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Passow CN, Henpita C, Shaw JH, Quackenbush CR, Warren WC, Schartl M, Arias-Rodriguez L, Kelley JL, Tobler M. The roles of plasticity and evolutionary change in shaping gene expression variation in natural populations of extremophile fish. Mol Ecol 2017; 26:6384-6399. [PMID: 28926156 DOI: 10.1111/mec.14360] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 12/22/2022]
Abstract
The notorious plasticity of gene expression responses and the complexity of environmental gradients complicate the identification of adaptive differences in gene regulation among populations. We combined transcriptome analyses in nature with common-garden and exposure experiments to establish cause-effect relationships between the presence of a physiochemical stressor and expression differences, as well as to test how evolutionary change and plasticity interact to shape gene expression variation in natural systems. We studied two evolutionarily independent population pairs of an extremophile fish (Poecilia mexicana) living in toxic, hydrogen sulphide (H2 S)-rich springs and adjacent nontoxic habitats and assessed genomewide expression patterns of wild-caught and common-garden-raised individuals exposed to different concentrations of H2 S. We found that 7.7% of genes that were differentially expressed between sulphidic and nonsulphidic ecotypes remained differentially expressed in the laboratory, indicating that sources of selection other than H2 S-or plastic responses to other environmental factors-contribute substantially to gene expression patterns observed in the wild. Concordantly differentially expressed genes in the wild and the laboratory were primarily associated with H2 S detoxification, sulphur processing and metabolic physiology. While shared, ancestral plasticity played a minor role in shaping gene expression variation observed in nature, we documented evidence for evolved population differences in the constitutive expression as well as the H2 S inducibility of candidate genes. Mechanisms underlying gene expression variation also varied substantially across the two ecotype pairs. These results provide a springboard for studying evolutionary modifications of gene regulatory mechanisms that underlie expression variation in locally adapted populations.
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Affiliation(s)
| | - Chathurika Henpita
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | - Jennifer H Shaw
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | - Corey R Quackenbush
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | - Manfred Schartl
- Physiological Chemistry, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany.,Hagler Institute for Advanced Studies and Department of Biology, Texas A&M University, College Station, TX, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, México
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, USA
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52
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Pearce SL, Clarke DF, East PD, Elfekih S, Gordon KHJ, Jermiin LS, McGaughran A, Oakeshott JG, Papanicolaou A, Perera OP, Rane RV, Richards S, Tay WT, Walsh TK, Anderson A, Anderson CJ, Asgari S, Board PG, Bretschneider A, Campbell PM, Chertemps T, Christeller JT, Coppin CW, Downes SJ, Duan G, Farnsworth CA, Good RT, Han LB, Han YC, Hatje K, Horne I, Huang YP, Hughes DST, Jacquin-Joly E, James W, Jhangiani S, Kollmar M, Kuwar SS, Li S, Liu NY, Maibeche MT, Miller JR, Montagne N, Perry T, Qu J, Song SV, Sutton GG, Vogel H, Walenz BP, Xu W, Zhang HJ, Zou Z, Batterham P, Edwards OR, Feyereisen R, Gibbs RA, Heckel DG, McGrath A, Robin C, Scherer SE, Worley KC, Wu YD. Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species. BMC Biol 2017; 15:63. [PMID: 28756777 PMCID: PMC5535293 DOI: 10.1186/s12915-017-0402-6] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/04/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Helicoverpa armigera and Helicoverpa zea are major caterpillar pests of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely polyphagous, and H. armigera has developed resistance to many insecticides. Here we use comparative genomics, transcriptomics and resequencing to elucidate the genetic basis for their properties as pests. RESULTS We find that, prior to their divergence about 1.5 Mya, the H. armigera/H. zea lineage had accumulated up to more than 100 more members of specific detoxification and digestion gene families and more than 100 extra gustatory receptor genes, compared to other lepidopterans with narrower host ranges. The two genomes remain very similar in gene content and order, but H. armigera is more polymorphic overall, and H. zea has lost several detoxification genes, as well as about 50 gustatory receptor genes. It also lacks certain genes and alleles conferring insecticide resistance found in H. armigera. Non-synonymous sites in the expanded gene families above are rapidly diverging, both between paralogues and between orthologues in the two species. Whole genome transcriptomic analyses of H. armigera larvae show widely divergent responses to different host plants, including responses among many of the duplicated detoxification and digestion genes. CONCLUSIONS The extreme polyphagy of the two heliothines is associated with extensive amplification and neofunctionalisation of genes involved in host finding and use, coupled with versatile transcriptional responses on different hosts. H. armigera's invasion of the Americas in recent years means that hybridisation could generate populations that are both locally adapted and insecticide resistant.
