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Clare CI, Nichols KM, Thrower FP, Berntson EA, Hale MC. Comparative genomics of rainbow trout ( Oncorhynchus mykiss): Is the genetic architecture of migratory behavior conserved among populations? Ecol Evol 2023; 13:e10241. [PMID: 37384247 PMCID: PMC10293719 DOI: 10.1002/ece3.10241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/01/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023] Open
Abstract
Rainbow trout (Oncorhynchus mykiss) are a partially migratory species wherein some individuals undergo long-distance anadromous migrations, and others stay as residents in their native freshwater streams. The decision to migrate is known to be highly heritable, and yet, the underlying genes and alleles associated with migration are not fully characterized. Here we used a pooled approach of whole-genome sequence data from migratory and resident trout of two native populations-Sashin Creek, Alaska and Little Sheep Creek, Oregon-to obtain a genome-wide perspective of the genetic architecture of resident and migratory life history. We calculated estimates of genetic differentiation, genetic diversity, and selection between the two phenotypes to locate regions of interest and then compared these associations between populations. We identified numerous genes and alleles associated with life history development in the Sashin Creek population with a notable area on chromosome 8 that may play a critical role in the development of the migratory phenotype. However, very few alleles appeared to be associated with life history development in the Little Sheep Creek system, suggesting population-specific genetic effects are likely important in the development of anadromy. Our results indicate that a migratory life history is not controlled by a singular gene or region but supports the idea that there are many independent ways for a migratory phenotype to emerge in a population. Therefore, conserving and promoting genetic diversity in migratory individuals is paramount to conserving these populations. Ultimately, our data add to a growing body of literature that suggests that population-specific genetic effects, likely mediated through environmental variation, contribute to life history development in rainbow trout.
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Affiliation(s)
| | - Krista M. Nichols
- Conservation Biology Division, Northwest Fisheries Science CenterNational Marine Fisheries Service, National Oceanic and Atmospheric AdministrationSeattleWashingtonUSA
| | - Frank P. Thrower
- Ted Stevens Marine Research Institute, Alaska Fisheries Science Center, NOAAJuneauAlaskaUSA
| | - Ewann A. Berntson
- Conservation Biology Division, Northwest Fisheries Science CenterNational Marine Fisheries Service, National Oceanic and Atmospheric AdministrationSeattleWashingtonUSA
| | - Matthew C. Hale
- Department of BiologyTexas Christian UniversityFort WorthTexasUSA
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2
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Zolotarenko AD, Shitova MV. Transcriptome Studies of Salmonid Fishes of the Genius Oncorhynchus. RUSS J GENET+ 2022. [DOI: 10.1134/s102279542207016x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Collins EE, Romero N, Zendt JS, Narum SR. Whole-Genome Resequencing to Evaluate Life History Variation in Anadromous Migration of Oncorhynchus mykiss. Front Genet 2022; 13:795850. [PMID: 35368705 PMCID: PMC8964970 DOI: 10.3389/fgene.2022.795850] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/24/2022] [Indexed: 12/04/2022] Open
Abstract
Anadromous fish experience physiological modifications necessary to migrate between vastly different freshwater and marine environments, but some species such as Oncorhynchus mykiss demonstrate variation in life history strategies with some individuals remaining exclusively resident in freshwater, whereas others undergo anadromous migration. Because there is limited understanding of genes involved in this life history variation across populations of this species, we evaluated the genomic difference between known anadromous (n = 39) and resident (n = 78) Oncorhynchus mykiss collected from the Klickitat River, WA, USA, with whole-genome resequencing methods. Sequencing of these collections yielded 5.64 million single-nucleotide polymorphisms that were tested for significant differences between resident and anadromous groups along with previously identified candidate gene regions. Although a few regions of the genome were marginally significant, there was one region on chromosome Omy12 that provided the most consistent signal of association with anadromy near two annotated genes in the reference assembly: COP9 signalosome complex subunit 6 (CSN6) and NACHT, LRR, and PYD domain–containing protein 3 (NLRP3). Previously identified candidate genes for anadromy within the inversion region of chromosome Omy05 in coastal steelhead and rainbow trout were not informative for this population as shown in previous studies. Results indicate that the significant region on chromosome Omy12 may represent a minor effect gene for male anadromy and suggests that this life history variation in Oncorhynchus mykiss is more strongly driven by other mechanisms related to environmental rearing such as epigenetic modification, gene expression, and phenotypic plasticity. Further studies into regulatory mechanisms of this trait are needed to understand drivers of anadromy in populations of this protected species.
