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D'Anatro A, Calvelo J, Feijóo M, Giorello FM. Differential expression analyses and detection of SNP loci associated with environmental variables: Are salinity and temperature factors involved in population differentiation and speciation in Odontesthes? COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101262. [PMID: 38861850 DOI: 10.1016/j.cbd.2024.101262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/13/2024]
Abstract
Environmental factors play a key role in individual adaptation to different local conditions. Because of this, studies about the physiological and genetic responses of individuals exposed to different natural environments offer clues about mechanisms involved in population differentiation, and as a subsequent result, speciation. Marine environments are especially suited to survey this kind of phenomena because they commonly harbor species adapted to different local conditions along a geographic continuum. Silversides belonging to Odontesthes are commonly distributed in tropical and temperate regions of South America and exhibit noticeable phenotypic plasticity, which allows them to adapt to contrasting environments. In this study, the genetic expression of O. argentinensis sampled along the Uruguayan Atlantic coast and estuarine adjacent areas was investigated. In addition, the correlation between individual genotypes and environmental variables was also analysed in O. argentinensis and O. bonariensis. Results obtained suggest a differential expression pattern of low magnitude among individuals from the different areas sampled and a correlation between several SNP loci and environmental variables. The analyses carried out did not show a clear differentiation among individuals sampled along different salinity regimens, but enriched GOTerms seem to be driven by water oxygen content. On the other hand, a total of 46 SNPs analysed in O. argentinensis and O. bonariensis showed a correlation with salinity and temperature. Although none of the correlated SNPs and corresponding genes from our both analyses were directly associated with hypoxia, genes related to the cardiovascular system and muscle cell differentiation were found. All these genes are interesting candidates for future studies since they are closely related to the differentially expressed genes. Although salinity was also mentioned as an important parameter limiting introgression between O. argentinensis and O. bonariensis, it was found that salinity does not drive differential expression in O. argentinensis, but rather oxygen levels. Moreover, salinity does not directly affect the structure and genetic divergence of the populations, they appear to be structured based on their degree of isolation and geographical distance between them. Further studies, like genome-wide analyses, could help to elucidate additional genes adapted to the different environments in these silverside species.
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Affiliation(s)
- Alejandro D'Anatro
- Laboratorio de Evolución y Sistemática, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay.
| | - Javier Calvelo
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Matías Feijóo
- Centro Universitario Regional Este, Sede Treinta y Tres, Universidad de la República, Treinta y Tres, Uruguay
| | - Facundo M Giorello
- Espacio de Biología Vegetal del Noreste, Centro Universitario de Tacuarembó, Universidad de la República, Tacuarembó, Uruguay
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Wingert JM, Ferrer J, Neves MP, Baumgartner D, Malabarba LR. A New Species of Silverside of the Genus Odontesthes (Atheriniformes: Atherinopsidae) with Hypertrophic Lips from a High-Altitude Basin in Southern Brazil. ICHTHYOLOGY & HERPETOLOGY 2022. [DOI: 10.1643/i2021136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Juliana M. Wingert
- Programa de Pós-Graduação em Biologia Animal, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91501–970 Porto Alegre, RS, Brazil; (JMW) ; (JF) ; (MPN) mayara-nevesbio@ hotma
| | - Juliano Ferrer
- Programa de Pós-Graduação em Biologia Animal, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91501–970 Porto Alegre, RS, Brazil; (JMW) ; (JF) ; (MPN) mayara-nevesbio@ hotma
| | - Mayara P. Neves
- Programa de Pós-Graduação em Biologia Animal, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91501–970 Porto Alegre, RS, Brazil; (JMW) ; (JF) ; (MPN) mayara-nevesbio@ hotma
| | - Dirceu Baumgartner
- Universidade Estadual do Oeste do Paraná, Programa de Pós-Graduação em Recursos Pesqueiros e Engenharia de Pesca, Paraná, Brazil; (DB)
| | - Luiz R. Malabarba
- Programa de Pós-Graduação em Biologia Animal, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91501–970 Porto Alegre, RS, Brazil; (JMW) ; (JF) ; (MPN) mayara-nevesbio@ hotma
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3
