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Diz AP, Romero MR, Galindo J, Saura M, Skibinski DOF, Rolán-Alvarez E. Proteomic analysis of F1 hybrids and intermediate variants in a littorina saxatilis hybrid zone. Curr Zool 2021; 68:351-359. [PMID: 35592345 PMCID: PMC9113252 DOI: 10.1093/cz/zoab054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 07/03/2021] [Indexed: 11/22/2022] Open
Abstract
Proteomic analysis was carried out on the Crab (upper-shore) and Wave (lower-shore) ecotypes of Littorina saxatilis from a hybrid zone at Silleiro Cape, Spain. Proteome profiles of individual snails were obtained. Protein expression in F1 hybrid snails bred in the laboratory and snails with intermediate shell phenotypes collected from the mid-shore were compared with Crab and Wave ecotypes using analytical approaches used to study dominance. Multivariate analysis over many protein spots showed that the F1 snails are distinct from both ecotypes but closer to the Wave ecotype. The intermediate snails are highly variable, some closer to the Crab and others to the Wave ecotype. Considered on a protein by protein basis, some proteins are significantly closer in expression to the Crab and others to the Wave ecotype for both F1 and intermediate snails. Furthermore, a significant majority of proteins were closer in expression to the Wave ecotype for the F1, consistent with the multivariate analysis. No such significant majority toward either the Crab or Wave ecotype was observed for the intermediate snails. The closer similarity of F1 and Wave ecotype expression patterns could be the result of similar selective pressures in the similar mid-shore and low-shore environments. For a significantly larger number of proteins, intermediate snails were closer in expression to the ecotype having the lower expression, for both Crab and Wave ecotypes. This is somewhat unexpected as lower expression might be expected to be an indication of impairment of function and lower fitness. Proteomic analysis could be important for the identification of candidate proteins useful for gaining improved understanding of adaptation and barriers to gene flow in hybrid zones.
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Affiliation(s)
- Angel P Diz
- Centro de Investigación Mariña (CIM-UVIGO), Universidade de Vigo, Vigo 36310, Spain
- Address Correspondence to Angel P. Diz. E-mail:
| | - Mónica R Romero
- Centro de Investigación Mariña (CIM-UVIGO), Universidade de Vigo, Vigo 36310, Spain
| | - Juan Galindo
- Centro de Investigación Mariña (CIM-UVIGO), Universidade de Vigo, Vigo 36310, Spain
| | - María Saura
- Departamento de Mejora Genética Animal, INIA, Madrid 28040, Spain
| | - David O F Skibinski
- Institute of Life Science, Swansea University Medical School, Swansea SA2 8PP, UK
| | - Emilio Rolán-Alvarez
- Centro de Investigación Mariña (CIM-UVIGO), Universidade de Vigo, Vigo 36310, Spain
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2
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Diz AP, Sánchez-Marín P. A Primer and Guidelines for Shotgun Proteomic Analysis in Non-model Organisms. Methods Mol Biol 2021; 2259:77-102. [PMID: 33687710 DOI: 10.1007/978-1-0716-1178-4_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
During the last decade, we have witnessed outstanding advances in proteomics led mostly by great technological improvements in mass spectrometry field allowing high-throughput production of high-quality data used for massive protein identification and quantification. From a practical viewpoint, these advances have been mainly exploited in research projects involving model organisms with abundant genomic and proteomic information available in public databases. However, there is a growing number of organisms of high interest in different disciplines, such as ecological, biotechnological, and evolutionary research, yet poorly represented in these databases. Important advances in massive parallel sequencing technology and easy accessibility of this technology to many research laboratories have made nowadays possible to produce customized genomic and proteomic databases of any organism. Along this line, the use of proteogenomic approaches by combining in the same analysis the data obtained from different omic levels has emerged as a very useful and powerful strategy to run shotgun proteomic experiments specially focused on non-model organisms. In this chapter, we provide detailed procedures to undertake shotgun quantitative proteomic experiments following either a label-free or an isobaric labeling approach in non-model organisms, emphasizing also a few key aspects related to experimental design and data analysis.