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Affiliation(s)
- S L Pearce
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - D F Clarke
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- School of Biological Sciences, University of Melbourne, Parkville, Vic, Australia
| | - P D East
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - S Elfekih
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - K H J Gordon
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia.
| | - L S Jermiin
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - A McGaughran
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - J G Oakeshott
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia.
| | - A Papanicolaou
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- Hawksbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - O P Perera
- Southern Insect Management Research Unit, USDA-ARS, Stoneville, MS, USA
| | - R V Rane
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- School of Biological Sciences, University of Melbourne, Parkville, Vic, Australia
| | - S Richards
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| | - W T Tay
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - T K Walsh
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - A Anderson
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - C J Anderson
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | - S Asgari
- School of Biological Sciences, University of Queensland, Brisbane St Lucia, QLD, Australia
| | - P G Board
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | | | - P M Campbell
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - T Chertemps
- Sorbonnes Universités, UPMC Université Paris 06, Institute of Ecology and Environmental Sciences of Paris, Paris, France
- National Institute for Agricultural Research (INRA), Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | | | - C W Coppin
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | | | - G Duan
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - C A Farnsworth
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - R T Good
- School of Biological Sciences, University of Melbourne, Parkville, Vic, Australia
| | - L B Han
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Y C Han
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - K Hatje
- Max Planck Institute for Biophysical Chemistry, Gottingen, Germany
| | - I Horne
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - Y P Huang
- Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - D S T Hughes
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - E Jacquin-Joly
- National Institute for Agricultural Research (INRA), Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - W James
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - S Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - M Kollmar
- Max Planck Institute for Biophysical Chemistry, Gottingen, Germany
| | - S S Kuwar
- Max Planck Institute of Chemical Ecology, Jena, Germany
| | - S Li
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - N-Y Liu
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
| | - M T Maibeche
- Sorbonnes Universités, UPMC Université Paris 06, Institute of Ecology and Environmental Sciences of Paris, Paris, France
- National Institute for Agricultural Research (INRA), Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - J R Miller
- J. Craig Venter Institute, Rockville, MD, USA
| | - N Montagne
- Sorbonnes Universités, UPMC Université Paris 06, Institute of Ecology and Environmental Sciences of Paris, Paris, France
| | - T Perry
- School of Biological Sciences, University of Melbourne, Parkville, Vic, Australia
| | - J Qu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - S V Song
- School of Biological Sciences, University of Melbourne, Parkville, Vic, Australia
| | - G G Sutton
- J. Craig Venter Institute, Rockville, MD, USA
| | - H Vogel
- Max Planck Institute of Chemical Ecology, Jena, Germany
| | - B P Walenz
- J. Craig Venter Institute, Rockville, MD, USA
| | - W Xu
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
| | - H-J Zhang
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, 400016, China
| | - Z Zou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - P Batterham
- School of Biological Sciences, University of Melbourne, Parkville, Vic, Australia
| | | | - R Feyereisen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej, Denmark
| | - R A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - D G Heckel
- Max Planck Institute of Chemical Ecology, Jena, Germany
| | - A McGrath
- CSIRO Black Mountain, GPO Box 1700, Canberra, ACT, 2600, Australia
| | - C Robin
- School of Biological Sciences, University of Melbourne, Parkville, Vic, Australia
| | - S E Scherer
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - K C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Y D Wu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
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