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Hodgins KA, Lai Z, Nurkowski K, Huang J, Rieseberg LH. The molecular basis of invasiveness: differences in gene expression of native and introduced common ragweed (Ambrosia artemisiifolia) in stressful and benign environments. Mol Ecol 2013; 22:2496-510. [PMID: 23294156 DOI: 10.1111/mec.12179] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 11/14/2012] [Accepted: 11/21/2012] [Indexed: 11/28/2022]
Abstract
Although the evolutionary and ecological processes that contribute to plant invasion have been the focus of much research, investigation into the molecular basis of invasion is just beginning. Common ragweed (Ambrosia artemisiifolia) is an annual weed native to North America and has been introduced to Europe where it has become invasive. Using a custom-designed NimbleGen oligoarray, we examined differences in gene expression between five native and six introduced populations of common ragweed in three different environments (control, light stress and nutrient stress), as well as two different time points. We identified candidate genes that may contribute to invasiveness in common ragweed based on differences in expression between native and introduced populations from Europe. Specifically, we found 180 genes where range explained a significant proportion of the variation in gene expression and a further 103 genes with a significant range by treatment interaction. Several of these genes are potentially involved in the metabolism of secondary compounds, stress response and the detoxification of xenobiotics. Previously, we found more rapid growth and greater reproductive success in introduced populations, particularly in benign and competitive (light stress) environments, and many of these candidate genes potentially underlie these growth differences. We also found expression differences among populations within each range, reflecting either local adaptation or neutral processes, although no associations with climate or latitude were identified. These data provide a first step in identifying genes that are involved with introduction success in an aggressive annual weed.
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Affiliation(s)
- Kathryn A Hodgins
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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Sun J, Wang M, Wang H, Zhang H, Zhang X, Thiyagarajan V, Qian PY, Qiu JW. De novo
assembly of the transcriptome of an invasive snail and its multiple ecological applications. Mol Ecol Resour 2012; 12:1133-44. [PMID: 22994926 DOI: 10.1111/1755-0998.12014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 08/08/2012] [Accepted: 08/14/2012] [Indexed: 11/28/2022]
Affiliation(s)
- J. Sun
- Department of Biology Hong Kong Baptist University Waterloo Road Hong Kong China
| | - M. Wang
- Department of Biology Hong Kong Baptist University Waterloo Road Hong Kong China
| | - H. Wang
- Division of Life Science Section of Marine Ecology and Biotechnology, Clear Water Bay Road The Hong Kong University of Science and Technology Hong Kong China
| | - H. Zhang
- Department of Biology Hong Kong Baptist University Waterloo Road Hong Kong China
| | - X. Zhang
- Laboratory of Disease Genomics and Individualized Medicine Beijing Institute of Genomics Chinese Academy of Sciences 7 Beitucheng West Road, Beijing 100029 China
| | - V. Thiyagarajan
- School of Biological Sciences and Swire Marine Institute The University of Hong Kong Pok Fu Lam Road Hong Kong China
| | - P. Y. Qian
- Division of Life Science Section of Marine Ecology and Biotechnology, Clear Water Bay Road The Hong Kong University of Science and Technology Hong Kong China
| | - J. W. Qiu
- Department of Biology Hong Kong Baptist University Waterloo Road Hong Kong China
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Prentis PJ, Woolfit M, Thomas-Hall SR, Ortiz-Barrientos D, Pavasovic A, Lowe AJ, Schenk PM. Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant. ANNALS OF BOTANY 2010; 106:1009-17. [PMID: 20929896 PMCID: PMC2990670 DOI: 10.1093/aob/mcq201] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND Invasive species pose a significant threat to global economies, agriculture and biodiversity. Despite progress towards understanding the ecological factors associated with plant invasions, limited genomic resources have made it difficult to elucidate the evolutionary and genetic factors responsible for invasiveness. This study presents the first expressed sequence tag (EST) collection for Senecio madagascariensis, a globally invasive plant species. METHODS We used pyrosequencing of one normalized and two subtractive libraries, derived from one native and one invasive population, to generate an EST collection. ESTs were assembled into contigs, annotated by BLAST comparison with the NCBI non-redundant protein database and assigned gene ontology (GO) terms from the Plant GO Slim ontologies. KEY RESULTS Assembly of the 221,746 sequence reads resulted in 12,442 contigs. Over 50 % (6183) of 12,442 contigs showed significant homology to proteins in the NCBI database, representing approx. 4800 independent transcripts. The molecular transducer GO term was significantly over-represented in the native (South African) subtractive library compared with the invasive (Australian) library. Based on NCBI BLAST hits and literature searches, 40 % of the molecular transducer genes identified in the South African subtractive library are likely to be involved in response to biotic stimuli, such as fungal, bacterial and viral pathogens. CONCLUSIONS This EST collection is the first representation of the S. madagascariensis transcriptome and provides an important resource for the discovery of candidate genes associated with plant invasiveness. The over-representation of molecular transducer genes associated with defence responses in the native subtractive library provides preliminary support for aspects of the enemy release and evolution of increased competitive ability hypotheses in this successful invasive. This study highlights the contribution of next-generation sequencing to better understanding the molecular mechanisms underlying ecological hypotheses that are important in successful plant invasions.