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Affiliation(s)
- Angel P Diz
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain. .,Marine Research Center, University of Vigo (CIM-UVIGO), Vigo, Spain.
| | - Paula Sánchez-Marín
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, Vigo, Spain
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3
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Klein AH, Ballard KR, Storey KB, Motti CA, Zhao M, Cummins SF. Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies. Brief Funct Genomics 2020; 18:377-394. [PMID: 31609407 DOI: 10.1093/bfgp/elz017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/06/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Here, we reviewed the recent advances involving gastropod omics ('gastropodomics') research from hundreds of publications and online genomics databases. By summarizing the current publicly available data, we present an insight for the design of useful data integrating tools and strategies for comparative omics studies in the future. Additionally, we discuss the future of omics applications in aquaculture, natural pharmaceutical biodiscovery and pest management, as well as to monitor the impact of environmental stressors.
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Affiliation(s)
- Anne H Klein
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kaylene R Ballard
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, Ottawa, ON, Canada K1S 5B6
| | - Cherie A Motti
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville Queensland 4810, Australia
| | - Min Zhao
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Scott F Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
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4
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Rivas MJ, Saura M, Pérez-Figueroa A, Panova M, Johansson T, André C, Caballero A, Rolán-Alvarez E, Johannesson K, Quesada H. Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation. Sci Rep 2018; 8:16147. [PMID: 30385764 PMCID: PMC6212547 DOI: 10.1038/s41598-018-33897-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/08/2018] [Indexed: 11/17/2022] Open
Abstract
Natural selection often produces parallel phenotypic changes in response to a similar adaptive challenge. However, the extent to which parallel gene expression differences and genomic divergence underlie parallel phenotypic traits and whether they are decoupled or not remains largely unexplored. We performed a population genomic study of parallel ecological adaptation among replicate ecotype pairs of the rough periwinkle (Littorina saxatilis) at a regional geographical scale (NW Spain). We show that genomic changes underlying parallel phenotypic divergence followed a complex pattern of both repeatable differences and of differences unique to specific ecotype pairs, in which parallel changes in expression or sequence are restricted to a limited set of genes. Yet, the majority of divergent genes were divergent either for gene expression or coding sequence, but not for both simultaneously. Overall, our findings suggest that divergent selection significantly contributed to the process of parallel molecular differentiation among ecotype pairs, and that changes in expression and gene sequence underlying phenotypic divergence could, at least to a certain extent, be considered decoupled processes.
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Affiliation(s)
- María José Rivas
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - María Saura
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Marina Panova
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Tomas Johansson
- Department of Biology, University of Lund, SE-223 62, Lund, Sweden
| | - Carl André
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Emilio Rolán-Alvarez
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Kerstin Johannesson
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Humberto Quesada
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain.
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5
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Ramos MV, Brito D, Freitas CDT, Gonçalves JFC, Porfirio CTMN, Lobo MDP, Monteiro-Moreira ACO, Souza LAC, Fernandes AV. Proteomic identification and purification of seed proteins from native Amazonian species displaying antifungal activity. PLANTA 2018; 248:197-209. [PMID: 29675765 DOI: 10.1007/s00425-018-2893-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/12/2018] [Indexed: 06/08/2023]
Abstract
Seeds of native species from the rain forest (Amazon) are source of chitinases and their protein extracts exhibited strong and broad antifungal activity. Numerous plant species native to the Amazon have not yet been chemically studied. Studies of seeds are scarcer, since adversities in accessing study areas and seasonality pose constant hurdles to systematic research. In this study, proteins were extracted from seeds belonging to endemic Amazon species and were investigated for the first time. Proteolytic activity, peptidase inhibitors, and chitinases were identified, but chitinolytic activity predominated. Four proteins were purified through chromatography and identified as lectin and chitinases by MS/MS analyses. The proteins were examined for inhibition of a phytopathogen (Fusarium oxysporum). Analyses by fluorescence microscopy suggested binding of propidium iodide to DNA of fungal spores, revealing that spore integrity was lost when accessed by the proteins. Further structural and functional analyses of defensive proteins belonging to species facing highly complex ecosystems such as Amazonia should be conducted, since these could provide new insights into specificity and synergism involving defense proteins of plants submitted to a very complex ecosystem.