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Affiliation(s)
- Erin E. Collins
- Hagerman Genetics Laboratory, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, United States
- *Correspondence: Erin E. Collins,
| | - Nicolas Romero
- Yakama Nation Fisheries, Yakima/Klickitat Fisheries Project, Klickitat, WA, United States
| | - Joseph S. Zendt
- Yakama Nation Fisheries, Yakima/Klickitat Fisheries Project, Klickitat, WA, United States
| | - Shawn R. Narum
- Hagerman Genetics Laboratory, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, United States
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4
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Fischer EK, Hauber ME, Bell AM. Back to the basics? Transcriptomics offers integrative insights into the role of space, time and the environment for gene expression and behaviour. Biol Lett 2021; 17:20210293. [PMID: 34520681 DOI: 10.1098/rsbl.2021.0293] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Fuelled by the ongoing genomic revolution, broadscale RNA expression surveys are fast replacing studies targeting one or a few genes to understand the molecular basis of behaviour. Yet, the timescale of RNA-sequencing experiments and the dynamics of neural gene activation are insufficient to drive real-time switches between behavioural states. Moreover, the spatial, functional and transcriptional complexity of the brain (the most commonly targeted tissue in studies of behaviour) further complicates inference. We argue that a Central Dogma-like 'back-to-basics' assumption that gene expression changes cause behaviour leaves some of the most important aspects of gene-behaviour relationships unexplored, including the roles of environmental influences, timing and feedback from behaviour-and the environmental shifts it causes-to neural gene expression. No perfect experimental solutions exist but we advocate that explicit consideration, exploration and discussion of these factors will pave the way toward a richer understanding of the complicated relationships between genes, environments, brain gene expression and behaviour over developmental and evolutionary timescales.
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Affiliation(s)
- Eva K Fischer
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois, Urbana-Champaign, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Mark E Hauber
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois, Urbana-Champaign, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Alison M Bell
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois, Urbana-Champaign, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801, USA
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5
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Hale MC, McLaughlin R, Wilson C, Mackereth R, Nichols KM. Differential gene expression associated with behavioral variation in ecotypes of Lake Superior brook trout (Salvelinus fontinalis). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 40:100884. [PMID: 34303261 DOI: 10.1016/j.cbd.2021.100884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/06/2021] [Accepted: 07/10/2021] [Indexed: 11/17/2022]
Abstract
Associations between behaviors and the development of different life history tactics have been documented in several species of salmon, trout, and charr. While it is well known that such behaviors are heritable the genes and molecular pathways connected to these behaviors remain unknown. We used an RNA-seq approach to identify genes and molecular pathways differentially regulated in brain tissue between "shy" and "bold" brook trout (Salvelinus fontinalis). A small number of genes were differentially expressed between the behavioral types at several months after hatching and two years of age. Pathway analysis revealed that EIF2 signaling differed consistently between shy and bold individuals suggesting large-scale differences in protein synthesis between behavioral types in the brain. Additionally, the RNA-seq data were used to find polymorphisms within the brook trout genome and a GWAS approach was used to test for statistical associations between genetic variants and behavior type. One allele located in a transcription factor (TSHZ3) contained a protein-coding non-synonymous SNP suggesting that functional variation within TSHZ3 is connected to the development of different behaviors. These results suggest that the molecular basis of behavioral development is complex and due to the differential expression of many genes involved in a wide-range of different molecular pathways.
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Affiliation(s)
- Matthew C Hale
- Department of Biology, Texas Christian University, Fort Worth, TX 76129, United States of America.
| | - Robert McLaughlin
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Chris Wilson
- Aquatic Biodiversity and Conservation Unit, Ontario Ministry of Natural Resources, Trent University, Peterborough, ON K9J 7B8, Canada
| | - Robert Mackereth
- Department of Biology, Lakehead University, Thunder Bay, ON P7B 5E1, Canada
| | - Krista M Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112, United States of America
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6
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Ali A, Thorgaard GH, Salem M. PacBio Iso-Seq Improves the Rainbow Trout Genome Annotation and Identifies Alternative Splicing Associated With Economically Important Phenotypes. Front Genet 2021; 12:683408. [PMID: 34335690 PMCID: PMC8321248 DOI: 10.3389/fgene.2021.683408] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 06/14/2021] [Indexed: 01/04/2023] Open
Abstract
Rainbow trout is an important model organism that has received concerted international efforts to study the transcriptome. For this purpose, short-read sequencing has been primarily used over the past decade. However, these sequences are too short of resolving the transcriptome complexity. This study reported a first full-length transcriptome assembly of the rainbow trout using single-molecule long-read isoform sequencing (Iso-Seq). Extensive computational approaches were used to refine and validate the reconstructed transcriptome. The study identified 10,640 high-confidence transcripts not previously annotated, in addition to 1,479 isoforms not mapped to the current Swanson reference genome. Most of the identified lncRNAs were non-coding variants of coding transcripts. The majority of genes had multiple transcript isoforms (average ∼3 isoforms/locus). Intron retention (IR) and exon skipping (ES) accounted for 56% of alternative splicing (AS) events. Iso-Seq improved the reference genome annotation, which allowed identification of characteristic AS associated with fish growth, muscle accretion, disease resistance, stress response, and fish migration. For instance, an ES in GVIN1 gene existed in fish susceptible to bacterial cold-water disease (BCWD). Besides, under five stress conditions, there was a commonly regulated exon in prolyl 4-hydroxylase subunit alpha-2 (P4HA2) gene. The reconstructed gene models and their posttranscriptional processing in rainbow trout provide invaluable resources that could be further used for future genetics and genomics studies. Additionally, the study identified characteristic transcription events associated with economically important phenotypes, which could be applied in selective breeding.
