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Lubna, Asaf S, Jan R, Asif S, Bilal S, Khan AL, Al-Rawahi AN, Kim KM, Al-Harrasi A. The complete plastome sequences of invasive weed Parthenium hysterophorus: genome organization, evolutionary significance, structural features, and comparative analysis. Sci Rep 2024; 14:4006. [PMID: 38369569 PMCID: PMC10874969 DOI: 10.1038/s41598-024-54503-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/13/2024] [Indexed: 02/20/2024] Open
Abstract
Parthenium hysterophorus, a globally widespread weed, poses a significant threat to agricultural ecosystems due to its invasive nature. We investigated the chloroplast genome of P. hysterophorus in this study. Our analysis revealed that the chloroplast genome of P. hysterophorus spans a length of 151,881 base pairs (bp). It exhibits typical quadripartite structure commonly found in chloroplast genomes, including inverted repeat regions (IR) of 25,085 bp, a small single copy (SSC) region of 18,052 bp, and a large single copy (LSC) region of 83,588 bp. A total of 129 unique genes were identified in P. hysterophorus chloroplast genomes, including 85 protein-coding genes, 36 tRNAs, and eight rRNAs genes. Comparative analysis of the P. hysterophorus plastome with those of related species from the tribe Heliantheae revealed both conserved structures and intriguing variations. While many structural elements were shared among the species, we identified a rearrangement in the large single-copy region of P. hysterophorus. Moreover, our study highlighted notable gene divergence in several specific genes, namely matK, ndhF, clpP, rps16, ndhA, rps3, and ndhD. Phylogenetic analysis based on the 72 shared genes placed P. hysterophorus in a distinct clade alongside another species, P. argentatum. Additionally, the estimated divergence time between the Parthenium genus and Helianthus (sunflowers) was approximately 15.1 million years ago (Mya). These findings provide valuable insights into the evolutionary history and genetic relationships of P. hysterophorus, shedding light on its divergence and adaptation over time.
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Affiliation(s)
- Lubna
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
| | - Rahmatullah Jan
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Saleem Asif
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Saqib Bilal
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
| | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Sugar Land, TX, 77479, USA
| | - Ahmed N Al-Rawahi
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Kyung-Min Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
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Hamidzadeh Moghadam S, Alebrahim MT, Mohebodini M, MacGregor DR. Genetic variation of Amaranthus retroflexus L. and Chenopodium album L. (Amaranthaceae) suggests multiple independent introductions into Iran. FRONTIERS IN PLANT SCIENCE 2023; 13:1024555. [PMID: 36684720 PMCID: PMC9847890 DOI: 10.3389/fpls.2022.1024555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Amaranthus retroflexus L. and Chenopodium album L. (Amaranthaceae) are weedy plants that cause severe ecological and economic damage. In this study, we collected DNA from three different countries and assessed genetic diversity using inter-simple sequence repeat (ISSR) markers. Our analysis shows both weed species have low genetic diversity within a population and high genetic diversity among populations, as well as a low value of gene flow among the populations. UPGMA clustering and principal coordinate analysis indicate four distinct groups for A. retroflexus L. and C. album L. exist. We detected significant isolation-by-distance for A. retroflexus L. and no significant correlation for C.album L. These conclusions are based data from 13 ISSR primers where the average percentage of polymorphism produced was 98.46% for A. retroflexus L. and 74.81% for C. album L.These data suggest that each population was independently introduced to the location from which it was sampled and these noxious weeds come armed with considerable genetic variability giving them the opportunity to manifest myriad traits that could be used to avoid management practices. Our results, albeit not definitive about this issue, do not support the native status of C. album L. in Iran.
