1
|
Flores AM, Christensen KA, Siah A, Koop BF. Insights from Hi-C data regarding the Pacific salmon louse (Lepeophtheirus salmonis) sex-chromosomes. G3 (Bethesda) 2024:jkae087. [PMID: 38683737 DOI: 10.1093/g3journal/jkae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/09/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Salmon lice, Lepeophtheirus salmonis (family Caligidae), are ectoparasites that have negatively impacted the salmon aquaculture industry and vulnerable wild salmon populations. Researchers have studied salmon lice to better understand their biology to develop effective control strategies. In this study, we updated the chromosome-level reference genome assembly of the Pacific subspecies of L. salmonis using Hi-C data. The previous version placed contigs/scaffolds using an Atlantic salmon louse genetic map. By utilizing Hi-C data from Pacific salmon lice, we were able to properly assign locations to contigs/scaffolds previously unplaced or misplaced. This resulted in a more accurate genome assembly and a more comprehensive characterization of the sex-chromosome unique to females (W). We found evidence that the same ZW-ZZ mechanism is common in both Atlantic and Pacific subspecies of salmon lice using PCR assays. The W-chromosome was approximately 800 kbp in size, which is ∼30 times smaller than the Z-chromosome (24 Mbp). The W-chromosome contained 61 annotated genes, including 32 protein-coding genes, 27 long non-coding RNA (lncRNA) genes, and 2 pseudogenes. Among these 61 genes, 39 genes shared homology to genes found on other chromosomes, while 20 were unique to the W-chromosome. Two genes of interest on the W-chromosome, prohibitin-2 and kinase suppressor of ras-2, were previously identified as potential sex-linked markers in the salmon louse. However, we prioritized the 20 unique genes on the W-chromosome as sex-determining candidates. This information furthers our understanding of the biology of this ectoparasite and may help in the development of more effective management strategies.
Collapse
Affiliation(s)
- Anne-Marie Flores
- Department of Biology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Kris A Christensen
- Department of Biology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Ahmed Siah
- British Columbia Centre for Aquatic Health Sciences, Campbell River, BC, V9W 2C2, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| |
Collapse
|
2
|
Rondeau EB, Christensen KA, Johnson HA, Sakhrani D, Biagi CA, Wetklo M, Despins CA, Leggatt RA, Minkley DR, Withler RE, Beacham TD, Koop BF, Devlin RH. Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function. G3 (Bethesda) 2023; 13:jkad127. [PMID: 37293843 PMCID: PMC10411575 DOI: 10.1093/g3journal/jkad127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/30/2023] [Accepted: 06/04/2023] [Indexed: 06/10/2023]
Abstract
Chum salmon are ecologically important to Pacific Ocean ecosystems and commercially important to fisheries. To improve the genetic resources available for this species, we sequenced and assembled the genome of a male chum salmon using Oxford Nanopore read technology and the Flye genome assembly software (contig N50: ∼2 Mbp, complete BUSCOs: ∼98.1%). We also resequenced the genomes of 59 chum salmon from hatchery sources to better characterize the genome assembly and the diversity of nucleotide variants impacting phenotype variation. With genomic sequences from a doubled haploid individual, we were able to identify regions of the genome assembly that have been collapsed due to high sequence similarity between homeologous (duplicated) chromosomes. The homeologous chromosomes are relics of an ancient salmonid-specific genome duplication. These regions were enriched with genes whose functions are related to the immune system and responses to toxins. From analyzing nucleotide variant annotations of the resequenced genomes, we were also able to identify genes that have increased levels of variants thought to moderately impact gene function. Genes related to the immune system and the detection of chemical stimuli (olfaction) had increased levels of these variants based on a gene ontology enrichment analysis. The tandem organization of many of the enriched genes raises the question of why they have this organization.
Collapse
Affiliation(s)
- Eric B Rondeau
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Kris A Christensen
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Hollie A Johnson
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Dionne Sakhrani
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
| | - Carlo A Biagi
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
| | - Mike Wetklo
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Cody A Despins
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Rosalind A Leggatt
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
| | - David R Minkley
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Ruth E Withler
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Terry D Beacham
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Robert H Devlin
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
| |
Collapse
|
3
|
Flores AM, Christensen KA, Campbell B, Koop BF, Taylor JS. Sablefish (Anoplopoma fimbria) chromosome-level genome assembly. G3 (Bethesda) 2023:7141347. [PMID: 37097026 DOI: 10.1093/g3journal/jkad089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/27/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023]
Abstract
Sablefish (Anoplopoma fimbria) are in the suborder Cottioidei, which also includes stickleback and lumpfish. This species inhabits coastal regions of the northeastern and northwestern Pacific Ocean from California to Japan. A commercial fishery for sablefish began to flourish in the 1960s, though a downward trend in stock biomass and landings has been observed since 2010. Aquaculture protocols have been developed for sablefish; eggs and sperm from wild-caught and hatchery-reared captive broodstock are used to generate offspring that reach market size in about two years. Parentage analyses show that survival in aquaculture varies among families. Growth rate and disease resistance also vary among individuals and cohorts, but the extent to which genetics and the environment contribute to this variation is unclear. The sablefish genome assembly reported here will form the foundation for SNP-based surveys designed to detect genetic markers associated with survival, growth rate, and pathogen resistance. Beyond its contribution to sablefish domestication, the sablefish genome can be a resource for the management of the wild sablefish fishery. The assembly generated in this study had a length of 653 Mbp, a scaffold N50 of 26.74 Mbp, a contig N50 of 2.57 Mbp, and contained more than 98% of the 3640 Actinopterygii core genes. We placed 620.9 Mbp (95% of the total) onto 24 chromosomes using a genetic map derived from six full-sib families and Hi-C contact data.
Collapse
Affiliation(s)
- Anne-Marie Flores
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia, V8W 2Y2, Canada
| | - Kris A Christensen
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia, V8W 2Y2, Canada
| | - Briony Campbell
- Golden Eagle Sablefish, 335 Walkers Hood Rd, Salt Spring Island, British Columbia, V8K 1N7, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia, V8W 2Y2, Canada
| | - John S Taylor
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia, V8W 2Y2, Canada
| |
Collapse
|
4
|
Rondeau EB, Christensen KA, Minkley DR, Leong JS, Chan MTT, Despins CA, Mueller A, Sakhrani D, Biagi CA, Rougemont Q, Normandeau E, Jones SJM, Devlin RH, Withler RE, Beacham TD, Naish KA, Yáñez JM, Neira R, Bernatchez L, Davidson WS, Koop BF. Population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome. G3 (Bethesda) 2023; 13:7033475. [PMID: 36759939 PMCID: PMC10085799 DOI: 10.1093/g3journal/jkad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 11/22/2022] [Accepted: 01/26/2023] [Indexed: 02/11/2023]
Abstract
Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that return from multiyear ocean migrations to spawn in rivers that flow to the Northern Pacific Ocean. Southern stocks of coho salmon in Canada and the United States have significantly declined over the past quarter century, and unfortunately, conservation efforts have not reversed this trend. To assist in stock management and conservation efforts, we generated a chromosome-level genome assembly. We also resequenced the genomes of 83 coho salmon across their North American range to identify nucleotide variants, and understand the demographic histories of these salmon by modeling effective population size from genome-wide data. From demographic history modeling, we observed reductions in effective population sizes between 3750-8000 years ago for several northern sampling sites, which may correspond to bottleneck events during recolonization after glacial retreat.
Collapse
Affiliation(s)
- Eric B Rondeau
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 2Y2, Canada.,Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC, V7V 1N6, Canada.,Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| | - Kris A Christensen
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 2Y2, Canada.,Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC, V7V 1N6, Canada
| | - David R Minkley
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 2Y2, Canada.,Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC, V7V 1N6, Canada
| | - Jong S Leong
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Michelle T T Chan
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC, V7V 1N6, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Cody A Despins
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Anita Mueller
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Dionne Sakhrani
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC, V7V 1N6, Canada
| | - Carlo A Biagi
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC, V7V 1N6, Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada.,Current: CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, 34293, France
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Robert H Devlin
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC, V7V 1N6, Canada
| | - Ruth E Withler
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| | - Terry D Beacham
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98105, USA
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santa Rosa 11735, La Pintana, Santiago, 8820808, Chile.,Millennium Nucleus of Austral Invasive Salmonids (INVASAL), Concepción, 4030000, Chile
| | - Roberto Neira
- Facultad de Ciencias Agronómicas, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, 8820808, Chile.,Millennium Nucleus of Austral Invasive Salmonids (INVASAL), Concepción, 4030000, Chile
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
| | - William S Davidson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Ben F Koop
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| |
Collapse
|
5
|
Rougemont Q, Xuereb A, Dallaire X, Moore JS, Normandeau E, Perreault-Payette A, Bougas B, Rondeau EB, Withler RE, Van Doornik DM, Crane PA, Naish KA, Garza JC, Beacham TD, Koop BF, Bernatchez L. Long-distance migration is a major factor driving local adaptation at continental scale in Coho salmon. Mol Ecol 2023; 32:542-559. [PMID: 35000273 DOI: 10.1111/mec.16339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/19/2021] [Accepted: 12/23/2021] [Indexed: 01/25/2023]
Abstract
Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species' homing behaviour may promote the establishment of local adaptation. We genotyped 7829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. The results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidate single nucleotide polymorphisms associated with long-distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.
Collapse
Affiliation(s)
- Quentin Rougemont
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada.,CEFE, Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier, Montpellier, France
| | - Amanda Xuereb
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Xavier Dallaire
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Jean-Sébastien Moore
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Alysse Perreault-Payette
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Bérénice Bougas
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Eric B Rondeau
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada.,Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Ruth E Withler
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Donald M Van Doornik
- National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Manchester Research Station, Port Orchard, Washington, USA
| | - Penelope A Crane
- Conservation Genetics Laboratory, U.S. Fish and Wildlife Service, Anchorage, Alaska, USA
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - John Carlos Garza
- Department of Ocean Sciences and Institute of Marine Sciences, University of California Santa Cruz, Santa Cruz, California, USA
| | - Terry D Beacham
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| |
Collapse
|
6
|
Xuereb A, Rougemont Q, Dallaire X, Moore J, Normandeau E, Bougas B, Perreault‐Payette A, Koop BF, Withler R, Beacham T, Bernatchez L. Re‐evaluating Coho salmon (
Oncorhynchus kisutch
) conservation units in Canada using genomic data. Evol Appl 2022; 15:1925-1944. [DOI: 10.1111/eva.13489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Amanda Xuereb
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Quentin Rougemont
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
- CEFE, Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS, Univ Montpellier, CNRS, EPHE, IRD Univ Paul Valéry Montpellier Montpellier France
| | - Xavier Dallaire
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Jean‐Sébastien Moore
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Eric Normandeau
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Bérénice Bougas
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Alysse Perreault‐Payette
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Ben F. Koop
- Department of Biology University of Victoria Victoria British Columbia Canada
| | - Ruth Withler
- Department of Fisheries and Ocean Pacific Biological Station Nanaimo British Columbia Canada
| | - Terry Beacham
- Department of Fisheries and Ocean Pacific Biological Station Nanaimo British Columbia Canada
| | - Louis Bernatchez
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| |
Collapse
|
7
|
Joshi J, Flores AM, Christensen KA, Johnson H, Siah A, Koop BF. An update of the salmon louse (Lepeophtheirus salmonis) reference genome assembly. G3 (Bethesda) 2022; 12:jkac087. [PMID: 35404448 PMCID: PMC9157166 DOI: 10.1093/g3journal/jkac087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/04/2022] [Indexed: 11/21/2022]
Abstract
Salmon lice have plagued the salmon farming industry and have negatively impacted salmon populations in the wild. In response, researchers have generated high density genetic maps, genome assemblies, transcriptomes, and whole-genome resequencing data to better understand this parasite. In this study, we used long-read sequencing technology to update the previous genome assemblies of Atlantic Ocean salmon lice with a more contiguous assembly and a more comprehensive gene catalog of Pacific Ocean salmon lice. We were also able to further characterize genomic features previously identified from other studies by using published resequenced genomes of 25 Atlantic and 15 Pacific salmon lice. One example was further characterizing the ZW sex chromosomes. For both the Atlantic and Pacific Ocean salmon lice subspecies, we found that the female W-chromosome is only a small fraction of the Z-chromosome and that the vast majority of the W and Z-chromosome do not contain conserved regions (i.e. pseudoautosomal regions). However, conserved orthologous protein sequences can still be identified between the W- and Z-chromosomes.
Collapse
Affiliation(s)
- Jay Joshi
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Anne-Marie Flores
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Kris A Christensen
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Hollie Johnson
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Ahmed Siah
- British Columbia Centre for Aquatic Health Sciences, Campbell River, BC V9W 2C2, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| |
Collapse
|
8
|
Salisbury S, McCracken GR, Perry R, Keefe D, Layton KKS, Kess T, Nugent CM, Leong JS, Bradbury IR, Koop BF, Ferguson MM, Ruzzante DE. The Genomic Consistency of the Loss of Anadromy in an Arctic Fish (Salvelinus alpinus). Am Nat 2022; 199:617-635. [DOI: 10.1086/719122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
9
|
Christensen KA, Rondeau EB, Sakhrani D, Biagi CA, Johnson H, Joshi J, Flores AM, Leelakumari S, Moore R, Pandoh PK, Withler RE, Beacham TD, Leggatt RA, Tarpey CM, Seeb LW, Seeb JE, Jones SJM, Devlin RH, Koop BF. The pink salmon genome: Uncovering the genomic consequences of a two-year life cycle. PLoS One 2021; 16:e0255752. [PMID: 34919547 PMCID: PMC8682878 DOI: 10.1371/journal.pone.0255752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/02/2021] [Indexed: 12/30/2022] Open
Abstract
Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A two-year life history of pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of a centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.