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Affiliation(s)
- Márcio V Ramos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará (UFC), Campus do Pici, Fortaleza, Ceará, Brazil.
| | - Daniel Brito
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará (UFC), Campus do Pici, Fortaleza, Ceará, Brazil
| | - Cléverson D T Freitas
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará (UFC), Campus do Pici, Fortaleza, Ceará, Brazil
| | | | - Camila T M N Porfirio
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará (UFC), Campus do Pici, Fortaleza, Ceará, Brazil
| | - Marina D P Lobo
- Universidade de Fortaleza (UNIFOR), Fortaleza, Ceará, Brazil
| | | | - Luiz A C Souza
- Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brazil
| | - Andreia V Fernandes
- Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brazil
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Diz AP, Álvarez-Rodríguez M, Romero MR, Rolán-Alvarez E, Galindo J. Limited proteomic response in the marine snail Melarhaphe neritoides after long-term emersion. Curr Zool 2018; 63:487-493. [PMID: 29492008 PMCID: PMC5804206 DOI: 10.1093/cz/zow110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/29/2016] [Indexed: 11/14/2022] Open
Abstract
Rocky intertidal organisms are commonly exposed to environmental gradients, promoting adaptations to these conditions. Emersion time varies along the intertidal range and in the supralittoral zone is frequently larger than a single tidal cycle, even lasting for weeks. The planktonic-dispersing gastropod Melarhaphe neritoides is a common species of the high shore, adapted to reduce water loss in order to survive during long-term emersion. In this study, we investigated the molecular response, at the proteome level, of M. neritoides collected in high-shore tide pools to a series of emersion periods, from 8 to 24 days, in laboratory conditions. We compared this response to individuals maintained submerged during this period, because this was their original habitat. We also included a reversion treatment in the study, in which emersed individuals were returned to the submerged conditions. Although we detected an increase in overall protein concentration with longer emersion periods, contrary to general expectation, the two dimensional electrophoresis (2DE)-based proteomic analysis did not show significant differences between the treatments at the level of individual protein spots, even after an emersion period of 24 days. Our results suggest that the metabolism remains unaltered independent of the treatment carried out or the changes are very subtle and therefore difficult to detect with our experimental design. We conclude that M. neritoides could be equally adapted to emersion and submersion without drastic physiological changes.
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Affiliation(s)
- Angel P Diz
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, 36310, Spain.,Toralla Marine Science Station (ECIMAT), Universidad de Vigo, Vigo, 36331, Spain
| | - Margarita Álvarez-Rodríguez
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, 36310, Spain.,Institute of Marine Research (IIM), CSIC, Vigo, 36208, Spain
| | - Mónica R Romero
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, 36310, Spain.,Toralla Marine Science Station (ECIMAT), Universidad de Vigo, Vigo, 36331, Spain
| | - Emilio Rolán-Alvarez
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, 36310, Spain.,Toralla Marine Science Station (ECIMAT), Universidad de Vigo, Vigo, 36331, Spain
| | - Juan Galindo
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, Vigo, 36310, Spain.,Toralla Marine Science Station (ECIMAT), Universidad de Vigo, Vigo, 36331, Spain
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7
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Boulding EG, Rivas MJ, González‐Lavín N, Rolán‐Alvarez E, Galindo J. Size selection by a gape-limited predator of a marine snail: Insights into magic traits for speciation. Ecol Evol 2016; 7:674-688. [PMID: 28116062 PMCID: PMC5243190 DOI: 10.1002/ece3.2659] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/24/2016] [Accepted: 11/05/2016] [Indexed: 12/22/2022] Open
Abstract