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Affiliation(s)
| | | | - Mehdi Mohebodini
- Department of Horticultural Sciences, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Dana R. MacGregor
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, United Kingdom
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Liu RL, Yang YB, Lee BR, Liu G, Zhang WG, Chen XY, Song XJ, Kang JQ, Zhu ZH. The dispersal-related traits of an invasive plant Galinsoga quadriradiata correlate with elevation during range expansion into mountain ranges. AOB PLANTS 2021; 13:plab008. [PMID: 34194688 PMCID: PMC8237851 DOI: 10.1093/aobpla/plab008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Detecting shifts in trait values among populations of an invasive plant is important for assessing invasion risks and predicting future spread. Although a growing number of studies suggest that the dispersal propensity of invasive plants increases during range expansion, there has been relatively little attention paid to dispersal patterns along elevational gradients. In this study, we tested the differentiation of dispersal-related traits in an invasive plant, Galinsoga quadriradiata, across populations at different elevations in the Qinling and Bashan Mountains in central China. Seed mass-area ratio (MAR), an important seed dispersal-related trait, of 45 populations from along an elevational gradient was measured, and genetic variation of 23 populations was quantified using inter-simple sequence repeat (ISSR) markers. Individuals from four populations were then planted in a greenhouse to compare their performance under shared conditions. Changing patterns of seed dispersal-related traits and populations genetic diversity along elevation were tested using linear regression. Mass-area ratio of G. quadriradiata increased, while genetic diversity decreased with elevation in the field survey. In the greenhouse, populations of G. quadriradiata sourced from different elevations showed a difference response of MAR. These results suggest that although rapid evolution may contribute to the range expansion of G. quadriradiata in mountain ranges, dispersal-related traits will also likely be affected by phenotypic plasticity. This challenges the common argument that dispersal ability of invasive plants increases along dispersal routes. Furthermore, our results suggest that high-altitude populations would be more effective at seed dispersal once they continue to expand their range downslope on the other side. Our experiment provides novel evidence that the spread of these high-altitude populations may be more likely than previously theorized and that they should thus be cautiously monitored.
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Affiliation(s)
- Rui-Ling Liu
- College of Life Sciences, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
| | - Ying-Bo Yang
- College of Life Sciences, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
| | - Benjamin R Lee
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gang Liu
- College of Life Sciences, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
| | - Wen-Gang Zhang
- College of Life Sciences, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
| | - Xiao-Yan Chen
- College of Life Sciences, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
| | - Xing-Jiang Song
- College of Life Sciences, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
| | - Ju-Qing Kang
- College of Life Sciences, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
| | - Zhi-Hong Zhu
- College of Life Sciences, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
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Nazareno AG, Neto LM, Buzatti RSDO, van den Berg C, Forzza RC. Four raised to one equals one: A genetic approach to the Pseudolaelia vellozicola complex does not follow a math rule. Ecol Evol 2020; 10:4562-4569. [PMID: 32551043 PMCID: PMC7297771 DOI: 10.1002/ece3.6148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 01/31/2020] [Accepted: 02/10/2020] [Indexed: 11/20/2022] Open
Abstract
Pseudolaelia is a genus endemic to the eastern Brazilian Atlantic Forest, consisting of 12 accepted species. Some Pseudolaelia species, such as P. vellozicola, P. aguadocensis, P. oliveirana, and P. regentii, referred to here as the PV complex, present extensive intra- and interpopulation morphological polymorphism, raising uncertainty regarding their circumscriptions. Although previous morphological analyses were used to solve the generic boundaries in the PV complex, persuasive genetic evidence is lacking. In order to test the hypothesis that the group under investigation contains only one taxon, amplification profiles of five intersimple sequence repeat (ISSR) markers were used to evaluate genetic diversity, genetic structure, and the relationships among the PV complex species. A total of 134 reproductive individuals were sampled in eight insular populations. Intrapopulation genetic analysis indicated low levels of genetic diversity. Analysis of genetic structure revealed that each of the eight sample locations can be considered unique biological populations as they are highly differentiated from each other. The Mantel test showed a high and positive correlation between genetic and geographic distance (r = .841, p < .002), indicating isolation by distance. The results are consistent with that expected for plants with insular geographical distribution. When testing for the null hypothesis, the low levels of genetic variation among species (F CT = 0.155) suggest that the populations constitute only one highly polymorphic species with a wide distribution.