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Affiliation(s)
- Ali Ali
- Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States
| | - Gary H. Thorgaard
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States
| | - Mohamed Salem
- Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States
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7
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Wynne R, Archer LC, Hutton SA, Harman L, Gargan P, Moran PA, Dillane E, Coughlan J, Cross TF, McGinnity P, Colgan TJ, Reed TE. Alternative migratory tactics in brown trout ( Salmo trutta) are underpinned by divergent regulation of metabolic but not neurological genes. Ecol Evol 2021; 11:8347-8362. [PMID: 34188891 PMCID: PMC8216917 DOI: 10.1002/ece3.7664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/15/2021] [Accepted: 04/18/2021] [Indexed: 12/03/2022] Open
Abstract
The occurrence of alternative morphs within populations is common, but the underlying molecular mechanisms remain poorly understood. Many animals, for example, exhibit facultative migration, where two or more alternative migratory tactics (AMTs) coexist within populations. In certain salmonid species, some individuals remain in natal rivers all their lives, while others (in particular, females) migrate to sea for a period of marine growth. Here, we performed transcriptional profiling ("RNA-seq") of the brain and liver of male and female brown trout to understand the genes and processes that differentiate between migratory and residency morphs (AMT-associated genes) and how they may differ in expression between the sexes. We found tissue-specific differences with a greater number of genes expressed differentially in the liver (n = 867 genes) compared with the brain (n = 10) between the morphs. Genes with increased expression in resident livers were enriched for Gene Ontology terms associated with metabolic processes, highlighting key molecular-genetic pathways underlying the energetic requirements associated with divergent migratory tactics. In contrast, smolt-biased genes were enriched for biological processes such as response to cytokines, suggestive of possible immune function differences between smolts and residents. Finally, we identified evidence of sex-biased gene expression for AMT-associated genes in the liver (n = 12) but not the brain. Collectively, our results provide insights into tissue-specific gene expression underlying the production of alternative life histories within and between the sexes, and point toward a key role for metabolic processes in the liver in mediating divergent physiological trajectories of migrants versus residents.
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Affiliation(s)
- Robert Wynne
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Louise C. Archer
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Stephen A. Hutton
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Luke Harman
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | | | - Peter A. Moran
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
- Present address:
Department of Ecological Science – Animal EcologyVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Eileen Dillane
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Jamie Coughlan
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Thomas F. Cross
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Philip McGinnity
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
- Marine InstituteNewportIreland
| | - Thomas J. Colgan
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
- Present address:
Institute of Organismic and Molecular EvolutionJohannes Gutenberg University MainzMainzGermany
| | - Thomas E. Reed
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
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8
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Salmón P, Jacobs A, Ahrén D, Biard C, Dingemanse NJ, Dominoni DM, Helm B, Lundberg M, Senar JC, Sprau P, Visser ME, Isaksson C. Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe. Nat Commun 2021; 12:2983. [PMID: 34016968 PMCID: PMC8137928 DOI: 10.1038/s41467-021-23027-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 04/01/2021] [Indexed: 02/03/2023] Open
Abstract
Urbanisation is increasing worldwide, and there is now ample evidence of phenotypic changes in wild organisms in response to this novel environment. Yet, the genetic changes and genomic architecture underlying these adaptations are poorly understood. Here, we genotype 192 great tits (Parus major) from nine European cities, each paired with an adjacent rural site, to address this major knowledge gap in our understanding of wildlife urban adaptation. We find that a combination of polygenic allele frequency shifts and recurrent selective sweeps are associated with the adaptation of great tits to urban environments. While haplotypes under selection are rarely shared across urban populations, selective sweeps occur within the same genes, mostly linked to neural function and development. Collectively, we show that urban adaptation in a widespread songbird occurs through unique and shared selective sweeps in a core-set of behaviour-linked genes.
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Affiliation(s)
- Pablo Salmón
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Lund, Sweden ,grid.8756.c0000 0001 2193 314XInstitute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Arne Jacobs
- grid.8756.c0000 0001 2193 314XInstitute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Dag Ahrén
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Lund, Sweden
| | - Clotilde Biard
- grid.462350.6Sorbonne Université, UPEC, Paris 7, CNRS, INRA, IRD, Institut d’Écologie et des Sciences de l’Environnement de Paris, iEES Paris, F-75005 Paris, France
| | - Niels J. Dingemanse
- grid.5252.00000 0004 1936 973XDepartment of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - Davide M. Dominoni
- grid.8756.c0000 0001 2193 314XInstitute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Barbara Helm
- grid.8756.c0000 0001 2193 314XInstitute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK ,grid.4830.f0000 0004 0407 1981Present Address: GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Max Lundberg
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Lund, Sweden
| | - Juan Carlos Senar
- grid.507605.10000 0001 1958 5537Museu de Ciències Naturals de Barcelona, Barcelona, Spain
| | - Philipp Sprau
- grid.5252.00000 0004 1936 973XDepartment of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - Marcel E. Visser
- grid.418375.c0000 0001 1013 0288Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Caroline Isaksson
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Lund, Sweden
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9
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Abstract
Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.
