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Huang Y, Cao J, Zhao M, Guo J, Li J, Wang R. The complete chloroplast genome sequence of an invasive plant, Tragopogon dubius Scopoli (asteraceae). Mitochondrial DNA B Resour 2024; 9:352-356. [PMID: 38487811 PMCID: PMC10939102 DOI: 10.1080/23802359.2024.2329668] [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: 01/03/2024] [Accepted: 03/07/2024] [Indexed: 03/17/2024] Open
Abstract
Tragopogon dubius Scopoli is native to Europe and western Asia and is considered an invasive plant in China. In this study, the complete chloroplast genome of T. dubius was obtained using high-throughput next-generation sequencing technology. The whole chloroplast genome was 153,017 bp long with a GC content of 38% and comprised 130 genes (86 protein-coding genes, 36 tRNA genes, and 8 rRNA genes). Phylogenetic analysis based on the concatenated chloroplast protein-coding sequences showed that T. dubius is most closely related to Tragopogon pratensis. This study provides valuable genetic data for further phylogenetic analysis and molecular identification of species in the genus Tragopogon.
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Affiliation(s)
- Yue Huang
- College of Life Science, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingjing Cao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengxin Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianying Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiamei Li
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Rui Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Ruan X, Wang Z, Su Y, Wang T. Population Genomics Reveals Gene Flow and Adaptive Signature in Invasive Weed Mikania micrantha. Genes (Basel) 2021; 12:1279. [PMID: 34440453 PMCID: PMC8394975 DOI: 10.3390/genes12081279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 11/28/2022] Open
Abstract
A long-standing and unresolved issue in invasion biology concerns the rapid adaptation of invaders to nonindigenous environments. Mikania micrantha is a notorious invasive weed that causes substantial economic losses and negative ecological consequences in southern China. However, the contributions of gene flow, environmental variables, and functional genes, all generally recognized as important factors driving invasive success, to its successful invasion of southern China are not fully understood. Here, we utilized a genotyping-by-sequencing approach to sequence 306 M. micrantha individuals from 21 invasive populations. Based on the obtained genome-wide single nucleotide polymorphism (SNP) data, we observed that all the populations possessed similar high levels of genetic diversity that were not constrained by longitude and latitude. Mikania micrantha was introduced multiple times and subsequently experienced rapid-range expansion with recurrent high gene flow. Using FST outliers, a latent factor mixed model, and the Bayesian method, we identified 38 outlier SNPs associated with environmental variables. The analysis of these outlier SNPs revealed that soil composition, temperature, precipitation, and ecological variables were important determinants affecting the invasive adaptation of M. micrantha. Candidate genes with outlier signatures were related to abiotic stress response. Gene family clustering analysis revealed 683 gene families unique to M. micrantha which may have significant implications for the growth, metabolism, and defense responses of M. micrantha. Forty-one genes showing significant positive selection signatures were identified. These genes mainly function in binding, DNA replication and repair, signature transduction, transcription, and cellular components. Collectively, these findings highlight the contribution of gene flow to the invasion and spread of M. micrantha and indicate the roles of adaptive loci and functional genes in invasive adaptation.
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Affiliation(s)
- Xiaoxian Ruan
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (X.R.); (Z.W.)
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (X.R.); (Z.W.)
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (X.R.); (Z.W.)
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen 518057, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou 510641, China
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Banerjee AK, Hou Z, Lin Y, Lan W, Tan F, Xing F, Li G, Guo W, Huang Y. Going with the flow: analysis of population structure reveals high gene flow shaping invasion pattern and inducing range expansion of Mikania micrantha in Asia. ANNALS OF BOTANY 2020; 125:1113-1126. [PMID: 32173740 PMCID: PMC7262463 DOI: 10.1093/aob/mcaa044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/12/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Mikania micrantha, a climbing perennial weed of the family Asteraceae, is native to Latin America and is highly invasive in the tropical belt of Asia, Oceania and Australia. This study was framed to investigate the population structure of M. micrantha at a large spatial scale in Asia and to identify how introduction history, evolutionary forces and landscape features influenced the genetic pattern of the species in this region. METHODS We assessed the genetic diversity and structure of 1052 individuals from 46 populations for 12 microsatellite loci. The spatial pattern of genetic variation was investigated by estimating the relationship between genetic distance and geographical, climatic and landscape resistances hypothesized to influence gene flow between populations. KEY RESULTS We found high genetic diversity of M. micrantha in this region, as compared with the genetic diversity parameters of other invasive species. Spatial and non-spatial clustering algorithms identified the presence of multiple genetic clusters and admixture between populations. Most of the populations showed heterozygote deficiency, primarily due to inbreeding, and the founder populations showed evidence of a genetic bottleneck. Persistent gene flow throughout the invasive range caused low genetic differentiation among populations and provided beneficial genetic variation to the marginal populations in a heterogeneous environment. Environmental suitability was found to buffer the detrimental effects of inbreeding at the leading edge of range expansion. Both linear and non-linear regression models demonstrated a weak relationship between genetic distance and geographical distance, as well as bioclimatic variables and environmental resistance surfaces. CONCLUSIONS These findings provide evidence that extensive gene flow and admixture between populations have influenced the current genetic pattern of M. micrantha in this region. High gene flow across the invaded landscape may facilitate adaptation, establishment and long-term persistence of the population, thereby indicating the range expansion ability of the species.
