 661500, ChinaManagement Bureau of Fenshuiling National Nature ReserveJinpingChina
| | - Ren-Chao Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, No. 135, Xin-Gang-Xi Road, Guangzhou 510275, ChinaSun Yat-sen UniversityGuangzhouChina
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, No. 135, Xin-Gang-Xi Road, Guangzhou 510275, ChinaSun Yat-sen UniversityGuangzhouChina
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