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González-Castro M, Cardoso YP, Hughes LC, Ortí G. Hybridization is strongly constrained by salinity during secondary contact between silverside fishes (Odontesthes, Atheriniformes). Heredity (Edinb) 2022; 129:233-243. [PMID: 35821279 PMCID: PMC9519950 DOI: 10.1038/s41437-022-00555-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 11/08/2022] Open
Abstract
This study investigates a contact zone between two silverside fish species (marine Odontesthes argentinensis and freshwater O. bonariensis) in the estuarine Mar Chiquita lagoon along the Atlantic coast in Argentina (MChL), in which intermediate morphs had been reported. It has been suggested that admixture and introgression occur in MChL between these two species, but direct genetic evidence is lacking. Leveraging samples collected over several years (n = 676), we document the spatial distribution of both species and intermediate morphs within this habitat and collect landmark-based morphometric and multilocus genetic data (9876 loci for n = 110 individuals) to test the hypothesis of hybridization. Our analysis unambiguously characterizes intermediate morphs as F1 or F2 hybrids. We show that the low frequency of hybrid individuals in MChL may be explained by uneven abundance of parental species, which in turn are strongly affected by water salinity, limiting the size of the contact zone. Although hybrids seem to be fertile, their fitness may be reduced by external and intrinsic factors that may limit their success and suggest that this is an unstable hybrid zone. Genetic distinctiveness of both parental species is strongly supported by genome-wide data, explaining a known pattern of mitonuclear discordance as a consequence of hybridization followed by mitochondrial introgression. A clear signature of population genetic structure was detected in O. argentinensis, distinguishing MChL residents from marine populations of this species, that also was supported by distinctive morphometric features among these groups. Previous hypotheses of speciation in these fishes are discussed in the light of the new findings.
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Affiliation(s)
- Mariano González-Castro
- Grupo de Biotaxonomía Morfológica y molecular de peces, IIMyC-CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Yamila P Cardoso
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
- Laboratorio de Sistemática y Biología Evolutiva, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Argentina.
- Department of Biological Sciences, George Washington University, Washington, DC, USA.
| | - Lily C Hughes
- Department of Biological Sciences, George Washington University, Washington, DC, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Guillermo Ortí
- Department of Biological Sciences, George Washington University, Washington, DC, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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4
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Gill transcriptome of the yellow peacock bass (Cichla ocellaris monoculus) exposed to contrasting physicochemical conditions. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01284-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Sebastian W, Sukumaran S, Gopalakrishnan A. Comparative mitogenomics of Clupeoid fish provides insights into the adaptive evolution of mitochondrial oxidative phosphorylation (OXPHOS) genes and codon usage in the heterogeneous habitats. Heredity (Edinb) 2022; 128:236-249. [PMID: 35256764 PMCID: PMC8986858 DOI: 10.1038/s41437-022-00519-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/17/2022] [Accepted: 02/17/2022] [Indexed: 11/09/2022] Open
Abstract
Clupeoid fish can be considered excellent candidates to understand the role of mitochondrial DNA in adaptive evolution, as they have colonized different habitats (marine, brackish, freshwater, tropical and temperate regions) over millions of years. Here, we investigate patterns of tRNA location, codon usage bias, and lineage-specific diversifying selection signals to provide novel insights into how evolutionary improvements of mitochondrial metabolic efficiency have allowed clupeids to adapt to different habitats. Based on whole mitogenome data of 70 Clupeoids with a global distribution we find that purifying selection was the dominant force acting and that the mutational deamination pressure in mtDNA was stronger than the codon/amino acid constraints. The codon usage pattern appears evolved to achieve high translational efficiency (codon/amino acid-related constraints), as indicated by the complementarity of most codons to the GT-saturated tRNA anticodon sites (retained by deamination-induced pressure) and usage of the codons of the tRNA genes situated near to the control region (fixed by deamination pressure) where transcription efficiency was high. The observed shift in codon preference patterns between marine and euryhaline/freshwater Clupeoids indicates possible selection for improved translational efficiency in mitochondrial genes while adapting to low-salinity habitats. This mitogenomic plasticity and enhanced efficiency of the metabolic machinery may have contributed to the evolutionary success and abundance of Clupeoid fish.