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Affiliation(s)
| | | | | | - Cássio van den Berg
- Department of Biological SciencesUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
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Shang L, Li LF, Song ZP, Wang Y, Yang J, Wang CC, Qiu SY, Huang JX, Nie M, Wolfe LM, Li B. High Genetic Diversity With Weak Phylogeographic Structure of the Invasive Spartina alterniflora (Poaceae) in China. FRONTIERS IN PLANT SCIENCE 2019; 10:1467. [PMID: 31850008 PMCID: PMC6896949 DOI: 10.3389/fpls.2019.01467] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
Biological invasion represents a global issue of concern due to its large negative impacts on native ecosystems and society. Elucidating the evolutionary history and genetic basis underpinning invasiveness is critical to understanding how alien species invade and adapt to novel environments. Smooth cordgrass (Spartina alterniflora, 2n = 6x = 62) is a notorious invasive species that causes heavily negative effects on native ecosystems worldwide. Here we addressed the evolutionary mechanisms underlying the invasion and dispersal history of this species along the China coast in the past decades. We employed nine microsatellites and three chloroplast fragments to investigate phylogeographic structure and genetic diversity of 11 native US and 11 invasive Chinese S. alterniflora populations. Demographic history simulation was also performed for both the native and invasive populations, respectively. Comparative genetic analyses of these natural populations revealed that although all the Chinese populations were introduced only once, high level of genetic diversity with weak geographic structure was observed. In particular, both the genetic features and mathematical simulation illustrated very recent population expansion in the Chinese populations. We found that genetic variants identified in native US populations were mixed in the Chinese populations, suggesting the recombination of these original variants during the invasion process. These genetic attributes indicate that Chinese populations might not have experienced a genetic bottleneck during the invasion process. High genetic diversity and genetic admixture might have contributed to the success of invasion of S. alterniflora in China. Our study provides a framework of how the smooth cordgrass spreads along the China coast as well as its potential genetic mechanisms underlying the invasion.
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Affiliation(s)
- Lei Shang
- Coastal Ecosystems Research Station of Yangtze River Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Eco-Chongming (IEC), Fudan University, Shanghai, China
- Institute of Forensic Science, Ministry of Public Security, Beijing, China
| | - Lin-Feng Li
- Coastal Ecosystems Research Station of Yangtze River Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Eco-Chongming (IEC), Fudan University, Shanghai, China
| | - Zhi-Ping Song
- Coastal Ecosystems Research Station of Yangtze River Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Eco-Chongming (IEC), Fudan University, Shanghai, China
| | - Yi Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ji Yang
- Key Laboratory of Biodiversity and Evolution, Fudan University, Shanghai, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, China
| | - Shi-Yun Qiu
- Coastal Ecosystems Research Station of Yangtze River Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Eco-Chongming (IEC), Fudan University, Shanghai, China
| | - Jing-Xin Huang
- Coastal Ecosystems Research Station of Yangtze River Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Eco-Chongming (IEC), Fudan University, Shanghai, China
- School of Energy and Environment Science, Yunan Normal University, Kunming, China
| | - Ming Nie
- Coastal Ecosystems Research Station of Yangtze River Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Eco-Chongming (IEC), Fudan University, Shanghai, China
| | - Lorne M. Wolfe
- Coastal Ecosystems Research Station of Yangtze River Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Eco-Chongming (IEC), Fudan University, Shanghai, China
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, South Africa
| | - Bo Li
- Coastal Ecosystems Research Station of Yangtze River Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Eco-Chongming (IEC), Fudan University, Shanghai, China
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Why are tall-statured energy grasses of polyploid species complexes potentially invasive? A review of their genetic variation patterns and evolutionary plasticity. Biol Invasions 2019. [DOI: 10.1007/s10530-019-02053-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Riverón-Giró FB, Raventós J, Damon A, García-González A, Mújica E. Spatio-temporal dynamics of the invasive orchid Oeceoclades maculata (Orchidaceae), in four different habitats in southeast Chiapas, Mexico. Biol Invasions 2019. [DOI: 10.1007/s10530-019-01945-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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