Collapse
Affiliation(s)
- Kris A. Christensen
- West Vancouver, Fisheries and Oceans Canada, British Columbia, Canada
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
- * E-mail: (KAC); (BFK)
| | - Eric B. Rondeau
- West Vancouver, Fisheries and Oceans Canada, British Columbia, Canada
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Dionne Sakhrani
- West Vancouver, Fisheries and Oceans Canada, British Columbia, Canada
| | - Carlo A. Biagi
- West Vancouver, Fisheries and Oceans Canada, British Columbia, Canada
| | - Hollie Johnson
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Jay Joshi
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Anne-Marie Flores
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Sreeja Leelakumari
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Richard Moore
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Pawan K. Pandoh
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Ruth E. Withler
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Terry D. Beacham
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | | | - Carolyn M. Tarpey
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - James E. Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Steven J. M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Robert H. Devlin
- West Vancouver, Fisheries and Oceans Canada, British Columbia, Canada
| | - Ben F. Koop
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
- * E-mail: (KAC); (BFK)
| |
Collapse
|
10
|
Skern-Mauritzen R, Malde K, Eichner C, Dondrup M, Furmanek T, Besnier F, Komisarczuk AZ, Nuhn M, Dalvin S, Edvardsen RB, Klages S, Huettel B, Stueber K, Grotmol S, Karlsbakk E, Kersey P, Leong JS, Glover KA, Reinhardt R, Lien S, Jonassen I, Koop BF, Nilsen F. The salmon louse genome: Copepod features and parasitic adaptations. Genomics 2021; 113:3666-3680. [PMID: 34403763 DOI: 10.1016/j.ygeno.2021.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/06/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022]
Abstract
Copepods encompass numerous ecological roles including parasites, detrivores and phytoplankton grazers. Nonetheless, copepod genome assemblies remain scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod found on salmonid fish. We present the 695.4 Mbp L. salmonis genome assembly containing ≈60% repetitive regions and 13,081 annotated protein-coding genes. The genome comprises 14 autosomes and a ZZ-ZW sex chromosome system. Assembly assessment identified 92.4% of the expected arthropod genes. Transcriptomics supported annotation and indicated a marked shift in gene expression after host attachment, including apparent downregulation of genes related to circadian rhythm coinciding with abandoning diurnal migration. The genome shows evolutionary signatures including loss of genes needed for peroxisome biogenesis, presence of numerous FNII domains, and an incomplete heme homeostasis pathway suggesting heme proteins to be obtained from the host. Despite repeated development of resistance against chemical treatments L. salmonis exhibits low numbers of many genes involved in detoxification.
Collapse
Affiliation(s)
| | - Ketil Malde
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway; Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Christiane Eichner
- Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Michael Dondrup
- Computational Biology Unit, Department of Informatics, University of Bergen, Thormøhlens Gate 55, 5008 Bergen, Norway
| | - Tomasz Furmanek
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Francois Besnier
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Anna Zofia Komisarczuk
- Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Michael Nuhn
- EMBL-The European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Sussie Dalvin
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Rolf B Edvardsen
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Sven Klages
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Carl von Linné Weg 10, D-50829 Köln, Germany
| | - Kurt Stueber
- Max Planck Genome Centre Cologne, Carl von Linné Weg 10, D-50829 Köln, Germany
| | - Sindre Grotmol
- Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Egil Karlsbakk
- Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Paul Kersey
- EMBL-The European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK; Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Jong S Leong
- Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Kevin A Glover
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway; Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Richard Reinhardt
- Max Planck Genome Centre Cologne, Carl von Linné Weg 10, D-50829 Köln, Germany
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Oluf Thesens vei 6, 1433 Ås, Norway
| | - Inge Jonassen
- Computational Biology Unit, Department of Informatics, University of Bergen, Thormøhlens Gate 55, 5008 Bergen, Norway
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Frank Nilsen
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway; Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway.
| |
Collapse
|
11
|
Kess T, Dempson JB, Lehnert SJ, Layton KKS, Einfeldt A, Bentzen P, Salisbury SJ, Messmer AM, Duffy S, Ruzzante DE, Nugent CM, Ferguson MM, Leong JS, Koop BF, O'Connell MF, Bradbury IR. Genomic basis of deep-water adaptation in Arctic Charr (Salvelinus alpinus) morphs. Mol Ecol 2021; 30:4415-4432. [PMID: 34152667 DOI: 10.1111/mec.16033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 12/30/2022]
Abstract
The post-glacial colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr (Salvelinus alpinus) provides the opportunity to study the genomic basis of adaptation to extreme deep-water environments. Colonization of deep-water (>50 m) habitats often requires extensive adaptation to cope with novel environmental challenges from high hydrostatic pressure, low temperature, and low light, but the genomic mechanisms underlying evolution in these environments are rarely known. Here, we compare genomic divergence between a deep-water morph adapted to depths of up to 288 m and a larger, piscivorous pelagic morph occupying shallower depths. Using both a SNP array and resequencing of whole nuclear and mitochondrial genomes, we find clear genetic divergence (FST = 0.11-0.15) between deep and shallow water morphs, despite an absence of morph divergence across the mitochondrial genome. Outlier analyses identified many diverged genomic regions containing genes enriched for processes such as gene expression and DNA repair, cardiac function, and membrane transport. Detection of putative copy number variants (CNVs) uncovered 385 genes with CNVs distinct to piscivorous morphs, and 275 genes with CNVs distinct to deep-water morphs, enriched for processes associated with synapse assembly. Demographic analyses identified evidence for recent and local morph divergence, and ongoing reductions in diversity consistent with postglacial colonization. Together, these results show that Arctic Charr morph divergence has occurred through genome-wide differentiation and elevated divergence of genes underlying multiple cellular and physiological processes, providing insight into the genomic basis of adaptation in a deep-water habitat following postglacial recolonization.
Collapse
Affiliation(s)
- Tony Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - J Brian Dempson
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Sarah J Lehnert
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Kara K S Layton
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Anthony Einfeldt
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Paul Bentzen
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | | | - Amber M Messmer
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Steven Duffy
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | | | - Cameron M Nugent
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Moira M Ferguson
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Jong S Leong
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Michael F O'Connell
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Ian R Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| |
Collapse
|
12
|
López ME, Cádiz MI, Rondeau EB, Koop BF, Yáñez JM. Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information. Sci Rep 2021; 11:9685. [PMID: 33958603 PMCID: PMC8102513 DOI: 10.1038/s41598-021-86154-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/08/2021] [Indexed: 01/01/2023] Open
Abstract
Animal domestication and artificial selection give rise to gradual changes at the genomic level in populations. Subsequent footprints of selection, known as selection signatures or selective sweeps, have been traced in the genomes of many animal livestock species by exploiting variation in linkage disequilibrium patterns and/or reduction of genetic diversity. Domestication of most aquatic species is recent in comparison with land animals, and salmonids are one of the most important fish species in aquaculture. Coho salmon (Oncorhynchus kisutch), cultivated primarily in Chile, has been subjected to breeding programs to improve growth, disease resistance traits, and flesh color. This study aimed to identify selection signatures that may be involved in adaptation to culture conditions and traits of productive interest. To do so, individuals of two domestic populations cultured in Chile were genotyped with 200 thousand SNPs, and analyses were conducted using iHS, XP-EHH and CLR. Several signatures of selection on different chromosomal regions were detected across both populations. Some of the identified regions under selection contained genes such anapc2, alad, chp2 and myn, which have been previously associated with body weight in Atlantic salmon, or sec24d and robo1, which have been associated with resistance to Piscirickettsia salmonis in coho salmon. Findings in our study can contribute to an integrated genome-wide map of selection signatures, to help identify the genetic mechanisms of phenotypic diversity in coho salmon.
Collapse
Affiliation(s)
- M E López
- Department of Aquatic Resources, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| | - M I Cádiz
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - E B Rondeau
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - B F Koop
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - J M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile. .,Núcleo Milenio INVASAL, Concepción, Chile.
| |
Collapse
|
13
|
Gillard GB, Grønvold L, Røsæg LL, Holen MM, Monsen Ø, Koop BF, Rondeau EB, Gundappa MK, Mendoza J, Macqueen DJ, Rohlfs RV, Sandve SR, Hvidsten TR. Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication. Genome Biol 2021; 22:103. [PMID: 33849620 PMCID: PMC8042706 DOI: 10.1186/s13059-021-02323-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address this knowledge gap, we used a comparative phylogenetic model and transcriptomic data from seven species to infer selection on gene expression in duplicated genes (ohnologs) following the salmonid WGD 80-100 million years ago. RESULTS We find rare cases of tissue-specific expression evolution but pervasive expression evolution affecting many tissues, reflecting strong selection on maintenance of genome stability following genome doubling. Ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards lower expression and possible pseudogenization. Loss of expression in one ohnolog is significantly associated with transposable element insertions in promoters and likely driven by selection on gene dosage including selection on stoichiometric balance. We also find symmetric expression shifts, and these are associated with genes under strong evolutionary constraints such as ribosome subunit genes. This possibly reflects selection operating to achieve a gene dose reduction while avoiding accumulation of "toxic mutations". Mechanistically, ohnolog regulatory divergence is dictated by the number of bound transcription factors in promoters, with transposable elements being one likely source of novel binding sites driving tissue-specific gains in expression. CONCLUSIONS Our results imply pervasive adaptive expression evolution following WGD to overcome the immediate challenges posed by genome doubling and to exploit the long-term genetic opportunities for novel phenotype evolution.
Collapse
Affiliation(s)
- Gareth B Gillard
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Lars Grønvold
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Line L Røsæg
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Matilde Mengkrog Holen
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Øystein Monsen
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, Canada
| | - Eric B Rondeau
- Department of Biology, University of Victoria, Victoria, Canada
| | - Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - John Mendoza
- Department of Computer Science, San Francisco State University, San Francisco, USA
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Rori V Rohlfs
- Department of Biology, San Francisco State University, San Francisco, USA
| | - Simen R Sandve
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Torgeir R Hvidsten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| |
Collapse
|
14
|
Christensen KA, Rondeau EB, Minkley DR, Leong JS, Nugent CM, Danzmann RG, Ferguson MM, Stadnik A, Devlin RH, Muzzerall R, Edwards M, Davidson WS, Koop BF. Retraction: The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly. PLoS One 2021; 16:e0247083. [PMID: 33561157 PMCID: PMC7872265 DOI: 10.1371/journal.pone.0247083] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
15
|
Christensen KA, Le Luyer J, Chan MTT, Rondeau EB, Koop BF, Bernatchez L, Devlin RH. Assessing the effects of genotype-by-environment interaction on epigenetic, transcriptomic, and phenotypic response in a Pacific salmon. G3 (Bethesda) 2021; 11:jkab021. [PMID: 33712817 PMCID: PMC8022943 DOI: 10.1093/g3journal/jkab021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/13/2021] [Indexed: 12/24/2022]
Abstract
Genotype-by-environment (GxE) interactions are non-parallel reaction norms among individuals with different genotypes in response to different environmental conditions. GxE interactions are an extension of phenotypic plasticity and consequently studying such interactions improves our ability to predict effects of different environments on phenotype as well as the fitness of genetically distinct organisms and their capacity to interact with ecosystems. Growth hormone transgenic coho salmon grow much faster than non-transgenics when raised in tank environments, but show little difference in growth when reared in nature-like streams. We used this model system to evaluate potential mechanisms underlying this growth rate GxE interaction, performing RNA-seq to measure gene transcription and whole-genome bisulfite sequencing to measure gene methylation in liver tissue. Gene ontology (GO) term analysis revealed stress as an important biological process potentially influencing growth rate GxE interactions. While few genes with transcription differences also had methylation differences, in promoter or gene regions, many genes were differentially methylated between tank and stream environments. A GO term analysis of differentially methylated genes between tank and stream environments revealed increased methylation in the stream environment of more than 95% of the differentially methylated genes, many with biological processes unrelated to liver function. The lower nutritional condition of the stream environment may cause increased negative regulation of genes less vital for liver tissue function than when fish are reared in tanks with unlimited food availability. These data show a large effect of rearing environment both on gene expression and methylation, but it is less clear that the detected epigenetic marks are responsible for the observed altered growth and physiological responses.