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Affiliation(s)
- M. Lisette Delgado
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Daniel E. Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
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10
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Delgado ML, Manosalva A, Urbina MA, Habit E, Link O, Ruzzante DE. Genomic basis of the loss of diadromy in Galaxias maculatus: Insights from reciprocal transplant experiments. Mol Ecol 2020; 29:4857-4870. [PMID: 33048403 DOI: 10.1111/mec.15686] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/18/2022]
Abstract
Diadromy is known for having major effects on the distribution and richness of aquatic species, and so does its loss. The loss of diadromy has led to the diversification of many species, yet research focusing on understanding its molecular basis and consequences are limited. This is particularly true for amphidromous species despite being the most abundant group of diadromous species. Galaxias maculatus, an amphidromous species and one of the most widely distributed fishes in the Southern Hemisphere, exhibits many instances of nonmigratory or resident populations. The existence of naturally replicated resident populations in Patagonia can serve as an ideal system for the study of the mechanisms that lead to the loss of the diadromy and its ecological and evolutionary consequences. Here, we studied two adjacent river systems in which resident populations are genetically differentiated yet derived from the same diadromous population. By combining a reciprocal transplant experiment with genomic data, we showed that the two resident populations followed different evolutionary pathways by exhibiting a differential response in their capacity to survive in salt water. While one resident population was able to survive salt water, the other was not. Genomic analyses provided insights into the genes that distinguished (a) migratory from nonmigratory populations; (b) populations that can vs those that cannot survive a saltwater environment; and (c) between these resident populations. This study demonstrates that the loss of diadromy can be achieved by different pathways and that environmental (selection) and random (genetic drift) forces shape this dynamic evolutionary process.
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Affiliation(s)
| | - Aliro Manosalva
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA, Universidad de Concepción, Concepción, Chile
| | - Mauricio A Urbina
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Instituto Milenio de Oceanografía (IMO), Universidad de Concepción, Concepción, Chile
| | - Evelyn Habit
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA, Universidad de Concepción, Concepción, Chile
| | - Oscar Link
- Departamento de Ingeniería Civil, Facultad de Ingeniería, Universidad de Concepción, Concepción, Chile
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11
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Transcriptome analysis of the brain provides insights into the regulatory mechanism for Coilia nasus migration. BMC Genomics 2020; 21:410. [PMID: 32552858 PMCID: PMC7302372 DOI: 10.1186/s12864-020-06816-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/09/2020] [Indexed: 11/10/2022] Open
Abstract
Background Coilia nasus (C. nasus) is an important anadromous fish species that resides in the Yangtze River of China, and has high ecological and economical value. However, wild resources have suffered from a serious reduction in population, attributed to the over-construction of water conservancy projects, overfishing, and environmental pollution. The Ministry of Agriculture and Rural Affairs of the People’s Republic of China has issued a notice banning the commercial fishing of wild C. nasus in the Yangtze River. Wild C. nasus populations urgently need to recover. A better understanding of C. nasus migration patterns is necessary to maximize the efficiency of conservation efforts. Juvenile C. nasus experience a simultaneous effect of increasing salinity and cold stress during seaward migration, and the brain plays a comprehensive regulatory role during this process. Therefore, to explore the early seaward migration regulation mechanism of juvenile C. nasus, we performed a comparative transcriptome analysis on the brain of juvenile C. nasus under salinity and cold stress simultaneously. Results Relevant neurotransmitters, receptors, and regulatory proteins from three categories of regulatory pathway play synergistic regulatory roles during the migration process: neuronal signaling, the sensory system, and environmental adaptation. The significant differential expression of growth-related hormones, thyroid receptors, haptoglobin, and prolactin receptors was similar to the results of relevant research on salmonids and steelhead trout. Conclusions This study revealed a regulatory network that the brain of juvenile C. nasus constructs during migration, thereby providing basic knowledge on further studies could build on. This study also revealed key regulatory genes similar to salmonids and steelhead trout, thus, this study will lay a theoretical foundation for further study on migration regulation mechanism of anadromous fish species.