The intertidal snail Littorina saxatilis has repeatedly evolved two parallel ecotypes assumed to be wave adapted and predatory shore crab adapted, but the magnitude and targets of predator‐driven selection are unknown. In Spain, a small, wave ecotype with a large aperture from the lower shore and a large, thick‐shelled crab ecotype from the upper shore meet in the mid‐shore and show partial size‐assortative mating. We performed complementary field tethering and laboratory predation experiments; the first set compared the survival of two different size‐classes of the crab ecotype while the second compared the same size‐class of the two ecotypes. In the first set, the large size‐class of the crab ecotype survived significantly better than the small size‐class both on the upper shore and in the laboratory. In the second set, the small size‐class of the crab ecotype survived substantially better than that of the wave ecotype both on the upper shore and in the laboratory. Shell‐breaking predation on tethered snails was almost absent within the lower shore. In the laboratory shore crabs (Pachygrapsus marmoratus) with larger claw heights selected most strongly against the small size‐class of the crab ecotype, whereas those with medium claw heights selected most strongly against the thin‐shelled wave ecotype. Sexual maturity occurred at a much larger size in the crab ecotype than in the wave ecotype. Our results showed that selection on the upper shore for rapid attainment of a size refuge from this gape‐limited predator favors large size, thick shells, and late maturity. Model parameterization showed that size‐selective predation restricted to the upper shore resulted in the evolution of the crab ecotype despite gene flow from the wave ecotype snails living on the lower shore. These results on gape‐limited predation and previous ones showing size‐assortative mating between ecotypes suggest that size may represent a magic trait for the thick‐shelled ecotype.
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Affiliation(s)
- Elizabeth G. Boulding
- Integrative BiologyUniversity of GuelphGuelphONCanada
- Departamento de Bioquímica, Genética e InmunologíaFacultad de BiologíaUniversidade de VigoVigoSpain
- ECIMAT, Estación de Ciencias Mariñas de TorallaUniversidade de VigoVigoSpain
| | - María José Rivas
- Departamento de Bioquímica, Genética e InmunologíaFacultad de BiologíaUniversidade de VigoVigoSpain
- ECIMAT, Estación de Ciencias Mariñas de TorallaUniversidade de VigoVigoSpain
| | - Nerea González‐Lavín
- Departamento de Bioquímica, Genética e InmunologíaFacultad de BiologíaUniversidade de VigoVigoSpain
- ECIMAT, Estación de Ciencias Mariñas de TorallaUniversidade de VigoVigoSpain
| | - Emilio Rolán‐Alvarez
- Departamento de Bioquímica, Genética e InmunologíaFacultad de BiologíaUniversidade de VigoVigoSpain
- ECIMAT, Estación de Ciencias Mariñas de TorallaUniversidade de VigoVigoSpain
| | - Juan Galindo
- Departamento de Bioquímica, Genética e InmunologíaFacultad de BiologíaUniversidade de VigoVigoSpain
- ECIMAT, Estación de Ciencias Mariñas de TorallaUniversidade de VigoVigoSpain
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8
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Denoël M, Ficetola GF. Heterochrony in a complex world: disentangling environmental processes of facultative paedomorphosis in an amphibian. J Anim Ecol 2014; 83:606-15. [PMID: 24180255 DOI: 10.1111/1365-2656.12173] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/23/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Mathieu Denoël
- Laboratory of Fish and Amphibian Ethology; Behavioural Biology Unit; Department of Biology, Ecology and Evolution; University of Liege; 22 Quai van Beneden 4020 Liege Belgium
| | - Gentile F. Ficetola
- Department of Environmental and Earth Sciences; University of Milano-Bicocca; 1 Piazza della Scienza 20126 Milano Italy
- Laboratory of Alpine Ecology (LECA); CNRS UMR 5553; Joseph Fourier University; 38041 Grenoble France
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Evidence from morphological and genetic data confirms that Colossendeis tenera Hilton, 1943 (Arthropoda: Pycnogonida), does not belong to the Colossendeis megalonyx Hoek, 1881 complex. ORG DIVERS EVOL 2013. [DOI: 10.1007/s13127-012-0120-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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