Collapse
Affiliation(s)
- Kris A Christensen
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1N6, Canada
- Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Jérémy Le Luyer
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V OA6, Canada
| | - Michelle T T Chan
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1N6, Canada
- Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Eric B Rondeau
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1N6, Canada
- Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V OA6, Canada
| | - Robert H Devlin
- Fisheries and Oceans Canada, West Vancouver, BC V7V 1N6, Canada
| |
Collapse
|
16
|
Chan MTT, Muttray A, Sakhrani D, Woodward K, Kim JH, Christensen KA, Koop BF, Devlin RH. Sexually Dimorphic Growth Stimulation in a Strain of Growth Hormone Transgenic Coho Salmon (Oncorhynchus kisutch). Mar Biotechnol (NY) 2021; 23:140-148. [PMID: 33481139 PMCID: PMC7929968 DOI: 10.1007/s10126-020-10012-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
Growth hormone (GH) transgenic fish often exhibit remarkable transformations in growth rate and other phenotypes relative to wild-type. The 5750A transgenic coho salmon strain exhibits strong sexually dimorphic growth, with females possessing growth stimulation at a level typical of that seen for both sexes in other strains harbouring the same gene construct (e.g. M77), while males display a modest level of growth stimulation. GH mRNA levels were significantly higher in females than in males of the 5750A strain but equivalent in the M77 strain, indicating sex and transgene insertion locus altered transgene expression. We found that acute estradiol treatments did not influence GH expression in either strain (5750A and M77) or the transgene promoter (metallothionein-B), suggesting that estradiol level was not a significant factor influencing transgene activity. The feminization of XX and XY fish of the 5750A and M77 strains generated all-female groups and resulted in equalized growth of the two genetic sexes, suggesting that the presence of the Y chromosome was not directly capable of influencing the GH transgene-mediated growth in a physiological female conditions. These data suggest that the difference in growth rate seen between the sexes in the 5750A strain arises from non-estradiol-mediated sex influences on gene regulation at the transgene locus. This study shows how genetic factors and transgene insertion sites can influence transgene expression with significant consequent effects on phenotype.
Collapse
Affiliation(s)
- Michelle T T Chan
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC, V7V 1N6, Canada.
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
| | - Annette Muttray
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC, V7V 1N6, Canada
- New York Institute of Technology, #1700-701 West Georgia Street, Vancouver, BC, V7Y 1K8, Canada
| | - Dionne Sakhrani
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC, V7V 1N6, Canada
| | - Krista Woodward
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC, V7V 1N6, Canada
| | - Jin-Hyoung Kim
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC, V7V 1N6, Canada
- Division of Life Sciences, Korea Polar Research Institute, 26 Sondomirae-ro, Yeonsu-gu, Incheon, 21990, South Korea
| | - Kris A Christensen
- Department of Biology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Robert H Devlin
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC, V7V 1N6, Canada
| |
Collapse
|
17
|
Salisbury SJ, McCracken GR, Perry R, Keefe D, Layton KK, Kess T, Nugent CM, Leong JS, Bradbury IR, Koop BF, Ferguson MM, Ruzzante DE. Limited genetic parallelism underlies recent, repeated incipient speciation in geographically proximate populations of an Arctic fish (
Salvelinus alpinus
). Mol Ecol 2020; 29:4280-4294. [DOI: 10.1111/mec.15634] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/20/2020] [Accepted: 08/24/2020] [Indexed: 12/16/2022]
Affiliation(s)
| | | | - Robert Perry
- Department of Environment Fish and Wildlife Division Government of Yukon Whitehorse YT Canada
| | - Donald Keefe
- Department of Environment and Conservation Wildlife Division Government of Newfoundland and Labrador Corner Brook NL Canada
| | - Kara K.S. Layton
- Department of Fisheries and Oceans Northwest Atlantic Fisheries Centre St. John's NL Canada
- Department of Ocean Sciences Memorial University of Newfoundland St. John's NL Canada
| | - Tony Kess
- Department of Fisheries and Oceans Northwest Atlantic Fisheries Centre St. John's NL Canada
| | - Cameron M. Nugent
- Department of Integrative Biology University of Guelph Guelph ON Canada
| | - Jong S. Leong
- Department of Biology University of Victoria Victoria BC Canada
| | - Ian R. Bradbury
- Department of Biology Dalhousie University Halifax NS Canada
- Department of Fisheries and Oceans Northwest Atlantic Fisheries Centre St. John's NL Canada
- Department of Ocean Sciences Memorial University of Newfoundland St. John's NL Canada
| | - Ben F. Koop
- Department of Biology University of Victoria Victoria BC Canada
- Centre for Biomedical Research University of Victoria Victoria BC Canada
| | - Moira M. Ferguson
- Department of Integrative Biology University of Guelph Guelph ON Canada
| | | |
Collapse
|
18
|
Rougemont Q, Moore JS, Leroy T, Normandeau E, Rondeau EB, Withler RE, Van Doornik DM, Crane PA, Naish KA, Garza JC, Beacham TD, Koop BF, Bernatchez L. Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon. PLoS Genet 2020; 16:e1008348. [PMID: 32845885 PMCID: PMC7478589 DOI: 10.1371/journal.pgen.1008348] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/08/2020] [Accepted: 06/24/2020] [Indexed: 12/24/2022] Open
Abstract
A thorough reconstruction of historical processes is essential for a comprehensive understanding of the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded recently, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored. Reconstruction of a species’ past demographic history from genetic data can highlight historical factors that have shaped the distribution of genetic diversity along its genome and its geographic range. Here, we combine genotyping-by-sequencing with demographic modelling to address these issues in the Coho salmon, a Pacific salmon of conservation concern in some parts of its range, notably in the south. Our demographic reconstructions reveal a linear decrease in genetic diversity toward the north of the species range, supporting the hypothesis of a northern route of postglacial recolonization from a single major southern refugium. As predicted by theory, we also observed a higher proportion of deleterious mutations in the most distant populations from this refugium. Beyond this general pattern, among-site variation in the proportion of deleterious mutations is consistent with different local trends in effective population sizes. Our results highlight the potential importance of understanding historical factors that have shaped geographic patterns of the distribution of deleterious mutations in order to implement effective management programs for the conservation of wild populations. Such fundamental knowledge of human historical demography is now having major impacts on health sciences, and we argue it is time to integrate such approaches in conservation science as well.
Collapse
Affiliation(s)
- Quentin Rougemont
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- * E-mail:
| | - Jean-Sébastien Moore
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Thibault Leroy
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Department of Botany & Biodiversity Research, University of Vienna, Vienna, Austria
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Eric B. Rondeau
- Centre for Biomedical Research, University of Victoria, Victoria, BC, Canada
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Ruth E. Withler
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Donald M. Van Doornik
- National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Manchester Research Station, Port Orchard, Washington, United States of America
| | - Penelope A. Crane
- Conservation Genetics Laboratory, U.S. Fish and Wildlife Service, Anchorage, Alaska, United States of America
| | - Kerry A. Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States of America
| | - John Carlos Garza
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service and Institute of Marine Sciences, University of California–Santa Cruz, Santa Cruz, California, United States of America
| | - Terry D. Beacham
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Ben F. Koop
- Centre for Biomedical Research, University of Victoria, Victoria, BC, Canada
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| |
Collapse
|
19
|
Layton KKS, Dempson B, Snelgrove PVR, Duffy SJ, Messmer AM, Paterson IG, Jeffery NW, Kess T, Horne JB, Salisbury SJ, Ruzzante DE, Bentzen P, Côté D, Nugent CM, Ferguson MM, Leong JS, Koop BF, Bradbury IR. Resolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fish. Evol Appl 2020; 13:1055-1068. [PMID: 32431752 PMCID: PMC7232759 DOI: 10.1111/eva.12922] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 01/02/2020] [Indexed: 12/11/2022] Open
Abstract
The resiliency of populations and species to environmental change is dependent on the maintenance of genetic diversity, and as such, quantifying diversity is central to combating ongoing widespread reductions in biodiversity. With the advent of next-generation sequencing, several methods now exist for resolving fine-scale population structure, but the comparative performance of these methods for genetic assignment has rarely been tested. Here, we evaluate the performance of sequenced microsatellites and a single nucleotide polymorphism (SNP) array to resolve fine-scale population structure in a critically important salmonid in north eastern Canada, Arctic Charr (Salvelinus alpinus). We also assess the utility of sequenced microsatellites for fisheries applications by quantifying the spatial scales of movement and exploitation through genetic assignment of fishery samples to rivers of origin and comparing these results with a 29-year tagging dataset. Self-assignment and simulation-based analyses of 111 genome-wide microsatellite loci and 500 informative SNPs from 28 populations of Arctic Charr in north-eastern Canada identified largely river-specific genetic structure. Despite large differences (~4X) in the number of loci surveyed between panels, mean self-assignment accuracy was similar with the microsatellite loci and the SNP panel (>90%). Subsequent analysis of 996 fishery-collected samples using the microsatellite panel revealed that larger rivers contribute greater numbers of individuals to the fishery and that coastal fisheries largely exploit individuals originating from nearby rivers, corroborating results from traditional tagging experiments. Our results demonstrate the efficacy of sequence-based microsatellite genotyping to advance understanding of fine-scale population structure and harvest composition in northern and understudied species.
Collapse
Affiliation(s)
- Kara K. S. Layton
- Department of Ocean SciencesMemorial University of NewfoundlandSt. John'sNLCanada
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Brian Dempson
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Paul V. R. Snelgrove
- Department of Ocean SciencesMemorial University of NewfoundlandSt. John'sNLCanada
| | - Steven J. Duffy
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Amber M. Messmer
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | | | - Nicholas W. Jeffery
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNSCanada
| | - Tony Kess
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - John B. Horne
- National Oceanic and Atmospheric AdministrationSouthwest Fisheries Science CenterLa JollaCAUSA
| | | | | | - Paul Bentzen
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| | - David Côté
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | | | | | - Jong S. Leong
- Department of BiologyUniversity of VictoriaVictoriaBCCanada
| | - Ben F. Koop
- Department of BiologyUniversity of VictoriaVictoriaBCCanada
- Centre for Biomedical ResearchUniversity of VictoriaVictoriaBCCanada
| | - Ian R. Bradbury
- Department of Ocean SciencesMemorial University of NewfoundlandSt. John'sNLCanada
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
- Department of BiologyDalhousie UniversityHalifaxNSCanada
| |
Collapse
|
20
|
Jacobs A, Carruthers M, Yurchenko A, Gordeeva NV, Alekseyev SS, Hooker O, Leong JS, Minkley DR, Rondeau EB, Koop BF, Adams CE, Elmer KR. Parallelism in eco-morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish. PLoS Genet 2020; 16:e1008658. [PMID: 32302300 PMCID: PMC7164584 DOI: 10.1371/journal.pgen.1008658] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 02/06/2020] [Indexed: 01/05/2023] Open
Abstract
Understanding the extent to which ecological divergence is repeatable is essential for predicting responses of biodiversity to environmental change. Here we test the predictability of evolution, from genotype to phenotype, by studying parallel evolution in a salmonid fish, Arctic charr (Salvelinus alpinus), across eleven replicate sympatric ecotype pairs (benthivorous-planktivorous and planktivorous-piscivorous) and two evolutionary lineages. We found considerable variability in eco-morphological divergence, with several traits related to foraging (eye diameter, pectoral fin length) being highly parallel even across lineages. This suggests repeated and predictable adaptation to environment. Consistent with ancestral genetic variation, hundreds of loci were associated with ecotype divergence within lineages of which eight were shared across lineages. This shared genetic variation was maintained despite variation in evolutionary histories, ranging from postglacial divergence in sympatry (ca. 10-15kya) to pre-glacial divergence (ca. 20-40kya) with postglacial secondary contact. Transcriptome-wide gene expression (44,102 genes) was highly parallel across replicates, involved biological processes characteristic of ecotype morphology and physiology, and revealed parallelism at the level of regulatory networks. This expression divergence was not only plastic but in part genetically controlled by parallel cis-eQTL. Lastly, we found that the magnitude of phenotypic divergence was largely correlated with the genetic differentiation and gene expression divergence. In contrast, the direction of phenotypic change was mostly determined by the interplay of adaptive genetic variation, gene expression, and ecosystem size. Ecosystem size further explained variation in putatively adaptive, ecotype-associated genomic patterns within and across lineages, highlighting the role of environmental variation and stochasticity in parallel evolution. Together, our findings demonstrate the parallel evolution of eco-morphology and gene expression within and across evolutionary lineages, which is controlled by the interplay of environmental stochasticity and evolutionary contingencies, largely overcoming variable evolutionary histories and genomic backgrounds.