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12
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Iversen M, Mulugeta T, Gellein Blikeng B, West AC, Jørgensen EH, Rød Sandven S, Hazlerigg D. RNA profiling identifies novel, photoperiod-history dependent markers associated with enhanced saltwater performance in juvenile Atlantic salmon. PLoS One 2020; 15:e0227496. [PMID: 32267864 PMCID: PMC7141700 DOI: 10.1371/journal.pone.0227496] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 12/09/2019] [Indexed: 12/20/2022] Open
Abstract
Atlantic salmon migrate to sea following completion of a developmental process known as smolting, which establishes a seawater (SW) tolerant phenotype. Smolting is stimulated by exposure to long photoperiod or continuous light (LL) following a period of exposure to short photoperiod (SP), and this leads to major changes in gill ion exchange and osmoregulatory function. Here, we performed an RNAseq experiment to discover novel genes involved in photoperiod-dependent remodeling of the gill. This revealed a novel cohort of genes whose expression rises dramatically in fish transferred to LL following SP exposure, but not in control fish maintained continuously on LL or on SP. A follow-up experiment revealed that the SP-history dependence of LL induction of gene expression varies considerably between genes. Some genes were inducible by LL exposure after only 2 weeks exposure to SP, while others required 8 weeks prior SP exposure for maximum responsiveness to LL. Since subsequent SW growth performance is also markedly improved following 8 weeks SP exposure, these photoperiodic history-dependent genes may be useful predictive markers for full smolt development.
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Affiliation(s)
- Marianne Iversen
- Department of Arctic and Marine Biology, UiT -The Arctic University of Norway, Tromsø, Norway
| | - Teshome Mulugeta
- Department of Animal and Aquaculture Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Børge Gellein Blikeng
- Department of Arctic and Marine Biology, UiT -The Arctic University of Norway, Tromsø, Norway
| | | | - Even Hjalmar Jørgensen
- Department of Arctic and Marine Biology, UiT -The Arctic University of Norway, Tromsø, Norway
| | - Simen Rød Sandven
- Centre for Integrative Genetics, Department of Animal and Aquaculture Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - David Hazlerigg
- Department of Arctic and Marine Biology, UiT -The Arctic University of Norway, Tromsø, Norway
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13
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Morro B, Doherty MK, Balseiro P, Handeland SO, MacKenzie S, Sveier H, Albalat A. Plasma proteome profiling of freshwater and seawater life stages of rainbow trout (Oncorhynchus mykiss). PLoS One 2020; 15:e0227003. [PMID: 31899766 PMCID: PMC6941806 DOI: 10.1371/journal.pone.0227003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/09/2019] [Indexed: 01/18/2023] Open
Abstract
The sea-run phenotype of rainbow trout (Oncorhynchus mykiss), like other anadromous salmonids, present a juvenile stage fully adapted to life in freshwater known as parr. Development in freshwater is followed by the smolt stage, where preadaptations needed for seawater life are developed making fish ready to migrate to the ocean, after which event they become post-smolts. While these three life stages have been studied using a variety of approaches, proteomics has never been used for such purpose. The present study characterised the blood plasma proteome of parr, smolt and post-smolt rainbow trout using a gel electrophoresis liquid chromatography tandem mass spectrometry approach alone or in combination with low-abundant protein enrichment technology (combinatorial peptide ligand library). In total, 1,822 proteins were quantified, 17.95% of them being detected only in plasma post enrichment. Across all life stages, the most abundant proteins were ankyrin-2, DNA primase large subunit, actin, serum albumin, apolipoproteins, hemoglobin subunits, hemopexin-like proteins and complement C3. When comparing the different life stages, 17 proteins involved in mechanisms to cope with hyperosmotic stress and retinal changes, as well as the downregulation of nonessential processes in smolts, were significantly different between parr and smolt samples. On the other hand, 11 proteins related to increased growth in post-smolts, and also related to coping with hyperosmotic stress and to retinal changes, were significantly different between smolt and post-smolt samples. Overall, this study presents a series of proteins with the potential to complement current seawater-readiness assessment tests in rainbow trout, which can be measured non-lethally in an easily accessible biofluid. Furthermore, this study represents a first in-depth characterisation of the rainbow trout blood plasma proteome, having considered three life stages of the fish and used both fractionation alone or in combination with enrichment methods to increase protein detection.