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Affiliation(s)
- Peter J Prentis
- Australian Centre for Evolutionary Biology and Biodiversity, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia.
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Yan Y, Wang Z, Tian W, Dong Z, Spencer DF. Generation and analysis of expressed sequence tags from the medicinal plant Salvia miltiorrhiza. SCIENCE CHINA-LIFE SCIENCES 2010; 53:273-85. [DOI: 10.1007/s11427-010-0005-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2009] [Accepted: 11/05/2009] [Indexed: 12/28/2022]
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Horvath D. Genomics for weed science. Curr Genomics 2010; 11:47-51. [PMID: 20808523 PMCID: PMC2851116 DOI: 10.2174/138920210790217972] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 07/08/2009] [Accepted: 07/08/2009] [Indexed: 12/29/2022] Open
Abstract
Numerous genomic-based studies have provided insight to the physiological and evolutionary processes involved in developmental and environmental processes of model plants such as arabidopsis and rice. However, far fewer efforts have been attempted to use genomic resources to study physiological and evolutionary processes of weedy plants. Genomics-based tools such as extensive EST databases and microarrays have been developed for a limited number of weedy species, although application of information and resources developed for model plants and crops are possible and have been exploited. These tools have just begun to provide insights into the response of these weeds to herbivore and pathogen attack, survival of extreme environmental conditions, and interaction with crops. The potential of these tools to illuminate mechanisms controlling the traits that allow weeds to invade novel habitats, survive extreme environments, and that make weeds difficult to eradicate have potential for both improving crops and developing novel methods to control weeds.
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Affiliation(s)
- David Horvath
- USDA-ARS, Bioscience Research Laboratory, 1605 Albrecht Blvd. Fargo, ND 58105, USA
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Broz AK, Manter DK, Bowman G, Müller-Schärer H, Vivanco JM. Plant origin and ploidy influence gene expression and life cycle characteristics in an invasive weed. BMC PLANT BIOLOGY 2009; 9:33. [PMID: 19309502 PMCID: PMC2670832 DOI: 10.1186/1471-2229-9-33] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 03/23/2009] [Indexed: 05/24/2023]
Abstract
BACKGROUND Ecological, evolutionary and physiological studies have thus far provided an incomplete picture of why some plants become invasive; therefore we used genomic resources to complement and advance this field. In order to gain insight into the invasive mechanism of Centaurea stoebe we compared plants of three geo-cytotypes, native Eurasian diploids, native Eurasian tetraploids and introduced North American tetraploids, grown in a common greenhouse environment. We monitored plant performance characteristics and life cycle habits and characterized the expression of genes related to constitutive defense and genome stability using quantitative PCR. RESULTS Plant origin and ploidy were found to have a significant effect on both life cycle characteristics and gene expression, highlighting the importance of comparing appropriate taxonomic groups in studies of native and introduced plant species. We found that introduced populations of C. stoebe exhibit reduced expression of transcripts related to constitutive defense relative to their native tetraploid counterparts, as might be expected based on ideas of enemy release and rapid evolution. Measurements of several vegetative traits were similar for all geo-cytotypes; however, fecundity of tetraploids was significantly greater than diploids, due in part to their polycarpic nature. A simulation of seed production over time predicts that introduced tetraploids have the highest fecundity of the three geo-cytotypes. CONCLUSION Our results suggest that characterizing gene expression in an invasive species using populations from both its native and introduced range can provide insight into the biology of plant invasion that can complement traditional measurements of plant performance. In addition, these results highlight the importance of using appropriate taxonomic units in ecological genomics investigations.