Collapse
Affiliation(s)
- Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Madeleine Carruthers
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Andrey Yurchenko
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Natalia V. Gordeeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Sergey S. Alekseyev
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Oliver Hooker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Loch Lomond, Glasgow, United Kingdom
| | - Jong S. Leong
- Biology/Centre for Biomedical Research, University of Victoria, British Columbia, Canada
| | - David R. Minkley
- Biology/Centre for Biomedical Research, University of Victoria, British Columbia, Canada
| | - Eric B. Rondeau
- Biology/Centre for Biomedical Research, University of Victoria, British Columbia, Canada
| | - Ben F. Koop
- Biology/Centre for Biomedical Research, University of Victoria, British Columbia, Canada
| | - Colin E. Adams
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Loch Lomond, Glasgow, United Kingdom
| | - Kathryn R. Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| |
Collapse
|
21
|
Pearse DE, Barson NJ, Nome T, Gao G, Campbell MA, Abadía-Cardoso A, Anderson EC, Rundio DE, Williams TH, Naish KA, Moen T, Liu S, Kent M, Moser M, Minkley DR, Rondeau EB, Brieuc MSO, Sandve SR, Miller MR, Cedillo L, Baruch K, Hernandez AG, Ben-Zvi G, Shem-Tov D, Barad O, Kuzishchin K, Garza JC, Lindley ST, Koop BF, Thorgaard GH, Palti Y, Lien S. Publisher Correction: Sex-dependent dominance maintains migration supergene in rainbow trout. Nat Ecol Evol 2019; 4:170. [PMID: 31819240 DOI: 10.1038/s41559-019-1076-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Collapse
Affiliation(s)
- Devon E Pearse
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA.
| | - Nicola J Barson
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Torfinn Nome
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Guangtu Gao
- National Center for Cool and Cold Water Aquaculture, USDA-ARS, Kearneysville, WV, USA
| | - Matthew A Campbell
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Alicia Abadía-Cardoso
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Baja California, Mexico
| | - Eric C Anderson
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - David E Rundio
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - Thomas H Williams
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, WA, Seattle, USA
| | | | - Sixin Liu
- National Center for Cool and Cold Water Aquaculture, USDA-ARS, Kearneysville, WV, USA
| | - Matthew Kent
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Michel Moser
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - David R Minkley
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Eric B Rondeau
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Marine S O Brieuc
- School of Aquatic and Fishery Sciences, University of Washington, WA, Seattle, USA
| | - Simen Rød Sandve
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Michael R Miller
- Department of Animal Science, University of California, CA, Davis, USA
| | | | | | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, IL, Urbana, USA
| | | | | | | | | | - John Carlos Garza
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - Steven T Lindley
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Gary H Thorgaard
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, WA, Pullman, USA
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, USDA-ARS, Kearneysville, WV, USA.
| | - Sigbjørn Lien
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| |
Collapse
|
22
|
Pearse DE, Barson NJ, Nome T, Gao G, Campbell MA, Abadía-Cardoso A, Anderson EC, Rundio DE, Williams TH, Naish KA, Moen T, Liu S, Kent M, Moser M, Minkley DR, Rondeau EB, Brieuc MSO, Sandve SR, Miller MR, Cedillo L, Baruch K, Hernandez AG, Ben-Zvi G, Shem-Tov D, Barad O, Kuzishchin K, Garza JC, Lindley ST, Koop BF, Thorgaard GH, Palti Y, Lien S. Sex-dependent dominance maintains migration supergene in rainbow trout. Nat Ecol Evol 2019; 3:1731-1742. [DOI: 10.1038/s41559-019-1044-6] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/18/2019] [Indexed: 11/09/2022]
Abstract
AbstractMales and females often differ in their fitness optima for shared traits that have a shared genetic basis, leading to sexual conflict. Morphologically differentiated sex chromosomes can resolve this conflict and protect sexually antagonistic variation, but they accumulate deleterious mutations. However, how sexual conflict is resolved in species that lack differentiated sex chromosomes is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 55-Mb double-inversion supergene that mediates sex-specific migratory tendency through sex-dependent dominance reversal, an alternative mechanism for resolving sexual conflict. The double inversion contains key photosensory, circadian rhythm, adiposity and sex-related genes and displays a latitudinal frequency cline, indicating environmentally dependent selection. Our results show sex-dependent dominance reversal across a large autosomal supergene, a mechanism for sexual conflict resolution capable of protecting sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutations associated with typical heteromorphic sex chromosomes.
Collapse
|
23
|
Magadan S, Krasnov A, Hadi-Saljoqi S, Afanasyev S, Mondot S, Lallias D, Castro R, Salinas I, Sunyer O, Hansen J, Koop BF, Lefranc MP, Boudinot P. Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires. Front Immunol 2019; 10:2541. [PMID: 31798572 PMCID: PMC6866254 DOI: 10.3389/fimmu.2019.02541] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/14/2019] [Indexed: 12/11/2022] Open
Abstract
In teleost fish as in mammals, humoral adaptive immunity is based on B lymphocytes expressing highly diverse immunoglobulins (IG). During B cell differentiation, IG loci are subjected to genomic rearrangements of V, D, and J genes, producing a unique antigen receptor expressed on the surface of each lymphocyte. During the course of an immune response to infections or immunizations, B cell clones specific of epitopes from the immunogen are expanded and activated, leading to production of specific antibodies. Among teleost fish, salmonids comprise key species for aquaculture. Rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) are especially important from a commercial point of view and have emerged as critical models for fish immunology. The growing interest to capture accurate and comprehensive antibody responses against common pathogens and vaccines has resulted in recent efforts to sequence the IG repertoire in these species. In this context, a unified and standardized nomenclature of salmonid IG heavy chain (IGH) genes is urgently required, to improve accuracy of annotation of adaptive immune receptor repertoire dataset generated by high-throughput sequencing (AIRRseq) and facilitate comparisons between studies and species. Interestingly, the assembly of salmonids IGH genomic sequences is challenging due to the presence of two large size duplicated IGH loci and high numbers of IG genes and pseudogenes. We used data available for Atlantic salmon to establish an IMGT standardized nomenclature of IGH genes in this species and then applied the IMGT rules to the rainbow trout IGH loci to set up a nomenclature, which takes into account the specificities of Salmonid loci. This unique, consistent nomenclature for Salmonid IGH genes was then used to construct IMGT sequence reference directories allowing accurate annotation of AIRRseq data. The complex issues raised by the genetic diversity of salmon and trout strains are discussed in the context of IG repertoire annotation.
Collapse
Affiliation(s)
- Susana Magadan
- Immunology Laboratory, Biomedical Research Center, University of Vigo, Vigo, Spain
- Department of Biology, Center of Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United States
| | - Aleksei Krasnov
- Nofima AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Tromsø, Norway
| | - Saida Hadi-Saljoqi
- IMGT®, The International ImMunoGeneTics Information System® (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier, France
| | - Sergey Afanasyev
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Saint Petersburg, Russia
| | - Stanislas Mondot
- MICALIS, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Delphine Lallias
- Génétique Animale et Biologie Intégrative (GABI), INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Rosario Castro
- Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, France
| | - Irene Salinas
- Department of Biology, Center of Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United States
| | - Oriol Sunyer
- Pathobiology Department, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - John Hansen
- Western Fisheries Research Center, U.S. Geological Survey, Seattle, WA, United States
| | - Ben F. Koop
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System® (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier, France
| | - Pierre Boudinot
- Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, France
| |
Collapse
|
24
|
Lehnert SJ, Christensen KA, Vandersteen WE, Sakhrani D, Pitcher TE, Heath JW, Koop BF, Heath DD, Devlin RH. Carotenoid pigmentation in salmon: variation in expression at BCO2-l locus controls a key fitness trait affecting red coloration. Proc Biol Sci 2019; 286:20191588. [PMID: 31615356 DOI: 10.1098/rspb.2019.1588] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Carotenoids are primarily responsible for the characteristic red flesh coloration of salmon. Flesh coloration is an economically and evolutionarily significant trait that varies inter- and intra-specifically, yet the underlying genetic mechanism is unknown. Chinook salmon (Oncorhynchus tshawytscha) represents an ideal system to study carotenoid variation as, unlike other salmonids, they exhibit extreme differences in carotenoid utilization due to genetic polymorphisms. Here, we crossed populations of Chinook salmon with fixed differences in flesh coloration (red versus white) for a genome-wide association study to identify loci associated with pigmentation. Here, the beta-carotene oxygenase 2-like (BCO2-l) gene was significantly associated with flesh colour, with the most significant single nucleotide polymorphism explaining 66% of the variation in colour. BCO2 gene disruption is linked to carotenoid accumulation in other taxa, therefore we hypothesize that an ancestral mutation partially disrupting BCO2-l activity (i.e. hypomorphic mutation) allowed the deposition and accumulation of carotenoids within Salmonidae. Indeed, we found elevated transcript levels of BCO2-l in white Chinook salmon relative to red. The long-standing mystery of why salmon are red, while no other fishes are, is thus probably explained by a hypomorphic mutation in the proto-salmonid at the time of divergence of red-fleshed salmonid genera (approx. 30 Ma).
Collapse
Affiliation(s)
- S J Lehnert
- Fisheries and Oceans Canada, West Vancouver, British Columbia, Canada.,Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | - K A Christensen
- Fisheries and Oceans Canada, West Vancouver, British Columbia, Canada.,University of Victoria, Victoria, British Columbia, Canada
| | - W E Vandersteen
- Fisheries and Oceans Canada, West Vancouver, British Columbia, Canada
| | - D Sakhrani
- Fisheries and Oceans Canada, West Vancouver, British Columbia, Canada
| | - T E Pitcher
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada.,Department of Integrative Biology, University of Windsor, Windsor, Ontario, Canada
| | - J W Heath
- Yellow Island Aquaculture Ltd., Quadra Island, British Columbia, Canada
| | - B F Koop
- University of Victoria, Victoria, British Columbia, Canada
| | - D D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada.,Department of Integrative Biology, University of Windsor, Windsor, Ontario, Canada
| | - R H Devlin
- Fisheries and Oceans Canada, West Vancouver, British Columbia, Canada
| |
Collapse
|
25
|
Barría A, Christensen KA, Yoshida G, Jedlicki A, Leong JS, Rondeau EB, Lhorente JP, Koop BF, Davidson WS, Yáñez JM. Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon ( Oncorhynchus kisutch) Breeding Population Using a High-Density SNP Array. Front Genet 2019; 10:498. [PMID: 31191613 PMCID: PMC6539196 DOI: 10.3389/fgene.2019.00498] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 05/07/2019] [Indexed: 12/19/2022] Open
Abstract
The estimation of linkage disequilibrium between molecular markers within a population is critical when establishing the minimum number of markers required for association studies, genomic selection, and inferring historical events influencing different populations. This work aimed to evaluate the extent and decay of linkage disequilibrium in a coho salmon breeding population using a high-density SNP array. Linkage disequilibrium was estimated between a total of 93,502 SNPs found in 64 individuals (33 dams and 31 sires) from the breeding population. The markers encompass all 30 coho salmon chromosomes and comprise 1,684.62 Mb of the genome. The average density of markers per chromosome ranged from 48.31 to 66 per 1 Mb. The minor allele frequency averaged 0.26 (with a range from 0.22 to 0.27). The overall average linkage disequilibrium among SNPs pairs measured as r2 was 0.10. The Average r2 value decreased with increasing physical distance, with values ranging from 0.21 to 0.07 at a distance lower than 1 kb and up to 10 Mb, respectively. An r2 threshold of 0.2 was reached at distance of approximately 40 Kb. Chromosomes Okis05, Okis15 and Okis28 showed high levels of linkage disequilibrium (>0.20 at distances lower than 1 Mb). Average r2 values were lower than 0.15 for all chromosomes at distances greater than 4 Mb. An effective population size of 43 was estimated for the population 10 generations ago, and 325, for 139 generations ago. Based on the effective number of chromosome segments, we suggest that at least 74,000 SNPs would be necessary for an association mapping study and genomic predictions. Therefore, the SNP panel used allowed us to capture high-resolution information in the farmed coho salmon population. Furthermore, based on the contemporary Ne, a new mate allocation strategy is suggested to increase the effective population size.
Collapse
Affiliation(s)
- Agustín Barría
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Kris A Christensen
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, Canada
| | - Grazyella Yoshida
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Ana Jedlicki
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Jong S Leong
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, Canada
| | - Eric B Rondeau
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, Canada
| | | | - Ben F Koop
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, Canada
| | - William S Davidson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile.,Nucleo Milenio INVASAL, Concepcion, Chile
| |
Collapse
|
26
|
Christensen KA, Sakhrani D, Rondeau EB, Richards J, Koop BF, Devlin RH. Effect of triploidy on liver gene expression in coho salmon (Oncorhynchus kisutch) under different metabolic states. BMC Genomics 2019; 20:336. [PMID: 31053056 PMCID: PMC6500012 DOI: 10.1186/s12864-019-5655-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 03/27/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Triploid coho salmon are excellent models for studying gene dosage and the effects of increased cell volume on gene expression. Triploids have an additional haploid genome in each cell and have fewer but larger cells than diploid coho salmon to accommodate the increased genome size. Studying gene expression in triploid coho salmon provides insight into how gene expression may have been affected after the salmonid-specific genome duplication which occurred some 90 MYA. Triploid coho salmon are sterile and consequently can live longer and grow larger than diploid congeners in many semelparous species (spawning only once) because they never reach maturity and post-spawning mortality is averted. Triploid fishes are also of interest to the commercial sector (larger fish are more valuable) and to fisheries management since sterile fish can potentially minimize negative impacts of escaped fish in the wild. RESULTS The vast majority of genes in liver tissue had similar expression levels between diploid and triploid coho salmon, indicating that the same amount of mRNA transcripts were being produced per gene copy (positive gene dosage effects) within a larger volume cell. Several genes related to nutrition and compensatory growth were differentially expressed between diploid and triploid salmon, indicating that some loci are sensitive to cell size and/or DNA content per cell. To examine how robust expression between ploidies is under different conditions, a genetic/metabolic modifier in the form of different doses of a growth hormone transgene was used to assess gene expression under conditions that the genome has not naturally experienced or adapted to. While many (up to 1400) genes were differentially expressed between non-transgenic and transgenic fish, relatively few genes were differentially expressed between diploids and triploids with similar doses of the transgene. These observations indicate that the small effect of ploidy on gene expression is robust to large changes in physiological state. CONCLUSIONS These findings are of interest from a gene regulatory perspective, but also valuable for understanding phenotypic effects in triploids, transgenics, and triploid transgenics that could affect their utility in culture conditions and their fitness and potential consequences of release into nature.