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Affiliation(s)
- Bernat Morro
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Mary K. Doherty
- Institute of Health Research and Innovation, Centre for Health Science, University of the Highlands and Islands, Inverness, Scotland, United Kingdom
| | | | | | - Simon MacKenzie
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
- NORCE AS, Universitetet i Bergen, Bergen, Norway
| | - Harald Sveier
- Lerøy Seafood Group ASA, Universitetet i Bergen, Bergen, Norway
| | - Amaya Albalat
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
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14
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Weinstein SY, Thrower FP, Nichols KM, Hale MC. A large-scale chromosomal inversion is not associated with life history development in rainbow trout from Southeast Alaska. PLoS One 2019; 14:e0223018. [PMID: 31539414 PMCID: PMC6754156 DOI: 10.1371/journal.pone.0223018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/11/2019] [Indexed: 01/12/2023] Open
Abstract
In studying the causative mechanisms behind migration and life history, the salmonids-salmon, trout, and charr-are an exemplary taxonomic group, as life history development is known to have a strong genetic component. A double inversion located on chromosome 5 in rainbow trout (Oncorhynchus mykiss) is associated with life history development in multiple populations, but the importance of this inversion has not been thoroughly tested in conjunction with other polymorphisms in the genome. To that end, we used a high-density SNP chip to genotype 192 F1 migratory and resident rainbow trout and focused our analyses to determine whether this inversion is important in life history development in a well-studied population of rainbow trout from Southeast Alaska. We identified 4,994 and 436 SNPs-predominantly outside of the inversion region-associated with life history development in the migrant and resident familial lines, respectively. Although F1 samples showed genomic patterns consistent with the double inversion on chromosome 5 (reduced observed and expected heterozygosity and an increase in linkage disequilibrium), we found no statistical association between the inversion and life history development. Progeny produced by crossing resident trout and progeny produced by crossing migrant trout both consisted of a mix of migrant and resident individuals, irrespective of the individuals' inversion haplotype on chromosome 5. This suggests that although the inversion is present at a low frequency, it is not strongly associated with migration as it is in populations of Oncorhynchus mykiss from lower latitudes.
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Affiliation(s)
- Spencer Y. Weinstein
- Department of Biology, Texas Christian University, Fort Worth, United States of America
| | - Frank P. Thrower
- Ted Stevens Marine Research Institute, Alaska Fisheries Center, NOAA, Juneau, AK, United States of America
| | - Krista M. Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, Seattle, WA, United States of America
| | - Matthew C. Hale
- Department of Biology, Texas Christian University, Fort Worth, United States of America
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15
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Hsu HY, Chen HW, Han YS. Habitat Partitioning and its Possible Genetic Background Between Two Sympatrically Distributed Eel Species in Taiwan. Zool Stud 2019; 58:e27. [PMID: 31966328 PMCID: PMC6917558 DOI: 10.6620/zs.2019.58-27] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 07/19/2019] [Indexed: 12/14/2022]
Abstract
The geographical distributions of the Japanese eel (Anguilla japonica) and Giant-mottled eel (A. marmorata) overlap in many regions in East Asia and therefore suffer from interspecific competition in the same rivers. After a long period of adaptation, the Japanese eel and Giant-mottled eel may exhibit habitat partitioning in the rivers to diminish the interspecific competition between them. In this study, we conducted a field investigation in the Fengshan River in Taiwan to survey the habitat distributions of the Japanese eel and Giant-mottled eel throughout a river. Moreover, we investigated whether their habitat distributions are related to their swimming and upstream migration. Thus, the mRNA expression levels of several candidate genes that may be associated with the swimming and upstream migration of eel were examined in the glass eels of the Japanese eel and Giant-mottled eel. Field investigation indicated that the Japanese eel mainly inhabited the lower and middle reaches of the Fengshan River, but the Giant- mottled eel was distributed over the middle to upper reaches. The mRNA expression levels of fMYH, dio2, gria3, and neurod1 were higher in the Giant-mottled eel than in the Japanese eel, implying that Giant- mottled eels might have better swimming bursts and more active upstream migration than Japanese eels. These results suggest that there is a habitat partition at which these two eel species coexist in a river, and their habitat distributions may be linked to their swimming bursts and upstream migration. Determining the habitat distributions of freshwater eels is important for developing applicable plans for eel conservation and resource management.
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Affiliation(s)
- Hsiang-Yi Hsu
- Institute of Fisheries Science, College of Life Science,
National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei 106, Taiwan.
| | - Hsiao-Wei Chen
- Institute of Fisheries Science, College of Life Science,
National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei 106, Taiwan.
| | - Yu-San Han
- Institute of Fisheries Science, College of Life Science,
National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei 106, Taiwan.
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16
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Campbell MA, Hale MC, McKinney GJ, Nichols KM, Pearse DE. Long-Term Conservation of Ohnologs Through Partial Tetrasomy Following Whole-Genome Duplication in Salmonidae. G3 (BETHESDA, MD.) 2019; 9:2017-2028. [PMID: 31010824 PMCID: PMC6553544 DOI: 10.1534/g3.119.400070] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/18/2019] [Indexed: 01/01/2023]
Abstract
Whole-genome duplications (WGDs) have occurred repeatedly and broadly throughout the evolutionary history of eukaryotes. However, the effects of WGD on genome function and evolution remain unclear. The salmonid WGD that occurred approximately 88 million years ago presents an excellent opportunity for studying the effects of WGD as ∼10-15% of each salmonid genome still exhibits tetrasomic inheritance. Herein, we utilized the rainbow trout (Oncorhynchus mykiss) genome assembly and brain transcriptome data to examine the fate of gene pairs (ohnologs) following the salmonid whole-genome duplication. We find higher sequence identity between ohnologs located within known tetrasomic regions than between ohnologs found in disomic regions, and that tetrasomically inherited ohnologs showed greater similarity in patterns of gene expression and per ohnolog were lower expressed, than disomically inherited ohnologs. Enrichment testing for Gene Ontology terms identified 49 over-represented terms in tetrasomically inherited ohnologs compared to disomic ohnologs. However, why these ohnologs are retained as tetrasomic is difficult to answer. It could be that we have identified salmonid specific "dangerous duplicates", that is, genes that cannot take on new roles following WGD. Alternatively, there may be adaptive advantages for retaining genes as functional duplicates in tetrasomic regions, as presumably, movement of these genes into disomic regions would affect both their sequence identity and their gene expression patterns.