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Affiliation(s)
- Wilson Sebastian
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - Sandhya Sukumaran
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India.
| | - A Gopalakrishnan
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
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6
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Du H, Xiong S, Lv H, Zhao S, Manyande A. Comprehensive analysis of transcriptomics and metabolomics to understand the flesh quality regulation of crucian carp (Carassius auratus) treated with short term micro-flowing water system. Food Res Int 2021; 147:110519. [PMID: 34399497 DOI: 10.1016/j.foodres.2021.110519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 05/26/2021] [Accepted: 06/09/2021] [Indexed: 12/21/2022]
Abstract
The short term micro-flowing purification system (STMFPS) has been shown to improve the flesh quality of freshwater fish. However, few studies have focused on the involved underlying mechanisms. This study explored the effect of STMFPS on the flesh quality of market-size freshwater fish based on the combination of metabolomics and transcriptomics methods. The UPLC-QTOF/MS based metabolomics method was utilized to screen metabolites and predict the possible major metabolic pathways during different STMFPS treatment periods (0 d, 1 d, 5 d and 9 d). Furthermore, the transcriptomic data demonstrated that the differentially expressed genes detected in crucian carp muscle were 2915, 7852 and 7183 after 1 d, 5 d and 9 d STMFPS treatment. Results showed that the TCA cycle, ornithine cycle, purine metabolism and amino acid catabolism play important roles in improving the flesh quality of crucian carp. This study may help to understand the mechanism of improving the flesh quality of aquatic products using STMFPS.
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Affiliation(s)
- Hongying Du
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China; National R & D Branch Center for Conventional Freshwater Fish Processing, Wuhan, Hubei 430070, PR China
| | - Shanbai Xiong
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China; National R & D Branch Center for Conventional Freshwater Fish Processing, Wuhan, Hubei 430070, PR China.
| | - Hao Lv
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Siming Zhao
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China; National R & D Branch Center for Conventional Freshwater Fish Processing, Wuhan, Hubei 430070, PR China
| | - Anne Manyande
- School of Human and Social Sciences, University of West London, Middlesex TW8 9GA, UK
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Calvelo J, D'Anatro A. Mitochondrial genome architecture and phylogenetic relationships of Odontesthes argentinensis within Atherinomorpha. Genetica 2021; 149:129-141. [PMID: 33817771 DOI: 10.1007/s10709-021-00116-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 03/15/2021] [Indexed: 12/30/2022]
Abstract
Silversides are a widely distributed group across South America, with several species occupying marine, freshwater and estuarine environments. Several authors suggest main transitions among these environments took place during Pleistocene, and were accompanied with rapid speciation events. This scenario produced very limited genetic and morphological differentiation among the species. However, most of these surveys have an incomplete coverage of the intraspecific genetic diversity of the taxa studied. In this work, we reconstructed six mitochondrial genomes of O. argentinensis using transcriptomic data, and used them-in combination with several nuclear markers retrieved from the same transcriptomes-to explore the effect of additional coverage of intraspecific diversity of this species in phylogenetic reconstructions. Unlike previous works, phylogenetic analyses failed to identify O. argentinensis as a monophyletic group in relation with closely related taxa. Our results suggest that several species of the genus, especially those related to O. argentinensis, need further taxonomic revision.
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Affiliation(s)
- Javier Calvelo
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay
| | - Alejandro D'Anatro
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay.