Collapse
Affiliation(s)
- Kris A Christensen
- Fisheries and Oceans Canada, West Vancouver, BC, Canada.,Department of Biology, University of Victoria, Victoria, BC, Canada
| | | | - Eric B Rondeau
- Fisheries and Oceans Canada, West Vancouver, BC, Canada.,Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Jeffery Richards
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | | |
Collapse
|
27
|
Danzmann RG, Norman JD, Rondeau EB, Messmer AM, Kent MP, Lien S, Igboeli O, Fast MD, Koop BF. A genetic linkage map for the salmon louse (Lepeophtheirus salmonis): evidence for high male:female and inter-familial recombination rate differences. Mol Genet Genomics 2018; 294:343-363. [PMID: 30460550 DOI: 10.1007/s00438-018-1513-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/15/2018] [Indexed: 01/28/2023]
Abstract
A salmon louse (Lepeophtheirus salmonis salmonis) genetic linkage map was constructed to serve as a genomic resource for future investigations into the biology of this important marine parasitic copepod species, and to provide insights into the inheritance patterns of genetic markers in this species. SNP genotyping of 8 families confirmed the presence of 15 linkage groups based upon the assignment of 93,773 markers. Progeny sample size weight adjusted map sizes in males (with the exception of SL12 and SL15) ranged in size from 96.50 cM (SL11) to 134.61 cM (SL06), and total combined map steps or bins ranged from 143 (SL09) to 203 (SL13). The SL12 male map was the smallest linkage group with a weight-averaged size of 3.05 cM with 6 recombination bins. Male:female specific recombination rate differences are 10.49:1 and represent one of the largest reported sex-specific differences for any animal species. Recombination ratio differences (M:F) ranged from 1.0 (SL12) to 29:1 (SL15). The number of markers exhibiting normal Mendelian segregation within the sex linkage group SL15 was extremely low (N = 80) in comparison to other linkage groups genotyped [range: 1459 (SL12)-10206 markers (SL05)]. Re-evaluation of Mendelian inheritance patterns of markers unassigned to any mapping parent according to hemizygous segregation patterns (models presented) identified matches for many of these markers to hemizygous patterns. The greatest proportion of these markers assigned to SL15 (N increased to 574). Inclusion of the hemizygous markers revised SL15 sex-specific recombination rate differences to 28:1. Recombination hot- and coldspots were identified across all linkage groups with all linkage groups possessing multiple peaks. Nine of 13 linkage groups evaluated possessed adjacent domains with hot-coldspot transitional zones. The most common pattern was for one end of the linkage to show elevated recombination in addition to internal regions. For SL01 and SL06, however, a terminal region with high recombination was not evident while a central domain possessing extremely high-recombination levels was present. High levels of recombination were weakly coupled to higher levels of SNP variation within domains, but this association was very strong for the central domains of SL01 and SL06. From the pooled paternal half-sib lots (several virgin females placed with 1 male), only 1 or two surviving family lots were obtained. Surviving families possessed parents where both the male and female possessed either inherently low or high recombination rates. This study provides insight into the organization of the sea louse genome, and describes large differences in recombination rate that exist among individuals of the same sex, and between the sexes. These differences in recombination rate may be coupled to the capabilities of this species to adapt to environmental and pharmaceutical treatments, given that family survivorship appears to be enhanced when parents have similar recombination levels.
Collapse
Affiliation(s)
- Roy G Danzmann
- Department of Integrative Biology, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
| | - Joseph D Norman
- Department of Integrative Biology, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.,The Hospital for Sick Children, 686 Bay St., Toronto, ON, M5G 0A4, Canada
| | - Eric B Rondeau
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8W 3N5, Canada
| | - Amber M Messmer
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8W 3N5, Canada
| | - Matthew P Kent
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, 1432, As, Norway
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, 1432, As, Norway
| | - Okechukwu Igboeli
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada
| | - Mark D Fast
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada
| | - Ben F Koop
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8W 3N5, Canada
| |
Collapse
|
28
|
Agusti-Ridaura C, Dondrup M, Horsberg TE, Leong JS, Koop BF, Bravo S, Mendoza J, Kaur K. Caligus rogercresseyi acetylcholinesterase types and variants: a potential marker for organophosphate resistance. Parasit Vectors 2018; 11:570. [PMID: 30376873 PMCID: PMC6208076 DOI: 10.1186/s13071-018-3151-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/14/2018] [Indexed: 12/17/2022] Open
Abstract
Background Control of the sea louse Caligus rogercresseyi in the Chilean salmonid industry is reliant on chemical treatments. Azamethiphos was introduced in 2013, although other organophosphates were previously used. In 2014, reduced sensitivity to azamethiphos was detected in the Los Lagos Region using bioassays. The main target of organophosphates is the enzyme acetylcholinesterase (AChE). Mutations in the AChE gene are the main cause of organophosphate resistance in arthropods, including other sea lice. In the present study, we aimed to characterize C. rogercresseyi AChE(s) gene(s) and to study the association between AChE variants and azamethiphos resistance in this sea louse species. Methods Samples of adult male and female C. rogercresseyi were collected in the Los Lagos Region in 2014. Twenty-four hour exposure bioassays with azamethiphos were performed to select sensitive and resistant lice. The full-length cDNA coding sequences encoding for two AChEs in C. rogercresseyi were molecularly characterized. One of the AChE genes was screened by direct sequencing in the azamethiphos-selected lice to search for variants. An additional louse sampling was performed before and after an azamethiphos treatment in the field in 2017 to validate the findings. Results The molecular analysis revealed two putative AChEs in C. rogercresseyi. In silico analysis and 3D modelling of the protein sequences identified both of them as invertebrate AChE type 1; they were named C. rogercresseyi AChE1a and 1b. AChE1a had the characteristics of the main synaptic AChE, while AChE1b lacked some of the important amino acids of a typical AChE. A missense change found in the main synaptic AChE (1a), F318F/V (F290 in Torpedo californica), was associated with survival of C. rogercresseyi at high azamethiphos concentrations (bioassays and field treatment). The amino acid change was located in the acyl pocket of the active-site gorge of the protein. Conclusions The present study demonstrates the presence of two types of AChE1 genes in C. rogercresseyi. Although enzymatic assays are needed, AChE1a is most probably the main synaptic AChE. The function of AChE1b is unknown, but evidence points to a scavenger role. The AChE1a F/V318 variant is most probably involved in organophosphate resistance, and can be a good marker for resistance monitoring. Electronic supplementary material The online version of this article (10.1186/s13071-018-3151-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Celia Agusti-Ridaura
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Sea Lice Research Centre, Postboks 369 Sentrum, Oslo, NO-0102, Norway.
| | - Michael Dondrup
- Department of Informatics, University of Bergen, Sea Lice Research Centre, Thormøhlensgate 55, N-5008, Bergen, Norway
| | - Tor E Horsberg
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Sea Lice Research Centre, Postboks 369 Sentrum, Oslo, NO-0102, Norway
| | - Jong S Leong
- Biology Department, Centre for Biomedical Research, University of Victoria, Station CSC, PO Box 1700, Victoria, BC, V8W 2Y2, Canada
| | - Ben F Koop
- Biology Department, Centre for Biomedical Research, University of Victoria, Station CSC, PO Box 1700, Victoria, BC, V8W 2Y2, Canada
| | - Sandra Bravo
- Universidad Austral de Chile, Casilla 1327, Puerto Montt, Chile
| | - Julio Mendoza
- Cermaq Chile, Diego Portales 2000, Puerto Montt, Chile
| | - Kiranpreet Kaur
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Sea Lice Research Centre, Postboks 369 Sentrum, Oslo, NO-0102, Norway
| |
Collapse
|
29
|
Christensen KA, Rondeau EB, Minkley DR, Leong JS, Nugent CM, Danzmann RG, Ferguson MM, Stadnik A, Devlin RH, Muzzerall R, Edwards M, Davidson WS, Koop BF. The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly. PLoS One 2018; 13:e0204076. [PMID: 30212580 PMCID: PMC6136826 DOI: 10.1371/journal.pone.0204076] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/31/2018] [Indexed: 01/17/2023] Open
Abstract
Arctic charr have a circumpolar distribution, persevere under extreme environmental conditions, and reach ages unknown to most other salmonids. The Salvelinus genus is primarily composed of species with genomes that are structured more like the ancestral salmonid genome than most Oncorhynchus and Salmo species of sister genera. It is thought that this aspect of the genome may be important for local adaptation (due to increased recombination) and anadromy (the migration of fish from saltwater to freshwater). In this study, we describe the generation of a new genetic map, the sequencing and assembly of the Arctic charr genome (GenBank accession: GCF_002910315.2) using the newly created genetic map and a previous genetic map, and present several analyses of the Arctic charr genes and genome assembly. The newly generated genetic map consists of 8,574 unique genetic markers and is similar to previous genetic maps with the exception of three major structural differences. The N50, identified BUSCOs, repetitive DNA content, and total size of the Arctic charr assembled genome are all comparable to other assembled salmonid genomes. An analysis to identify orthologous genes revealed that a large number of orthologs could be identified between salmonids and many appear to have highly conserved gene expression profiles between species. Comparing orthologous gene expression profiles may give us a better insight into which genes are more likely to influence species specific phenotypes.
Collapse
Affiliation(s)
- Kris A. Christensen
- Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, West Vancouver, British Columbia, Canada
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
- Simon Fraser University, Molecular Biology and Biochemistry, Burnaby, British Columbia, Canada
| | - Eric B. Rondeau
- Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, West Vancouver, British Columbia, Canada
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
| | - David R. Minkley
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
| | - Jong S. Leong
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
| | - Cameron M. Nugent
- University of Guelph, Department of Integrative Biology, Guelph, Ontario, Canada
| | - Roy G. Danzmann
- University of Guelph, Department of Integrative Biology, Guelph, Ontario, Canada
| | - Moira M. Ferguson
- University of Guelph, Department of Integrative Biology, Guelph, Ontario, Canada
| | - Agnieszka Stadnik
- Simon Fraser University, Molecular Biology and Biochemistry, Burnaby, British Columbia, Canada
| | - Robert H. Devlin
- Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, West Vancouver, British Columbia, Canada
| | | | | | - William S. Davidson
- Simon Fraser University, Molecular Biology and Biochemistry, Burnaby, British Columbia, Canada
| | - Ben F. Koop
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
| |
Collapse
|
30
|
von Schalburg KR, Rondeau EB, Leong JS, Davidson WS, Koop BF. Regulatory processes that control haploid expression of salmon sperm mRNAs. BMC Res Notes 2018; 11:639. [PMID: 30176937 PMCID: PMC6122464 DOI: 10.1186/s13104-018-3749-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/30/2018] [Indexed: 11/12/2022] Open
Abstract
Objective Various stages of mRNA processing are necessary for functionally important genes required during late-stage sperm differentiation. Protein–RNA complexes form that edit, stabilize, store, deliver, localize and regulate translation of sperm mRNAs. These regulatory processes are often directed by recognition sequence elements and the particular composition of the proteins associated with the mRNAs. Previous work has shown that the cAMP response element modulator (CREM), estrogen receptor-alpha (ERα) and forkhead box L2A (FOXL2A) proteins are present in late-stage salmon sperm. Here we investigate whether these and other regulatory proteins might control processing of mRNAs not expressed until the haploid stage of development. We also examine regulatory processes that prepare and present mRNAs that generate unique products essential for differentiating sperm (i.e. for flagellar assembly and function). Results We provide evidence for potential sperm-specific recognition elements in 5′-untranslated regions (utrs) that may bind CREM, ERα, FOXL2A, Y-box and other proteins. We show that changes within the 5′-utrs and open reading frames of some sperm genes lead to distinct protein termini that may provide specific interfaces necessary for localization and function within the paternal gamete. Electronic supplementary material The online version of this article (10.1186/s13104-018-3749-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kristian R von Schalburg
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
| | - Eric B Rondeau
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Jong S Leong
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - William S Davidson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Ben F Koop
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 3N5, Canada
| |
Collapse
|
31
|
Poley JD, Braden LM, Messmer AM, Igboeli OO, Whyte SK, Macdonald A, Rodriguez J, Gameiro M, Rufener L, Bouvier J, Wadowska DW, Koop BF, Hosking BC, Fast MD. High level efficacy of lufenuron against sea lice (Lepeophtheirus salmonis) linked to rapid impact on moulting processes. Int J Parasitol Drugs Drug Resist 2018; 8:174-188. [PMID: 29627513 PMCID: PMC6039351 DOI: 10.1016/j.ijpddr.2018.02.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 02/26/2018] [Accepted: 02/28/2018] [Indexed: 11/29/2022]
Abstract
Drug resistance in the salmon louse Lepeophtheirus salmonis is a global issue for Atlantic salmon aquaculture. Multiple resistance has been described across most available compound classes with the exception of the benzoylureas. To target this gap in effective management of L. salmonis and other species of sea lice (e.g. Caligus spp.), Elanco Animal Health is developing an in-feed treatment containing lufenuron (a benzoylurea) to be administered prior to seawater transfer of salmon smolts and to provide long-term protection of salmon against sea lice infestations. Benzoylureas disrupt chitin synthesis, formation, and deposition during all moulting events. However, the mechanism(s) of action are not yet fully understood and most research completed to date has focused on insects. We exposed the first parasitic stage of L. salmonis to 700 ppb lufenuron for three hours and observed over 90% reduction in survival to the chalimus II life stage on the host, as compared to vehicle controls. This agrees with a follow up in vivo administration study on the host, which showed >95% reduction by the chalimus I stage. Transcriptomic responses of salmon lice exposed to lufenuron included genes related to moulting, epithelial differentiation, solute transport, and general developmental processes. Global metabolite profiles also suggest that membrane stability and fluidity is impacted in treated lice. These molecular signals are likely the underpinnings of an abnormal moulting process and cuticle formation observed ultrastructurally using transmission electron microscopy. Treated nauplii-staged lice exhibited multiple abnormalities in the integument, suggesting that the coordinated assembly of the epi- and procuticle is impaired. In all cases, treatment with lufenuron had rapid impacts on L. salmonis development. We describe multiple experiments to characterize the efficacy of lufenuron on eggs, larvae, and parasitic stages of L. salmonis, and provide the most comprehensive assessment of the physiological responses of a marine arthropod to a benzoylurea chemical.