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Affiliation(s)
- Achyut Kumar Banerjee
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhuangwei Hou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuting Lin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wentao Lan
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fengxiao Tan
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fen Xing
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Guanghe Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wuxia Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Yelin Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- For correspondence. E-mail
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Unraveling the Chloroplast Genomes of Two Prosopis Species to Identify Its Genomic Information, Comparative Analyses and Phylogenetic Relationship. Int J Mol Sci 2020; 21:ijms21093280. [PMID: 32384622 PMCID: PMC7247323 DOI: 10.3390/ijms21093280] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/14/2020] [Accepted: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
Genus Prosopis (family Fabaceae) are shrubby trees, native to arid and semi-arid regions of Asia, Africa, and America and known for nitrogen fixation. Here, we have sequenced the complete chloroplast (cp) genomes of two Prosopis species (P. juliflora and P. cineraria) and compared them with previously sequenced P. glandulosa, Adenanthera microsperma, and Parkia javanica belonging to the same family. The complete genome sequences of Prosopis species and related species ranged from 159,389 bp (A. microsperma) to 163,677 bp (P. cineraria). The overall GC contents of the genomes were almost the similar (35.9–36.6%). The P. juliflora and P. cineraria genomes encoded 132 and 131 genes, respectively, whereas both the species comprised of 85 protein-coding genes higher than other compared species. About 140, 134, and 129 repeats were identified in P. juliflora, P. cineraria and P. glandulosa cp genomes, respectively. Similarly, the maximum number of simple sequence repeats were determined in P. juliflora (88), P. cineraria (84), and P. glandulosa (78). Moreover, complete cp genome comparison determined a high degree of sequence similarity among P. juliflora, P. cineraria, and P. glandulosa, however some divergence in the intergenic spacers of A. microsperma and Parkia javanica were observed. The phylogenetic analysis showed that P. juliflora is closer to P. cineraria than P. glandulosa.
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Zhang Q, Zhai J, Chen G, Lin W, Peng C. The Changing Distribution of Anthocyanin in Mikania micrantha Leaves as an Adaption to Low-Temperature Environments. PLANTS (BASEL, SWITZERLAND) 2019; 8:E456. [PMID: 31717889 PMCID: PMC6918224 DOI: 10.3390/plants8110456] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 10/24/2019] [Accepted: 10/24/2019] [Indexed: 11/23/2022]
Abstract
Anthocyanins, a protective substance in plant leaves, can accumulate in large quantities under low-temperature induction. In order to explore the effect of anthocyanins in Mikania micrantha leaves, the Rubisco, photosynthesis, pigments, and antioxidative capacity in mature leaves (ML) and young leaves (YL) of M. micrantha were investigated in winter. YL were red on both the adaxial and abaxial surfaces, while ML was red on the abaxial surfaces and green on the adaxial surfaces. Compared with ML, the relative expression of the genes related to anthocyanin synthesis and anthocyanin content were significantly higher in YL. Antioxidants such as flavonoids and total phenols were found in higher quantities, and the total antioxidant capacity was also significantly higher in YL. However, in ML, the Rubisco and chlorophyll content related to photosynthesis were significantly higher. The stomata of ML displayed a larger aperture than YL, and the stomatal conductance and photosynthetic rate were significantly higher in ML. The results suggested that M. micrantha leaves could better adapt to the winter environment through changing the distribution of anthocyanins in leaves of different maturity.
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Affiliation(s)
| | | | | | | | - Changlian Peng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (Q.Z.); (J.Z.); (G.C.); (W.L.)
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Zhang Q, Zhai J, Shao L, Lin W, Peng C. Accumulation of Anthocyanins: An Adaptation Strategy of Mikania micrantha to Low Temperature in Winter. FRONTIERS IN PLANT SCIENCE 2019; 10:1049. [PMID: 31555311 PMCID: PMC6726734 DOI: 10.3389/fpls.2019.01049] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/29/2019] [Indexed: 05/03/2023]
Abstract
The accumulation of anthocyanins in leaves and stems of Mikania micrantha improves its adaptability to low-temperature environments during winter in areas where this species is invasive. The accumulation of anthocyanins in M. micrantha causes the plants to exhibit red coloration when encountering low-temperature environments during winter. Many studies have reported that the accumulation of anthocyanins near the plant surface filters light and improves photoprotection. However, the results of this study showed that the main role of anthocyanins accumulation in M. micrantha during winter was to increase both antioxidant capability and tolerance to low temperature. The results showed that the anthocyanin contents were significantly higher in red leaves and stems than in green leaves and stems, with more than 60-fold greater content in red leaves than in green leaves. In addition, the total antioxidant capability was significantly greater in red leaves and stems than in green leaves and stems. After 4°C treatment for 12 h, a large amount of reactive oxygen species accumulated in green leaves and stems, and the maximum photochemical efficiency decreased significantly. Compared with that of the green leaves, the net photosynthetic rate of red leaves was significantly higher. The biomass statistics revealed that the dry matter accumulation of M. micrantha plants with relatively large amounts of anthocyanins was significantly greater than that of plants with relatively low anthocyanin levels during the same period. Our results suggest that the accumulation of anthocyanins during winter is an adaptation strategy of M. micrantha to low winter temperatures.