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8
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Rajkov J, El Taher A, Böhne A, Salzburger W, Egger B. Gene expression remodelling and immune response during adaptive divergence in an African cichlid fish. Mol Ecol 2020; 30:274-296. [PMID: 33107988 DOI: 10.1111/mec.15709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/08/2020] [Accepted: 10/19/2020] [Indexed: 11/29/2022]
Abstract
Variation in gene expression contributes to ecological speciation by facilitating population persistence in novel environments. Likewise, immune responses can be of relevance in speciation driven by adaptation to different environments. Previous studies examining gene expression differences between recently diverged ecotypes have often relied on only one pair of populations, targeted the expression of only a subset of genes or used wild-caught individuals. Here, we investigated the contribution of habitat-specific parasites and symbionts and the underlying immunological abilities of ecotype hosts to adaptive divergence in lake-river population pairs of the cichlid fish Astatotilapia burtoni. To shed light on the role of phenotypic plasticity in adaptive divergence, we compared parasite and microbiota communities, immune response, and gene expression patterns of fish from natural habitats and a lake-like pond set-up. In all investigated population pairs, lake fish were more heavily parasitized than river fish, in terms of both parasite taxon composition and infection abundance. The innate immune response in the wild was higher in lake than in river populations and was elevated in a river population exposed to lake parasites in the pond set-up. Environmental differences between lake and river habitat and their distinct parasite communities have shaped differential gene expression, involving genes functioning in osmoregulation and immune response. Most changes in gene expression between lake and river samples in the wild and in the pond set-up were based on a plastic response. Finally, gene expression and bacterial communities of wild-caught individuals and individuals acclimatized to lake-like pond conditions showed shifts underlying adaptive phenotypic plasticity.
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Affiliation(s)
- Jelena Rajkov
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Athimed El Taher
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Astrid Böhne
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Walter Salzburger
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Bernd Egger
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
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Hughes LC, Cardoso YP, Sommer JA, Cifuentes R, Cuello M, Somoza GM, González‐Castro M, Malabarba LR, Cussac V, Habit EM, Betancur‐R. R, Ortí G. Biogeography, habitat transitions and hybridization in a radiation of South American silverside fishes revealed by mitochondrial and genomic RAD data. Mol Ecol 2020; 29:738-751. [DOI: 10.1111/mec.15350] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/23/2019] [Accepted: 01/03/2020] [Indexed: 01/23/2023]
Affiliation(s)
- Lily C. Hughes
- Department of Biological Sciences George Washington University Washington DC USA
- Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington DC USA
| | - Yamila P. Cardoso
- Laboratorio de Sistemática y Biología Evolutiva‐CONICET Facultad de Ciencias Naturales y Museo Universidad Nacional de La Plata La Plata Argentina
| | - Julie A. Sommer
- Vice Chancellor for Research Office University of Nebraska Medical Center Omaha NE USA
| | - Roberto Cifuentes
- Departmento de Sistemas Acuáticos Facultad de Ciencias Ambientales y Centro EULA Universidad de Concepción y Centro de Investigaciones en Ecosistemas Patagónicos Concepción Chile
| | - Mariela Cuello
- Facultad de Ciencias Naturales y Museo Universidad Nacional de La Plata‐CONICET Buenos Aires Argentina
| | - Gustavo M. Somoza
- Instituto Tecnológico de Chascomus (CONICET‐UNSAM) Chascomús, Buenos Aires Argentina
| | - Mariano González‐Castro
- Grupo de Biotaxonomía Morfológica y molecular de peces IIMyC‐CONICET Universidad Nacional de Mar del Plata Mar del Plata Argentina
| | - Luiz R. Malabarba
- Departamento de Zoologia Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
| | - Victor Cussac
- Centro Científico Tecnológico CONICET Patagonia Norte – Universidad Nacional del Comahue Bariloche, Rio Negro Argentina
| | - Evelyn M. Habit
- Departmento de Sistemas Acuáticos Facultad de Ciencias Ambientales y Centro EULA Universidad de Concepción y Centro de Investigaciones en Ecosistemas Patagónicos Concepción Chile
| | - Ricardo Betancur‐R.
- Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington DC USA
- Department of Biology University of Oklahoma Norman OK USA
| | - Guillermo Ortí
- Department of Biological Sciences George Washington University Washington DC USA
- Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington DC USA
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10
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González-Castro M, Rosso JJ, Delpiani SM, Mabragaña E, Díaz de Astarloa JM. Inferring boundaries among fish species of the new world silversides (Atherinopsidae; genus Odontesthes): new evidences of incipient speciation between marine and brackish populations of Odontesthes argentinensis. Genetica 2019; 147:217-229. [PMID: 31069611 DOI: 10.1007/s10709-019-00066-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/02/2019] [Indexed: 11/24/2022]
Abstract
Species of new world silversides (Actinopterygii; Atherinopsidae; genus Odontesthes) possess economic relevance, biological interest and ecological importance. In the present paper we: (A) investigate the molecular diversity in marine species of Odontesthes from the South West Atlantic Ocean (SWAO), and analyse their interspecific relationships and divergence by means of DNA Barcoding, including its freshwater congeners, as well. (B) Explore the suitability of DNA Barcoding to analyse the diversity and distribution of haplotypes in Odontesthes argentinensis, the only well documented marine species from the SWAO that exhibit putative estuarine and marine populations. Molecular analysis revealed 100% of agreement between morphological identification and molecular identity. Odontesthes argentinensis, Odontesthes platensis, Odontesthes smitti, Odontesthes nigricans and Odontesthes incisa were assigned to five different barcode index numbers (BINs). Maximum-likelihood analysis showed that all marine species of Odontesthes clustered separately in a unique monophyletic phylogroup, comprising five well defined haplogroups, with genetic divergence between groups ranging from 2.75 to 7.11%. The genetic analysis including freshwater congeners showed that O. incisa clustered alone occupying a basal position. The Fst pairwise comparisons within O. argentinensis support the existence of three population groups: one conformed by Mar Chiquita Lagoon (MCh) specimens, and the others by Mar del Plata/Mar Chiquita coast and San Blas Bay coastal specimens, respectively. The AMOVA showed significant overall differentiation (Fst = 0.238; p = 0.00001) for the entire data set. The previous/present evidence is discussed, and strongly suggests that incipient speciation is occurring in O. argentinensis argentinean populations, and specimens from MCh would be considered at present as the leading candidate of a marine to freshwater incipient speciation event.
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Affiliation(s)
- Mariano González-Castro
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar Del Plata, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Juan José Rosso
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar Del Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Sergio Matías Delpiani
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar Del Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ezequiel Mabragaña
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar Del Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Juan Martín Díaz de Astarloa
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar Del Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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11
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Yi Y, Lv Y, You X, Chen J, Bian C, Huang Y, Xu J, Deng L, Shi Q. High throughput screening of small immune peptides and antimicrobial peptides from the Fish-T1K database. Genomics 2019; 111:215-221. [DOI: 10.1016/j.ygeno.2018.11.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 11/20/2018] [Accepted: 11/20/2018] [Indexed: 01/19/2023]
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12
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Brennan RS, Healy TM, Bryant HJ, La MV, Schulte PM, Whitehead A. Integrative Population and Physiological Genomics Reveals Mechanisms of Adaptation in Killifish. Mol Biol Evol 2018; 35:2639-2653. [PMID: 30102365 PMCID: PMC11325861 DOI: 10.1093/molbev/msy154] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Adaptive divergence between marine and freshwater (FW) environments is important in generating phyletic diversity within fishes, but the genetic basis of this process remains poorly understood. Genome selection scans can identify adaptive loci, but incomplete knowledge of genotype-phenotype connections makes interpreting their significance difficult. In contrast, association mapping (genome-wide association mapping [GWAS], random forest [RF] analyses) links genotype to phenotype, but offer limited insight into the evolutionary forces shaping variation. Here, we combined GWAS, RF, and selection scans to identify loci important in adaptation to FW environments. We utilized FW-native and brackish water (BW)-native populations of Atlantic killifish (Fundulus heteroclitus) as well as a naturally admixed population between the two. We measured morphology and multiple physiological traits that differ between populations and may contribute to osmotic adaptation (salinity tolerance, hypoxia tolerance, metabolic rate, body shape) and used a reduced representation approach for genome-wide genotyping. Our results show patterns of population divergence in physiological capabilities that are consistent with local adaptation. Population genomic scans between BW-native and FW-native populations identified genomic regions evolving by natural selection, whereas association mapping revealed loci that contribute to variation for each trait. There was substantial overlap in the genomic regions putatively under selection and loci associated with phenotypic traits, particularly for salinity tolerance, suggesting that these regions and genes are important for adaptive divergence between BW and FW environments. Together, these data provide insight into the mechanisms that enable diversification of fishes across osmotic boundaries.