Collapse
Affiliation(s)
- Jordan D Poley
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown PE, C1A 4P3, Canada.
| | - Laura M Braden
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown PE, C1A 4P3, Canada.
| | - Amber M Messmer
- Centre for Biomedical Research, Department of Biology, University of Victoria, Victoria BC, V8W 3N5, Canada.
| | - Okechukwu O Igboeli
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown PE, C1A 4P3, Canada.
| | - Shona K Whyte
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown PE, C1A 4P3, Canada.
| | - Alicia Macdonald
- Elanco Canada Limited, 150 Research Lane, Guelph, Ontario N1G 4T2, Canada.
| | - Jose Rodriguez
- Elanco Canada Limited, 150 Research Lane, Guelph, Ontario N1G 4T2, Canada.
| | - Marta Gameiro
- Elanco Canada Limited, 150 Research Lane, Guelph, Ontario N1G 4T2, Canada.
| | - Lucien Rufener
- Elanco Centre de Recherche Santé Animale SA, CH-1566 St.-Aubin, Switzerland; INVENesis LLC, Chemin de Belleroche 14, 2000 Neuchâtel, Switzerland.
| | - Jacques Bouvier
- Elanco Centre de Recherche Santé Animale SA, CH-1566 St.-Aubin, Switzerland; INVENesis LLC, Chemin de Belleroche 14, 2000 Neuchâtel, Switzerland.
| | - Dorota W Wadowska
- Electron Microscopy Laboratory, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, PEI, C1A 4P3, Canada.
| | - Ben F Koop
- Centre for Biomedical Research, Department of Biology, University of Victoria, Victoria BC, V8W 3N5, Canada.
| | - Barry C Hosking
- Elanco Canada Limited, 150 Research Lane, Guelph, Ontario N1G 4T2, Canada.
| | - Mark D Fast
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown PE, C1A 4P3, Canada.
| |
Collapse
|
32
|
Messmer AM, Leong JS, Rondeau EB, Mueller A, Despins CA, Minkley DR, Kent MP, Lien S, Boyce B, Morrison D, Fast MD, Norman JD, Danzmann RG, Koop BF. A 200K SNP chip reveals a novel Pacific salmon louse genotype linked to differential efficacy of emamectin benzoate. Mar Genomics 2018; 40:45-57. [PMID: 29673959 DOI: 10.1016/j.margen.2018.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 02/28/2018] [Accepted: 03/27/2018] [Indexed: 11/28/2022]
Abstract
Antiparasitic drugs such as emamectin benzoate (EMB) are relied upon to reduce the parasite load, particularly of the sea louse Lepeophtheirus salmonis, on farmed salmon. The decline in EMB treatment efficacy for this purpose is an important issue for salmon producers around the world, and particularly for those in the Atlantic Ocean where widespread EMB tolerance in sea lice is recognized as a significant problem. Salmon farms in the Northeast Pacific Ocean have not historically experienced the same issues with treatment efficacy, possibly due to the relatively large population of endemic salmonid hosts that serve to both redistribute surviving lice and dilute populations potentially under selection by introducing naïve lice to farms. Frequent migration of lice among farmed and wild hosts should limit the effect of farm-specific selection pressures on changes to the overall allele frequencies of sea lice in the Pacific Ocean. A previous study using microsatellites examined L. salmonis oncorhynchi from 10 Pacific locations from wild and farmed hosts and found no population structure. Recently however, a farm population of sea lice was detected where EMB bioassay exposure tolerance was abnormally elevated. In response, we have developed a Pacific louse draft genome that complements the previously-released Atlantic louse sequence. These genomes were combined with whole-genome re-sequencing data to design a highly sensitive 201,279 marker SNP array applicable for both subspecies (90,827 validated Pacific loci; 153,569 validated Atlantic loci). Notably, kmer spectrum analysis of the re-sequenced samples indicated that Pacific lice exhibit a large within-individual heterozygosity rate (average of 1 in every 72 bases) that is markedly higher than that of Atlantic individuals (1 in every 173 bases). The SNP chip was used to produce a high-density map for Atlantic sea louse linkage group 5 that was previously shown to be associated with EMB tolerance in Atlantic lice. Additionally, 478 Pacific louse samples from farmed and wild hosts obtained between 2005 and 2014 were also genotyped on the array. Clustering analysis allowed us to detect the apparent emergence of an otherwise rare genotype at a high frequency among the lice collected from two farms in 2013 that had reported elevated EMB tolerance. This genotype was not observed in louse samples collected from the same farm in 2010, nor in any lice sampled from other locations prior to 2013. However, this genotype was detected at low frequencies in louse samples from farms in two locations reporting elevated EMB tolerance in 2014. These results suggest that a rare genotype present in Pacific lice may be locally expanded in farms after EMB treatment. Supporting this hypothesis, 437 SNPs associated with this genotype were found to be in a region of linkage group 5 that overlaps the region associated with EMB resistance in Atlantic lice. Finally, five of the top diagnostic SNPs within this region were used to screen lice that had been subjected to an EMB survival assay, revealing a significant association between these SNPs and EMB treatment outcome. To our knowledge this work is the first report to identify a genetic link to altered EMB efficacy in L. salmonis in the Pacific Ocean.
Collapse
Affiliation(s)
- Amber M Messmer
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - Jong S Leong
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - Eric B Rondeau
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - Anita Mueller
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - Cody A Despins
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - David R Minkley
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - Matthew P Kent
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Brad Boyce
- Marine Harvest Canada, Campbell River, BC, Canada.
| | | | - Mark D Fast
- Department of Pathology and Microbiology, University of Prince Edward Island, Charlottetown, PEI C1A 4P3, Canada.
| | - Joseph D Norman
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; Present address: The Hospital for Sick Children, 686 Bay St., Toronto, ON M5G 0A4, Canada.
| | - Roy G Danzmann
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada; Centre for Biomedical Research, University of Victoria, Victoria, BC V8W 3N5, Canada.
| |
Collapse
|
33
|
Christensen KA, Leong JS, Sakhrani D, Biagi CA, Minkley DR, Withler RE, Rondeau EB, Koop BF, Devlin RH. Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome. PLoS One 2018; 13:e0195461. [PMID: 29621340 PMCID: PMC5886536 DOI: 10.1371/journal.pone.0195461] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/22/2018] [Indexed: 11/18/2022] Open
Abstract
When unifying genomic resources among studies and comparing data between species, there is often no better resource than a genome sequence. Having a reference genome for the Chinook salmon (Oncorhynchus tshawytscha) will enable the extensive genomic resources available for Pacific salmon, Atlantic salmon, and rainbow trout to be leveraged when asking questions related to the Chinook salmon. The Chinook salmon's wide distribution, long cultural impact, evolutionary history, substantial hatchery production, and recent wild-population decline make it an important research species. In this study, we sequenced and assembled the genome of a Chilliwack River Hatchery female Chinook salmon (gynogenetic and homozygous at all loci). With a reference genome sequence, new questions can be asked about the nature of this species, and its role in a rapidly changing world.
Collapse
Affiliation(s)
- Kris A. Christensen
- Fisheries and Oceans Canada, West Vancouver, BC, Canada
- University of Victoria, Victoria, BC, Canada
| | | | | | | | | | - Ruth E. Withler
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | | | - Ben F. Koop
- University of Victoria, Victoria, BC, Canada
| | | |
Collapse
|
34
|
Poley JD, Sutherland BJG, Fast MD, Koop BF, Jones SRM. Effects of the vertically transmitted microsporidian Facilispora margolisi and the parasiticide emamectin benzoate on salmon lice (Lepeophtheirus salmonis). BMC Genomics 2017; 18:630. [PMID: 28818044 PMCID: PMC5561633 DOI: 10.1186/s12864-017-4040-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 08/08/2017] [Indexed: 12/15/2022] Open
Abstract
Background Microsporidia are highly specialized, parasitic fungi that infect a wide range of eukaryotic hosts from all major taxa. Infections cause a variety of damaging effects on host physiology from increased stress to death. The microsporidian Facilispora margolisi infects the Pacific salmon louse (Lepeophtheirus salmonis oncorhynchi), an economically and ecologically important ectoparasitic copepod that can impact wild and cultured salmonids. Results Vertical transmission of F. margolisi was demonstrated by using PCR and in situ hybridization to identify and localize microsporidia in female L. salmonis and their offspring. Spores and developmental structures of F. margolisi were identified in 77% of F1 generation copepods derived from infected females while offspring from uninfected females all tested negative for the microsporidia. The transcriptomic response of the salmon louse to F. margolisi was profiled at both the copepodid larval stage and the pre-adult stage using microarray technology. Infected copepodids differentially expressed 577 transcripts related to stress, ATP generation and structural components of muscle and cuticle. The infection also impacted the response of the copepodid to the parasiticide emamectin benzoate (EMB) at a low dose of 1.0 ppb for 24 h. A set of 48 transcripts putatively involved in feeding and host immunomodulation were up to 8-fold underexpressed in the F. margolisi infected copepodids treated with EMB compared with controls or either stressor alone. Additionally, these infected lice treated with EMB also overexpressed 101 transcripts involved in stress resistance and signalling compared to the other groups. In contrast, infected pre-adult lice did not display a stress response, suggesting a decrease in microsporidian virulence associated with lice maturity. Furthermore, copepodid infectivity and moulting was not affected by the microsporidian infection. Conclusions This study demonstrated that F. margolisi is transmitted vertically between salmon louse generations and that biological impacts of infection differ depending on the stage of the copepod host. The infection caused significant perturbations of larval transcriptomes and therefore must be considered in future studies in which impacts to host development and environmental factors are assessed. Fitness impacts are probably minor, although the interaction between pesticide exposure and microsporidian infection merits further study. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4040-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jordan D Poley
- Atlantic Veterinary College, University of Prince Edward Island, Department of Pathology & Microbiology, 550 University Ave, Charlottetown, PE, C1A 4P3, Canada
| | - Ben J G Sutherland
- Centre for Biomedical Research, Department of Biology, University of Victoria, 3800 Finnerty Rd, Victoria, BC, V8W 3N5, Canada.,Institut de Biologie Intégrative et des Systèmes (IBIS), Département de biologie, Université Laval, 1030 Avenue de la Medecine, Québec, QC, G1V 0A6, Canada
| | - Mark D Fast
- Atlantic Veterinary College, University of Prince Edward Island, Department of Pathology & Microbiology, 550 University Ave, Charlottetown, PE, C1A 4P3, Canada
| | - Ben F Koop
- Centre for Biomedical Research, Department of Biology, University of Victoria, 3800 Finnerty Rd, Victoria, BC, V8W 3N5, Canada
| | - Simon R M Jones
- Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada.
| |
Collapse
|
35
|
Macqueen DJ, Primmer CR, Houston RD, Nowak BF, Bernatchez L, Bergseth S, Davidson WS, Gallardo-Escárate C, Goldammer T, Guiguen Y, Iturra P, Kijas JW, Koop BF, Lien S, Maass A, Martin SAM, McGinnity P, Montecino M, Naish KA, Nichols KM, Ólafsson K, Omholt SW, Palti Y, Plastow GS, Rexroad CE, Rise ML, Ritchie RJ, Sandve SR, Schulte PM, Tello A, Vidal R, Vik JO, Wargelius A, Yáñez JM. Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture. BMC Genomics 2017; 18:484. [PMID: 28655320 PMCID: PMC5488370 DOI: 10.1186/s12864-017-3862-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 06/14/2017] [Indexed: 11/21/2022] Open
Abstract
We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.