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Affiliation(s)
- Amanda K Broz
- Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO 80523-1173, USA
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO 80523-1173, USA
| | - Daniel K Manter
- USDA-ARS, Soil-Plant-Nutrient Research Unit, Fort Collins, CO 80526, USA
| | - Gillianne Bowman
- Département de Biologie/Ecologie & Evolution, Université de Fribourg/Pérolles, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Heinz Müller-Schärer
- Département de Biologie/Ecologie & Evolution, Université de Fribourg/Pérolles, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Jorge M Vivanco
- Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO 80523-1173, USA
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO 80523-1173, USA
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Broz AK, Manter DK, Callaway RM, Paschke MW, Vivanco JM. A molecular approach to understanding plant-plant interactions in the context of invasion biology. FUNCTIONAL PLANT BIOLOGY : FPB 2008; 35:1123-1134. [PMID: 32688860 DOI: 10.1071/fp08155] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2008] [Accepted: 08/05/2008] [Indexed: 06/11/2023]
Abstract
Competition is a major determinant of plant community structure, and can influence the size and reproductive fitness of a species. Therefore, competitive responses may arise from alterations in gene expression and plant function when an individual is confronted with new competitors. This study explored competition at the level of gene expression by hybridising transcripts from Centaurea maculosa Lam., one of North America's most invasive exotic plant species, to an Arabidopsis thaliana (L.) Heynh microarray chip. Centaurea was grown in competition with Festuca idahoensis Elmer, a native species that generally has weak competitive effects against Centaurea; Gaillardia aristata Pursh, a native species that tends to be a much stronger competitor against Centaurea; and alone (control). Some transcripts were induced or repressed to a similar extent regardless of the plant neighbour grown with Centaurea. Other transcripts showed differential expression that was specific to the competitor species, possibly indicating a species-specific aspect of the competitive response of Centaurea. These results are the first to identify genes in an invasive plant that are induced or repressed by plant neighbours and provide a new avenue of insight into the molecular aspects of plant competitive ability.
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Affiliation(s)
- Amanda K Broz
- Center for Rhizosphere Biology, Fort Collins, CO 80523, USA
| | - Daniel K Manter
- United States Department of Agriculture - Agricultural Research Station, Soil-Plant-Nutrient Research Unit, Fort Collins, CO 80526, USA
| | - Ragan M Callaway
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Mark W Paschke
- Forest Rangeland and Watershed Stewardship Department, Fort Collins, CO 80523, USA
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Natural variation in gene expression between wild and weedy populations of Helianthus annuus. Genetics 2008; 179:1881-90. [PMID: 18689879 DOI: 10.1534/genetics.108.091041] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The molecular genetic changes underlying the transformation of wild plants into agricultural weeds are poorly understood. Here we use a sunflower cDNA microarray to detect variation in gene expression between two wild (non-weedy) Helianthus annuus populations from Utah and Kansas and four weedy H. annuus populations collected from agricultural fields in Utah, Kansas, Indiana, and California. When grown in a common growth chamber environment, populations differed substantially in their gene expression patterns, indicating extensive genetic differentiation. Overall, 165 uni-genes, representing approximately 5% of total genes on the array, showed significant differential expression in one or more weedy populations when compared to both wild populations. This subset of genes is enriched for abiotic/biotic stimulus and stress response proteins, which may underlie niche transitions from the natural sites to agricultural fields for H. annuus. However, only a small proportion of the differentially expressed genes overlapped in multiple wild vs. weedy comparisons, indicating that most of the observed expression changes are due to local adaptation or neutral processes, as opposed to parallel genotypic adaptation to agricultural fields. These results are consistent with an earlier phylogeographic study suggesting that weedy sunflowers have evolved multiple times in different regions of the United States and further indicate that the evolution of weedy sunflowers has been accompanied by substantial gene expression divergence in different weedy populations.
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Minto RE, Blacklock BJ. Biosynthesis and function of polyacetylenes and allied natural products. Prog Lipid Res 2008; 47:233-306. [PMID: 18387369 PMCID: PMC2515280 DOI: 10.1016/j.plipres.2008.02.002] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Revised: 02/25/2008] [Accepted: 02/28/2008] [Indexed: 11/19/2022]
Abstract
Polyacetylenic natural products are a substantial class of often unstable compounds containing a unique carbon-carbon triple bond functionality, that are intriguing for their wide variety of biochemical and ecological functions, economic potential, and surprising mode of biosynthesis. Isotopic tracer experiments between 1960 and 1990 demonstrated that the majority of these compounds are derived from fatty acid and polyketide precursors. During the past decade, research into the metabolism of polyacetylenes has swiftly advanced, driven by the cloning of the first genes responsible for polyacetylene biosynthesis in plants, moss, fungi, and actinomycetes and the initial characterization of the gene products. The current state of knowledge of the biochemistry and molecular genetics of polyacetylenic secondary metabolic pathways will be presented together with an up-to-date survey of new terrestrial and marine natural products, their known biological activities, and a discussion of their likely metabolic origins.
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Affiliation(s)
- Robert E Minto
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 North Blackford Street, Indianapolis, IN 46202, United States.
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