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Affiliation(s)
- Reid S Brennan
- Department of Environmental Toxicology, University of California-Davis, Davis, CA
- Department of Biology, University of Vermont, Burlington, VT
| | - Timothy M Healy
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, CA
| | - Heather J Bryant
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
| | - Man Van La
- Department of Environmental Toxicology, University of California-Davis, Davis, CA
| | - Patricia M Schulte
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
| | - Andrew Whitehead
- Department of Environmental Toxicology, University of California-Davis, Davis, CA
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Silveira TLR, Domingues WB, Remião MH, Santos L, Barreto B, Lessa IM, Varela Junior AS, Martins Pires D, Corcini C, Collares T, Seixas FK, Robaldo RB, Campos VF. Evaluation of Reference Genes to Analyze Gene Expression in Silverside Odontesthes humensis Under Different Environmental Conditions. Front Genet 2018; 9:75. [PMID: 29593778 PMCID: PMC5861154 DOI: 10.3389/fgene.2018.00075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/19/2018] [Indexed: 01/12/2023] Open
Abstract
Some mammalian reference genes, which are widely used to normalize the qRT-PCR, could not be used for this purpose due to its high expression variation. The normalization with false reference genes leads to misinterpretation of results. The silversides (Odontesthes spp.) has been used as models for evolutionary, osmoregulatory and environmental pollution studies but, up to now, there are no studies about reference genes in any Odontesthes species. Furthermore, many studies on silversides have used reference genes without previous validations. Thus, present study aimed to was to clone and sequence potential reference genes, thereby identifying the best ones in Odontesthes humensis considering different tissues, ages and conditions. For this purpose, animals belonging to three ages (adults, juveniles, and immature) were exposed to control, Roundup®, and seawater treatments for 24 h. Blood samples were subjected to flow-cytometry and other collected tissues to RNA extraction; cDNA synthesis; molecular cloning; DNA sequencing; and qRT-PCR. The candidate genes tested included 18s, actb, ef1a, eif3g, gapdh, h3a, atp1a, and tuba. Gene expression results were analyzed using five algorithms that ranked the candidate genes. The flow-cytometry data showed that the environmental challenges could trigger a systemic response in the treated fish. Even during this systemic physiological disorder, the consensus analysis of gene expression revealed h3a to be the most stable gene expression when only the treatments were considered. On the other hand, tuba was the least stable gene in the control and gapdh was the least stable in both Roundup® and seawater groups. In conclusion, the consensus analyses of different tissues, ages, and treatments groups revealed that h3a is the most stable gene whereas gapdh and tuba are the least stable genes, even being considered two constitutive genes.