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Affiliation(s)
- Matthew A Campbell
- Fisheries Ecology Division, Southwest Fisheries Science Center, Santa Cruz, CA 95060
| | - Matthew C Hale
- Department of Biology, Texas Christian University, Fort Worth, TX 76129
| | - Garrett J McKinney
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195, and
| | - Krista M Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, Seattle, WA 98112
| | - Devon E Pearse
- Fisheries Ecology Division, Southwest Fisheries Science Center, Santa Cruz, CA 95060
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17
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Gavery MR, Nichols KM, Berejikian BA, Tatara CP, Goetz GW, Dickey JT, Van Doornik DM, Swanson P. Temporal Dynamics of DNA Methylation Patterns in Response to Rearing Juvenile Steelhead ( Oncorhynchus mykiss) in a Hatchery versus Simulated Stream Environment. Genes (Basel) 2019; 10:E356. [PMID: 31075961 PMCID: PMC6563097 DOI: 10.3390/genes10050356] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 12/17/2022] Open
Abstract
Genetic selection is often implicated as the underlying cause of heritable phenotypic differences between hatchery and wild populations of steelhead trout (Oncorhynchus mykiss) that also differ in lifetime fitness. Developmental plasticity, which can also affect fitness, may be mediated by epigenetic mechanisms such as DNA methylation. Our previous study identified significant differences in DNA methylation between adult hatchery- and natural-origin steelhead from the same population that could not be distinguished by DNA sequence variation. In the current study, we tested whether hatchery-rearing conditions can influence patterns of DNA methylation in steelhead with known genetic backgrounds, and assessed the stability of these changes over time. Eyed-embryos from 22 families of Methow River steelhead were split across traditional hatchery tanks or a simulated stream-rearing environment for 8 months, followed by a second year in a common hatchery tank environment. Family assignments were made using a genetic parentage analysis to account for relatedness among individuals. DNA methylation patterns were examined in the liver, a relatively homogeneous organ that regulates metabolic processes and somatic growth, of juveniles at two time points: after eight months of rearing in either a tank or stream environment and after a subsequent year of rearing in a common tank environment. Further, we analyzed DNA methylation in the sperm of mature 2-year-old males from the earlier described treatments to assess the potential of environmentally-induced changes to be passed to offspring. Hepatic DNA methylation changes in response to hatchery versus stream-rearing in yearling fish were substantial, but few persisted after a second year in the tank environment. However, the early rearing environment appeared to affect how fish responded to developmental and environmental signals during the second year since novel DNA methylation differences were identified in the livers of hatchery versus stream-reared fish after a year of common tank rearing. Furthermore, we found profound differences in DNA methylation due to age, irrespective of rearing treatment. This could be due to smoltification associated changes in liver physiology after the second year of rearing. Although few rearing-treatment effects were observed in the sperm methylome, strong family effects were observed. These data suggest limited potential for intergenerational changes, but highlight the importance of understanding the effects of kinship among studied individuals in order to properly analyze and interpret DNA methylation data in natural populations. Our work is the first to study family effects and temporal dynamics of DNA methylation patterns in response to hatchery-rearing.
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Affiliation(s)
- Mackenzie R Gavery
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St., Seattle, WA 98105, USA.
| | - Krista M Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 2725 Montlake Blvd. E., Seattle, WA 98112, USA.
| | - Barry A Berejikian
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 7305 Beach Dr. East, Port Orchard, WA 98366, USA.
| | - Christopher P Tatara
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 7305 Beach Dr. East, Port Orchard, WA 98366, USA.
| | - Giles W Goetz
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St., Seattle, WA 98105, USA.
| | - Jon T Dickey
- University of Washington, School of Aquatic and Fishery Sciences, 1122 NE Boat St., Seattle, WA 98105, USA.
| | - Donald M Van Doornik
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 7305 Beach Dr. East, Port Orchard, WA 98366, USA.
| | - Penny Swanson
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 2725 Montlake Blvd. E., Seattle, WA 98112, USA.