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Affiliation(s)
- Qilei Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Junjie Zhai
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Ling Shao
- College of Life Science, Zhao Qing University, Zhaoqing, China
| | - Wei Lin
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Changlian Peng
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
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Comparative transcriptome analysis of the invasive weed Mikania micrantha with its native congeners provides insights into genetic basis underlying successful invasion. BMC Genomics 2018; 19:392. [PMID: 29793434 PMCID: PMC5968712 DOI: 10.1186/s12864-018-4784-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/11/2018] [Indexed: 02/06/2023] Open
Abstract
Background Mikania micrantha H.B.K. (Asteraceae) is one of the world’s most invasive weeds which has been rapidly expanding in tropical Asia, including China, while its close relative M. cordata, the only Mikania species native to China, shows no harm to the local ecosystems. These two species are very similar in morphology but differ remarkably in several ecological and physiological traits, representing an ideal system for comparative analysis to investigate the genetic basis underlying invasion success. In this study, we performed RNA-sequencing on the invader M. micrantha and its native congener M. cordata in China, to unravel the genetic basis underlying the strong invasiveness of M. micrantha. For a more robust comparison, another non-invasive congener M. cordifolia was also sequenced and compared. Results A total of 52,179, 55,835, and 52,983 unigenes were obtained for M. micrantha, M. cordata, and M. cordifolia, respectively. Phylogenetic analyses and divergence time dating revealed a relatively recent split between M. micrantha and M. cordata, i.e., approximately 4.81 million years ago (MYA), after their divergence with M. cordifolia (8.70 MYA). Gene ontology classifications, pathway assignments and differential expression analysis revealed higher representation or significant up-regulation of genes associated with photosynthesis, energy metabolism, protein modification and stress response in M. micrantha than in M. cordata or M. cordifolia. Analysis of accelerated evolution and positive selection also suggested the importance of these related genes and processes to the adaptability and invasiveness of M. micrantha. Particularly, most (77 out of 112, i.e. 68.75%) positively selected genes found in M. micrantha could be classified into four groups, i.e., energy acquisition and utilization (10 genes), growth and reproduction (13 genes), protection and repair (34 genes), and signal transduction and expression regulation (20 genes), which may have contributed to the high adaptability of M. micrantha to various new environments and the capability to occupy a wider niche, reflected in its high invasiveness. Conclusions We characterized the transcriptomes of the invasive species M. micrantha and its non-invasive congeners, M. cordata and M. cordifolia. A comparison of their transcriptomes provided insights into the genetic basis of the high invasiveness of M. micrantha. Electronic supplementary material The online version of this article (10.1186/s12864-018-4784-9) contains supplementary material, which is available to authorized users.
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Liu W, Kong H, Zhou J, Fritsch PW, Hao G, Gong W. Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae. Int J Mol Sci 2018; 19:E1286. [PMID: 29693617 PMCID: PMC5983592 DOI: 10.3390/ijms19051286] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/16/2018] [Accepted: 04/19/2018] [Indexed: 11/17/2022] Open
Abstract
The subfamily Caesalpinioideae of the Fabaceae has long been recognized as non-monophyletic due to its controversial phylogenetic relationships. Cercis chuniana, endemic to China, is a representative species of Cercis L. placed within Caesalpinioideae in the older sense. Here, we report the whole chloroplast (cp) genome of C. chuniana and compare it to six other species from the Caesalpinioideae. Comparative analyses of gene synteny and simple sequence repeats (SSRs), as well as estimation of nucleotide diversity, the relative ratios of synonymous and nonsynonymous substitutions (dn/ds), and Kimura 2-parameter (K2P) interspecific genetic distances, were all conducted. The whole cp genome of C. chuniana was found to be 158,433 bp long with a total of 114 genes, 81 of which code for proteins. Nucleotide substitutions and length variation are present, particularly at the boundaries among large single copy (LSC), inverted repeat (IR) and small single copy (SSC) regions. Nucleotide diversity among all species was estimated to be 0.03, the average dn/ds ratio 0.3177, and the average K2P value 0.0372. Ninety-one SSRs were identified in C. chuniana, with the highest proportion in the LSC region. Ninety-seven species from the old Caesalpinioideae were selected for phylogenetic reconstruction, the analysis of which strongly supports the monophyly of Cercidoideae based on the new classification of the Fabaceae. Our study provides genomic information for further phylogenetic reconstruction and biogeographic inference of Cercis and other legume species.
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Affiliation(s)
- Wanzhen Liu
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Juan Zhou
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
| | - Peter W Fritsch
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX 76107, USA.
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
| | - Wei Gong
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
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