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Affiliation(s)
- Tony L R Silveira
- Laboratory of Structural Genomics, Biotechnology Graduate Program, Federal University of Pelotas, Pelotas, Brazil
| | - William B Domingues
- Laboratory of Structural Genomics, Biotechnology Graduate Program, Federal University of Pelotas, Pelotas, Brazil
| | - Mariana H Remião
- Laboratory of Structural Genomics, Biotechnology Graduate Program, Federal University of Pelotas, Pelotas, Brazil
| | - Lucas Santos
- Laboratory of Structural Genomics, Biotechnology Graduate Program, Federal University of Pelotas, Pelotas, Brazil
| | - Bruna Barreto
- Laboratory of Structural Genomics, Biotechnology Graduate Program, Federal University of Pelotas, Pelotas, Brazil
| | - Ingrid M Lessa
- Laboratory of Structural Genomics, Biotechnology Graduate Program, Federal University of Pelotas, Pelotas, Brazil
| | | | | | - Carine Corcini
- Veterinary Faculty, Federal University of Pelotas, Pelotas, Brazil
| | - Tiago Collares
- Laboratory of Cancer Biotechnology, Biotechnology Graduate Program, Federal University of Pelotas, Pelotas, Brazil
| | - Fabiana K Seixas
- Laboratory of Cancer Biotechnology, Biotechnology Graduate Program, Federal University of Pelotas, Pelotas, Brazil
| | - Ricardo B Robaldo
- Laboratory of Physiology, Institute of Biology, Federal University of Pelotas, Pelotas, Brazil
| | - Vinicius F Campos
- Laboratory of Structural Genomics, Biotechnology Graduate Program, Federal University of Pelotas, Pelotas, Brazil
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14
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Hughes LC, Somoza GM, Nguyen BN, Bernot JP, González-Castro M, Díaz de Astarloa JM, Ortí G. Transcriptomic differentiation underlying marine-to-freshwater transitions in the South American silversides Odontesthes argentinensis and O. bonariensis (Atheriniformes). Ecol Evol 2017; 7:5258-5268. [PMID: 28770064 PMCID: PMC5528240 DOI: 10.1002/ece3.3133] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 04/28/2017] [Accepted: 05/03/2017] [Indexed: 12/22/2022] Open
Abstract
Salinity gradients are critical habitat determinants for freshwater organisms. Silverside fishes in the genus Odontesthes have recently and repeatedly transitioned from marine to freshwater habitats, overcoming a strong ecological barrier. Genomic and transcriptomic changes involved in this kind of transition are only known for a few model species. We present new data and analyses of gene expression and microbiome composition in the gills of two closely related silverside species, marine O. argentinensis and freshwater O. bonariensis and find more than three thousand transcripts differentially expressed, with osmoregulatory/ion transport genes and immune genes showing very different expression patterns across species. Interspecific differences also involve more than one thousand transcripts with nonsynonymous SNPs in the coding sequences, most of which were not differentially expressed. In addition to characterizing gill transcriptomes from wild‐caught marine and freshwater fishes, we test experimentally the response to salinity increases by O. bonariensis collected from freshwater habitats. Patterns of expression in gill transcriptomes of O. bonariensis exposed to high salinity do not resemble O. argentinensis mRNA expression, suggesting lack of plasticity for adaptation to marine conditions in this species. The diversity of functions associated with both the differentially expressed set of transcripts and those with sequence divergence plus marked microbiome differences suggest that multiple abiotic and biotic factors in marine and freshwater habitats are driving transcriptomic differences between these species.
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Affiliation(s)
- Lily C Hughes
- Department of Biological Sciences The George Washington University Washington DC USA
| | - Gustavo M Somoza
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (CONICET-UNSAM) Chascomús Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Buenos Aires Argentina
| | - Bryan N Nguyen
- Department of Biological Sciences The George Washington University Washington DC USA.,Computational Biology Institute The George Washington University Washington DC USA
| | - James P Bernot
- Computational Biology Institute The George Washington University Washington DC USA.,Institute for Biomedical Sciences The George Washington University Washington DC USA
| | - Mariano González-Castro
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Buenos Aires Argentina.,Grupo de Biotaxonomía Morfológica y molecular de peces IIMyC-CONICET Universidad Nacional de Mar del PlataMar del Plata Argentina
| | - Juan Martín Díaz de Astarloa
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Buenos Aires Argentina.,Grupo de Biotaxonomía Morfológica y molecular de peces IIMyC-CONICET Universidad Nacional de Mar del PlataMar del Plata Argentina
| | - Guillermo Ortí
- Department of Biological Sciences The George Washington University Washington DC USA
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