Collapse
Affiliation(s)
- Daniel J. Macqueen
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ UK
| | - Craig R. Primmer
- Department of Biology, University of Turku, 20014 Turku, Finland
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG UK
| | - Barbara F. Nowak
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, TAS Australia
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6 Canada
| | - Steinar Bergseth
- The Research Council of Norway, Drammensveien 288, P.O. Box 564, NO-1327 Lysaker, Norway
| | - William S. Davidson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Cristian Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research, Department of Oceanography, Universidad de Concepción, 4030000 Concepción, Chile
| | - Tom Goldammer
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Fish Genetics Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Yann Guiguen
- INRA, UR1037 Fish Physiology and Genomics, Rennes, France
| | - Patricia Iturra
- Human Genetics Program ICBM Faculty of Medicine, University of Chile, Santiago, Chile
| | | | - Ben F. Koop
- Department of Biology, University of Victoria, Victoria, BC V8W 3N5 Canada
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Alejandro Maass
- Center for Mathematical Modelling, Department of Mathematical Engineering, University of Chile, 8370456 Santiago, Chile
- Center for Genome Regulation, University of Chile, 8370456 Santiago, Chile
| | - Samuel A. M. Martin
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ UK
| | - Philip McGinnity
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Martin Montecino
- Center for Biomedical Research, Universidad Andres Bello, 8370146 Santiago, Chile
- FONDAP Center for Genome Regulation, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, 8370146 Santiago, Chile
| | - Kerry A. Naish
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195 USA
| | - Krista M. Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd E, Seattle, WA 98112 USA
| | | | - Stig W. Omholt
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, NO-1432 Ås, Norway
- NTNU - Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, USDA ARS, 11861 Leetown Road, Kearneysville, WV 25430 USA
| | - Graham S. Plastow
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Caird E. Rexroad
- Office of National Programs, USDA ARS, 5601 Sunnyside Avenue, Beltsville, MD 20705-5148 USA
| | - Matthew L. Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, 1 Marine Lab Road, St. John’s, NL A1C 5S7 Canada
| | - Rachael J. Ritchie
- Genome British Columbia, Suite 400 – 575, West 8th Avenue, Vancouver, BC V5Z 0C4 Canada
| | - Simen R. Sandve
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Patricia M. Schulte
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC V6T 1Z4 Canada
| | - Alfredo Tello
- Instituto Tecnológico del Salmón S.A., INTESAL de SalmonChile, Puerto Montt, Chile
| | - Rodrigo Vidal
- Laboratory of Molecular Ecology, Genomics, and Evolutionary Studies, Department of Biology, University of Santiago, 9170022 Santiago, Chile
| | - Jon Olav Vik
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Anna Wargelius
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817 Bergen, Norway
| | - José Manuel Yáñez
- Faculty of Veterinary and Animal Sciences, University of Chile, Av. Santa Rosa 11735, Santiago, Chile & Aquainnovo, Cardonal s/n, Puerto Montt, Chile
| |
Collapse
|
36
|
Sutherland BJ, Covello JM, Friend SE, Poley JD, Koczka KW, Purcell SL, MacLeod TL, Donovan BR, Pino J, González-Vecino JL, Gonzalez J, Troncoso J, Koop BF, Wadsworth SL, Fast MD. Host–parasite transcriptomics during immunostimulant-enhanced rejection of salmon lice (Lepeophtheirus salmonis) by Atlantic salmon (Salmo salar). Facets (Ott) 2017. [DOI: 10.1139/facets-2017-0020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Salmon lice ( Lepeophtheirus salmonis) are important ectoparasites of wild and farmed salmonids and cause major losses to the salmon farming industry throughout the Northern Hemisphere. With the emergence of resistance to several commonly used parasiticides, novel control strategies and integration of multiple treatment options are needed, including host immunostimulation. Here, we investigate the effects of a functional feed containing a peptidoglycan and nucleotide formulation on L. salmonis infection of Atlantic salmon ( Salmo salar) by characterizing lice infection levels, the expression of several host immune genes, and the parasite transcriptomic response to the immunostimulated host. Although initial infection intensities were low, the low dose (LD) immunostimulant diet reduced the total lice burden by 50% relative to controls. Immunostimulant fed hosts up-regulated interleukin-1β in the skin and spleen. This gene has been implicated in successful responses of several salmonid species to salmon lice but is typically not observed in Atlantic salmon, suggesting a favorable influence on the immune response. Lice infecting LD immunostimulated salmon overexpressed genes putatively involved in parasite immunity, including carboxylesterases, and underexpressed genes putatively involved in feeding (e.g., proteases). These lice response genes further improve the characterization of the transcriptome of the non-model parasite by identifying genes potentially involved in evading host immunity.
Collapse
Affiliation(s)
- Ben J.G. Sutherland
- Centre for Biomedical Research, Department of Biology, University of Victoria, Victoria, BC V8W 3N5, Canada
| | - Jennifer M. Covello
- Hoplite Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
| | - Sarah E. Friend
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA
| | - Jordan D. Poley
- Hoplite Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
| | - Kim W. Koczka
- Centre for Biomedical Research, Department of Biology, University of Victoria, Victoria, BC V8W 3N5, Canada
| | - Sara L. Purcell
- Hoplite Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
| | - Tara L. MacLeod
- Hoplite Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
| | - Bridget R. Donovan
- Hoplite Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
| | - Jorge Pino
- EWOS/Cargill Innovation Center—Colaco, Colaco KM5, Puerto Montt, Chile
| | | | - Javier Gonzalez
- EWOS/Cargill Innovation Center—Colaco, Colaco KM5, Puerto Montt, Chile
| | - Jose Troncoso
- EWOS/Cargill Innovation Center—Colaco, Colaco KM5, Puerto Montt, Chile
| | - Ben F. Koop
- Centre for Biomedical Research, Department of Biology, University of Victoria, Victoria, BC V8W 3N5, Canada
| | | | - Mark D. Fast
- Hoplite Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA
| |
Collapse
|
37
|
Braden LM, Sutherland BJG, Koop BF, Jones SRM. Enhanced transcriptomic responses in the Pacific salmon louse Lepeophtheirus salmonis oncorhynchi to the non-native Atlantic Salmon Salmo salar suggests increased parasite fitness. BMC Genomics 2017; 18:110. [PMID: 28137252 PMCID: PMC5282744 DOI: 10.1186/s12864-017-3520-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/26/2017] [Indexed: 12/03/2022] Open
Abstract
Background Outcomes of infections with the salmon louse Lepeophtheirus salmonis vary considerably among its natural hosts (Salmo, Oncorhynchus spp.). Host-parasite interactions range from weak to strong host responses accompanied by high to low parasite abundances, respectively. Parasite behavioral studies indicate that the louse prefers the host Atlantic Salmon (Salmo salar), which is characterized by a weak immune response, and that this results in enhanced parasite reproduction and growth rates. Furthermore, parasite-derived immunosuppressive molecules (e.g., proteases) have been detected at higher amounts in response to the mucus of Atlantic Salmon relative to Coho Salmon (Oncorhynchus kisutch). However, the host-specific responses of the salmon louse have not been well characterized in either of the genetically distinct sub-species that occur in the Atlantic and Pacific Oceans. Results We assessed and compared the transcriptomic feeding response of the Pacific salmon louse (L. salmonis oncorhynchi,) while parasitizing the highly susceptible Atlantic Salmon and Sockeye Salmon (Oncorhynchus nerka) or the more resistant Coho Salmon (Oncorhynchus kisutch) using a 38 K oligonucleotide microarray. The response of the louse was enhanced both in the number of overexpressed genes and in the magnitude of expression while feeding on the non-native Atlantic Salmon, compared to either Coho or Sockeye Salmon. For example, putative virulence factors (e.g., cathepsin L, trypsin, carboxypeptidase B), metabolic enzymes (e.g., cytochrome B, cytochrome C), protein synthesis enzymes (e.g., ribosomal protein P2, 60S ribosomal protein L7), and reproduction-related genes (e.g., estrogen sulfotransferase) were overexpressed in Atlantic-fed lice, indicating heightened parasite fitness with this host species. In contrast, responses in Coho- or Sockeye-fed lice were more similar to those of parasites deprived of a host. To test for host acclimation by the parasite, we performed a reciprocal host transfer experiment and determined that the exaggerated response to Atlantic Salmon was independent of the initial host species, confirming our conclusion that the Pacific salmon louse exhibits an enhanced response to Atlantic Salmon. Conclusions This study characterized global transcriptomic responses of Pacific salmon lice during infection of susceptible and resistant hosts. Similar parasite responses during infection of Coho or Sockeye Salmon, despite differences in natural immunity to infection between these host species, indicate that host susceptibility status alone does not drive the parasite response. We identified an enhanced louse response after feeding on Atlantic Salmon, characterized by up-regulation of virulence factors, energy metabolism and reproductive-associated transcripts. In contrast, the responses of lice infecting Coho or Sockeye Salmon were weaker, with reduced expression of virulence factors. These observations indicate that the response of the louse is independent of host susceptibility and suggest that co-evolutionary host-parasite relationships may influence contemporary host-parasite interactions. This research improves our understanding of the susceptibility of Atlantic Salmon and may assist in the development of novel control measures against the salmon louse. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3520-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Laura M Braden
- Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada.,Present Address: Department of Pathology and Microbiology, Atlantic Veterinary College, Charlottetown, Prince Edward Island, Canada
| | - Ben J G Sutherland
- Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada.,Present Address: Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Ben F Koop
- Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
| | - Simon R M Jones
- Pacific Biological Station, Fisheries & Oceans Canada, Nanaimo, British Columbia, Canada.
| |
Collapse
|
38
|
Poley JD, Braden LM, Messmer AM, Whyte SK, Koop BF, Fast MD. Cypermethrin exposure induces metabolic and stress-related gene expression in copepodid salmon lice (Lepeophtheirus salmonis). Comp Biochem Physiol Part D Genomics Proteomics 2016; 20:74-84. [PMID: 27612154 DOI: 10.1016/j.cbd.2016.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 08/05/2016] [Accepted: 08/11/2016] [Indexed: 01/12/2023]
Abstract
Cypermethrin has been administered for decades to control salmon lice (Lepeophtheirus salmonis) infestations in Atlantic salmon farming regions globally. However, resistance to cypermethrin and other available therapeutants has threatened the sustainability of this growing industry. To better understand the effects of cypermethrin on L. salmonis, a 38K oligonucleotide microarray and RT-qPCR analyses were applied to pools of copepodid larvae exposed to 1.0ppb cypermethrin or seawater controls for 24h. Phenotypic assessments and global gene expression profiles showed a significant disruption of homeostasis in copepodid L. salmonis exposed to cypermethrin. Multiple degradative enzymes were overexpressed in cypermethrin-treated lice including five trypsin-like serine proteases and three cytochrome p450s CYP3a24 (p=0.03, fold change (FC)=3.8; GenBank accession no. JP326960.1), CYP6w1 (p=0.008, FC=5.3; GenBank accession no. JP317875.1), and CYP6d4 (p=0.01; FC=7.9; GenBank accession no. JP334550.1). These enzymes represent preliminary markers for understanding the physiological response of L. salmonis to cypermethrin exposure. A general stress response was also observed in cypermethrin-treated lice which included differential expression of cell signaling genes involved in the induction of cell growth, solute transport, and metabolism. Lastly, a consensus-based analysis was completed with two previously published L. salmonis transcriptome studies revealing genes that respond to cypermethrin, emamectin benzoate (another delousing agent) and hyposalinity. This included concordant differential expression of heat shock beta-1, ammonium transporter Rh types B, and 72kDa type IV collagenase across different L. salmonis studies. This is currently the most comprehensive transcriptome assessment of chemical exposure on the first infectious stage of L. salmonis, providing novel markers for studying drug resistance and general stress in this important parasite.
Collapse
Affiliation(s)
- Jordan D Poley
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, PE, C1A 4P3, Canada.
| | - Laura M Braden
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, PE, C1A 4P3, Canada.
| | - Amber M Messmer
- Centre for Biomedical Research, Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada.
| | - Shona K Whyte
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, PE, C1A 4P3, Canada.
| | - Ben F Koop
- Centre for Biomedical Research, Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada.
| | - Mark D Fast
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, PE, C1A 4P3, Canada.
| |
Collapse
|
39
|
Poley JD, Sutherland BJG, Jones SRM, Koop BF, Fast MD. Sex-biased gene expression and sequence conservation in Atlantic and Pacific salmon lice (Lepeophtheirus salmonis). BMC Genomics 2016; 17:483. [PMID: 27377915 PMCID: PMC4932673 DOI: 10.1186/s12864-016-2835-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/13/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Salmon lice, Lepeophtheirus salmonis (Copepoda: Caligidae), are highly important ectoparasites of farmed and wild salmonids, and cause multi-million dollar losses to the salmon aquaculture industry annually. Salmon lice display extensive sexual dimorphism in ontogeny, morphology, physiology, behavior, and more. Therefore, the identification of transcripts with differential expression between males and females (sex-biased transcripts) may help elucidate the relationship between sexual selection and sexually dimorphic characteristics. RESULTS Sex-biased transcripts were identified from transcriptome analyses of three L. salmonis populations, including both Atlantic and Pacific subspecies. A total of 35-43 % of all quality-filtered transcripts were sex-biased in L. salmonis, with male-biased transcripts exhibiting higher fold change than female-biased transcripts. For Gene Ontology and functional analyses, a consensus-based approach was used to identify concordantly differentially expressed sex-biased transcripts across the three populations. A total of 127 male-specific transcripts (i.e. those without detectable expression in any female) were identified, and were enriched with reproductive functions (e.g. seminal fluid and male accessory gland proteins). Other sex-biased transcripts involved in morphogenesis, feeding, energy generation, and sensory and immune system development and function were also identified. Interestingly, as observed in model systems, male-biased L. salmonis transcripts were more frequently without annotation compared to female-biased or unbiased transcripts, suggesting higher rates of sequence divergence in male-biased transcripts. CONCLUSIONS Transcriptome differences between male and female L. salmonis described here provide key insights into the molecular mechanisms controlling sexual dimorphism in L. salmonis. This analysis offers targets for parasite control and provides a foundation for further analyses exploring critical topics such as the interaction between sex and drug resistance, sex-specific factors in host-parasite relationships, and reproductive roles within L. salmonis.