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18
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Merlin C, Liedvogel M. The genetics and epigenetics of animal migration and orientation: birds, butterflies and beyond. ACTA ACUST UNITED AC 2019; 222:222/Suppl_1/jeb191890. [PMID: 30728238 DOI: 10.1242/jeb.191890] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Migration is a complex behavioural adaptation for survival that has evolved across the animal kingdom from invertebrates to mammals. In some taxa, closely related migratory species, or even populations of the same species, exhibit different migratory phenotypes, including timing and orientation of migration. In these species, a significant proportion of the phenotypic variance in migratory traits is genetic. In others, the migratory phenotype and direction is triggered by seasonal changes in the environment, suggesting an epigenetic control of their migration. The genes and epigenetic changes underpinning migratory behaviour remain largely unknown. The revolution in (epi)genomics and functional genomic tools holds great promise to rapidly move the field of migration genetics forward. Here, we review our current understanding of the genetic and epigenetic architecture of migratory traits, focusing on two emerging models: the European blackcap and the North American monarch butterfly. We also outline a vision of how technical advances and integrative approaches could be employed to identify and functionally validate candidate genes and cis-regulatory elements on these and other migratory species across both small and broad phylogenetic scales to significantly advance the field of genetics of animal migration.
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Affiliation(s)
- Christine Merlin
- Department of Biology and Center for Biological Clock Research, Texas A&M University, College Station, TX 77843, USA
| | - Miriam Liedvogel
- Max Planck Institute for Evolutionary Biology, Max Planck Research Group (MPRG) Behavioural Genomics, 24306 Plön, Germany
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19
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Houde ALS, Schulze AD, Kaukinen KH, Strohm J, Patterson DA, Beacham TD, Farrell AP, Hinch SG, Miller KM. Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 29:32-42. [PMID: 30419481 DOI: 10.1016/j.cbd.2018.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 10/13/2018] [Indexed: 11/30/2022]
Abstract
There is a paucity of information on the physiological changes that occur over the course of salmon early marine migration. Here we aim to provide insight on juvenile Coho salmon (Oncorhynchus kisutch) physiology using the changes in gene expression (cGRASP 44K microarray) of four tissues (brain, gill, muscle, and liver) across the parr to smolt transition in freshwater and through the first eight months of ocean residence. We also examined transcriptome changes with body size as a covariate. The strongest shift in the transcriptome for brain, gill, and muscle occurred between summer and fall in the ocean, representing physiological changes that we speculate may be associated with migration preparation to feeding areas. Metabolic processes in the liver were positively associated with body length, generally consistent with enhanced feeding opportunities. However, a notable exception to this metabolic pattern was for spring post-smolts sampled soon after entry into the ocean, which showed a pattern of gene expression more likely associated with depressed feeding or recent fasting. Overall, this study has revealed life stages that may be the most critical developmentally (fall post-smolt) and for survival (spring post-smolt) in the early marine environment. These life stages may warrant further investigation.
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Affiliation(s)
- Aimee Lee S Houde
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada; Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada
| | - Angela D Schulze
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada
| | - Jeffrey Strohm
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada
| | - David A Patterson
- Fisheries and Oceans Canada, School of Resource and Environmental Management, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Terry D Beacham
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada
| | - Anthony P Farrell
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Scott G Hinch
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7, Canada.
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20
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Evidence of sex-bias in gene expression in the brain transcriptome of two populations of rainbow trout (Oncorhynchus mykiss) with divergent life histories. PLoS One 2018; 13:e0193009. [PMID: 29447294 PMCID: PMC5814004 DOI: 10.1371/journal.pone.0193009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/03/2018] [Indexed: 11/19/2022] Open
Abstract
Sex-bias in gene expression is a mechanism that can generate phenotypic variance between the sexes, however, relatively little is known about how patterns of sex-bias vary during development, and how variable sex-bias is between different populations. To that end, we measured sex-bias in gene expression in the brain transcriptome of rainbow trout (Oncorhynchus mykiss) during the first two years of development. Our sampling included from the fry stage through to when O. mykiss either migrate to the ocean or remain resident and undergo sexual maturation. Samples came from two F1 lines: One from migratory steelhead trout and one from resident rainbow trout. All samples were reared in a common garden environment and RNA sequencing (RNA-seq) was used to estimate patterns of gene expression. A total of 1,716 (4.6% of total) genes showed evidence of sex-bias in gene expression in at least one time point. The majority (96.7%) of sex-biased genes were differentially expressed during the second year of development, indicating that patterns of sex-bias in expression are tied to key developmental events, such as migration and sexual maturation. Mapping of differentially expressed genes to the O. mykiss genome revealed that the X chromosome is enriched for female upregulated genes, and this may indicate a lack of dosage compensation in rainbow trout. There were many more sex-biased genes in the migratory line than the resident line suggesting differences in patterns of gene expression in the brain between populations subjected to different forces of selection. Overall, our results suggest that there is considerable variation in the extent and identity of genes exhibiting sex-bias during the first two years of life. These differentially expressed genes may be connected to developmental differences between the sexes, and/or between adopting a resident or migratory life history.
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