Collapse
Affiliation(s)
- Jordan D Poley
- Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, PE, C1A 4P3, Canada
| | - Ben J G Sutherland
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Rd, Victoria, BC, V8W 3 N5, Canada.,Present address: Département de biologie, Institut de Biologie Intégrative et des Systèms (IBIS), Université Laval, 1030 Avenue de la Medecine, Québec, QC, Canada
| | - Simon R M Jones
- Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6 N7, Canada
| | - Ben F Koop
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Rd, Victoria, BC, V8W 3 N5, Canada
| | - Mark D Fast
- Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, PE, C1A 4P3, Canada.
| |
Collapse
|
40
|
Rondeau EB, Laurie CV, Johnson SC, Koop BF. A PCR assay detects a male-specific duplicated copy of Anti-Müllerian hormone (amh) in the lingcod (Ophiodon elongatus). BMC Res Notes 2016; 9:230. [PMID: 27103037 PMCID: PMC4840878 DOI: 10.1186/s13104-016-2030-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/07/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Anti-Müllerian hormone (amh) or Müllerian-inhibiting substance (mis) is a member of the transforming growth factor-β family of hormones. This gene plays a key role in vertebrate male sex-determination by inhibiting the development of the Müllerian ducts, and has been shown to be the master sex-determinant in the Patagonian pejerrey. RESULTS In the lingcod, Ophiodon elongatus, both males and females share one copy of amh, however we have identified a second duplicate copy that appears solely in the male individuals. We have developed a PCR-based assay targeting the TGF-β domain of amh that provides a simple method with which to sex lingcod from a small amount of tissue. An analysis across 57 individuals gave a 100% success rate in identifying the phenotypic sex. CONCLUSIONS We present a simple method to sex lingcod through non-lethal tissue sampling. A third, independent, male-specific duplication of amh in a teleost fish has been identified in the lingcod.
Collapse
Affiliation(s)
- Eric B Rondeau
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Cassandra V Laurie
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Stewart C Johnson
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, V9T 6N7, Canada
| | - Ben F Koop
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 3N5, Canada.
| |
Collapse
|
41
|
Kim JH, Leong JS, Koop BF, Devlin RH. Multi-tissue transcriptome profiles for coho salmon (Oncorhynchus kisutch), a species undergoing rediploidization following whole-genome duplication. Mar Genomics 2015; 25:33-37. [PMID: 26614614 DOI: 10.1016/j.margen.2015.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/16/2015] [Accepted: 11/17/2015] [Indexed: 01/15/2023]
Abstract
Salmonids are an important family of fish both from economic and basic research perspectives, and have been subjected to extensive research at whole-animal and molecular levels. Most research to date has been conducted on Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), but more recently other salmonids have become a focus of study due to their interesting life histories and because of their potential for use in commercial aquaculture. However, molecular biology and genetic analyses for these emerging species are currently hampered due to the lack of extensive genomic resources. To overcome some of these limitations, we have constructed a 43,228 sequence transcriptome from 13 tissues from coho salmon, Oncorhynchus kisutch using de novo transcriptome assembly methods. The transcriptome profiling analysis has provided data distinguishing allelic variation from paralogues that arose during the recent whole-genome duplication event in this family, thus allowing simplified analysis of gene-specific expression. Additionally, 1599 novel coho sequences have been identified through comparison with transcriptomes from two other salmonids species (Atlantic salmon and rainbow trout), and with northern pike. The transcriptome presented here will be useful for genomic analysis of coho salmon and other closely related salmonid species.
Collapse
Affiliation(s)
- Jin-Hyoung Kim
- Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, 4160 Marine Drive, West Vancouver, British Columbia V7V 1N6, Canada
| | - Jong S Leong
- Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Robert H Devlin
- Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, 4160 Marine Drive, West Vancouver, British Columbia V7V 1N6, Canada.
| |
Collapse
|
42
|
Braden LM, Barker DE, Koop BF, Jones SRM. Differential modulation of resistance biomarkers in skin of juvenile and mature pink salmon, Oncorhynchus gorbuscha by the salmon louse, Lepeophtheirus salmonis. Fish Shellfish Immunol 2015; 47:7-14. [PMID: 26272636 DOI: 10.1016/j.fsi.2015.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 07/29/2015] [Accepted: 08/07/2015] [Indexed: 06/04/2023]
Abstract
Juvenile pink salmon larger than 0.7 g reject the sea louse, Lepeophtheirus salmonis, and are considered resistant to the infection. Robust innate defense responses in the skin contribute to the observed resistance. In contrast adult pink salmon captured at sea or shortly before spawning carry large numbers of the parasite, suggesting inability to control the infection. The purpose of this research is to better understand these apparently contradictory conclusions by comparing a suite of genetic and cellular markers of resistance to L. salmonis in the skin of juvenile and mature pink salmon. The expression of major histocompatibility factor II, C-reactive protein, interleukin-1β, interleukin-8 and cyclooxygenase-2 was down-regulated in mature but not juvenile pink salmon. Similarly, skin at the site of parasite attachment in juvenile salmon was highly populated with MHIIβ(+) and IL-1β(+) cells that were either absent, or at reduced levels at similar sites in mature salmon. In addition, mucocyte density was relatively low in the skin of mature salmon, irrespective of louse infection. In juveniles, the higher mucocyte density decreased following louse attachment. We show that in mature pink salmon, genetic and histological responses in skin are depressed and speculate that salmonid defense against L. salmonis is modulated by maturation.
Collapse
Affiliation(s)
- Laura M Braden
- Department of Biology, University of Victoria, Victoria, B.C., V8W 3N5, Canada
| | - Duane E Barker
- Fisheries & Aquaculture Department, Vancouver Island University, Nanaimo, B.C., V9R 5S5, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, B.C., V8W 3N5, Canada
| | - Simon R M Jones
- Department of Biology, University of Victoria, Victoria, B.C., V8W 3N5, Canada; Fisheries and Ocean Canada, Pacific Biological Station, Nanaimo, B.C., V9T 6N7, Canada.
| |
Collapse
|
43
|
Müller A, Sutherland BJG, Koop BF, Johnson SC, Garver KA. Infectious hematopoietic necrosis virus (IHNV) persistence in Sockeye Salmon: influence on brain transcriptome and subsequent response to the viral mimic poly(I:C). BMC Genomics 2015; 16:634. [PMID: 26306576 PMCID: PMC4549833 DOI: 10.1186/s12864-015-1759-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/07/2015] [Indexed: 11/10/2022] Open
Abstract
Background Sockeye Salmon are an iconic species widely distributed throughout the North Pacific. A devastating pathogen of Sockeye Salmon is infectious hematopoietic necrosis virus (IHNV, genus Novirhabdovirus, family Rhabdoviridae). It has been postulated that IHNV is maintained in salmon populations by persisting over the life of its host and/or by residing in natural reservoirs other than its susceptible hosts. Herein we demonstrate the presence of IHNV in the brain of Sockeye Salmon that survived an experimentally-induced outbreak, suggesting the presence of viral persistence in this susceptible species. To understand the viral persistent state in Sockeye Salmon we profiled the transcriptome to evaluate the host response in asymptomatic carriers and to determine what effects (if any) IHNV exposure may have on subsequent virus challenges. Results A laboratory disease model to simulate a natural IHNV outbreak in Sockeye Salmon resulted in over a third of the population incurring acute IHN disease and mortality during the first four months after initial exposure. Nine months post IHNV exposure, despite the absence of disease and mortality, a small percentage (<4 %) of the surviving population contained IHNV in brain. Transcriptome analysis in brain of asymptomatic virus carriers and survivors without virus exhibited distinct transcriptional profiles in comparison to naïve fish. Characteristic for carriers was the up-regulation of genes involved in antibody production and antigen presentation. In both carriers and survivors a down-regulation of genes related to cholesterol biosynthesis, resembling an antiviral mechanism observed in higher vertebrates was revealed along with differences in nervous system development. Moreover, following challenge with poly(I:C), survivors and carriers displayed an elevated antiviral immune response in comparison to naïve fish. Conclusions IHN virus persistence was identified in Sockeye Salmon where it elicited a unique brain transcriptome profile suggesting an ongoing adaptive immune response. IHNV carriers remained uncompromised in mounting efficient innate antiviral responses when exposed to a viral mimic. The capacity of IHNV to reside in asymptomatic hosts supports a virus carrier hypothesis and if proven infectious, could have significant epidemiological consequences towards maintaining and spreading IHNV among susceptible host populations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1759-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Anita Müller
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, V9T 6N7, British Columbia, Canada.
| | - Ben J G Sutherland
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5, Canada. .,Present address: Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada.
| | - Ben F Koop
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5, Canada.
| | - Stewart C Johnson
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, V9T 6N7, British Columbia, Canada.
| | - Kyle A Garver
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, V9T 6N7, British Columbia, Canada.
| |
Collapse
|
44
|
Grimholt U, Tsukamoto K, Azuma T, Leong J, Koop BF, Dijkstra JM. A comprehensive analysis of teleost MHC class I sequences. BMC Evol Biol 2015; 15:32. [PMID: 25888517 PMCID: PMC4364491 DOI: 10.1186/s12862-015-0309-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/16/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND MHC class I (MHCI) molecules are the key presenters of peptides generated through the intracellular pathway to CD8-positive T-cells. In fish, MHCI genes were first identified in the early 1990's, but we still know little about their functional relevance. The expansion and presumed sub-functionalization of cod MHCI and access to many published fish genome sequences provide us with the incentive to undertake a comprehensive study of deduced teleost fish MHCI molecules. RESULTS We expand the known MHCI lineages in teleosts to five with identification of a new lineage defined as P. The two lineages U and Z, which both include presumed peptide binding classical/typical molecules besides more derived molecules, are present in all teleosts analyzed. The U lineage displays two modes of evolution, most pronouncedly observed in classical-type alpha 1 domains; cod and stickleback have expanded on one of at least eight ancient alpha 1 domain lineages as opposed to many other teleosts that preserved a number of these ancient lineages. The Z lineage comes in a typical format present in all analyzed ray-finned fish species as well as lungfish. The typical Z format displays an unprecedented conservation of almost all 37 residues predicted to make up the peptide binding groove. However, also co-existing atypical Z sub-lineage molecules, which lost the presumed peptide binding motif, are found in some fish like carps and cavefish. The remaining three lineages, L, S and P, are not predicted to bind peptides and are lost in some species. CONCLUSIONS Much like tetrapods, teleosts have polymorphic classical peptide binding MHCI molecules, a number of classical-similar non-classical MHCI molecules, and some members of more diverged MHCI lineages. Different from tetrapods, however, is that in some teleosts the classical MHCI polymorphism incorporates multiple ancient MHCI domain lineages. Also different from tetrapods is that teleosts have typical Z molecules, in which the residues that presumably form the peptide binding groove have been almost completely conserved for over 400 million years. The reasons for the uniquely teleost evolution modes of peptide binding MHCI molecules remain an enigma.
Collapse
Affiliation(s)
| | - Kentaro Tsukamoto
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan.
| | - Teruo Azuma
- Fisheries Technology Division, National Research Institute of Fisheries Engineering, 7620-7, Hasaki, Kamisu-shi, Ibaraki, Japan.
| | - Jong Leong
- Centre for Biomedical Research, Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, Canada.
| | - Ben F Koop
- Centre for Biomedical Research, Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, Canada.
| | - Johannes M Dijkstra
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan.
| |
Collapse
|
45
|
Grimholt U, Hauge H, Hauge AG, Leong J, Koop BF. Chemokine receptors in Atlantic salmon. Dev Comp Immunol 2015; 49:79-95. [PMID: 25445904 DOI: 10.1016/j.dci.2014.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 11/09/2014] [Accepted: 11/10/2014] [Indexed: 06/04/2023]
Abstract
Teleost sequence data have revealed that many immune genes have evolved differently when compared to other vertebrates. Thus, each gene family needs functional studies to define the biological role of individual members within major species groups. Chemokine receptors, being excellent markers for various leukocyte subpopulations, are one such example where studies are needed to decipher individual gene function. The unique salmonid whole genome duplication that occurred approximately 95 million years ago has provided salmonids with many additional duplicates further adding to the complexity and diversity. Here we have performed a systematic study of these receptors in Atlantic salmon with particular focus on potential inflammatory receptors. Using the preliminary salmon genome data we identified 48 chemokine or chemokine-like receptors including orthologues to the ten receptors previously published in trout. We found expressed support for 40 of the bona fide salmon receptors. Eighteen of the chemokine receptors are duplicated, and when tested against a diploid sister group the majority were shown to be remnants of the 4R whole genome duplication with subsequent high sequence identity. The salmon chemokine receptor repertoire of 40 expressed bona fide genes is comparably larger than that found in humans with 23 receptors. Diversification has been a major driving force for these duplicate genes with the main variability residing in ligand binding and signalling domains.
Collapse
Affiliation(s)
| | - Helena Hauge
- Norwegian Veterinary Institute, P.O. Box 750 Sentrum, 0106 Oslo, Norway
| | | | - Jong Leong
- Centre for Biomedical Research, Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, Canada
| | - Ben F Koop
- Centre for Biomedical Research, Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, Canada
| |
Collapse
|
46
|
Braden LM, Koop BF, Jones SRM. Signatures of resistance to Lepeophtheirus salmonis include a TH2-type response at the louse-salmon interface. Dev Comp Immunol 2015; 48:178-91. [PMID: 25453579 DOI: 10.1016/j.dci.2014.09.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 09/26/2014] [Accepted: 09/26/2014] [Indexed: 05/08/2023]
Abstract
Disease outbreaks with the salmon louse Lepeophtheirus salmonis cause significant economic losses in mariculture operations worldwide. Variable innate immune responses at the louse-attachment site contribute to differences in susceptibility among species such that members of Salmo spp. are more susceptible to infection than those of some Oncorhynchus spp. Relatively little is known about the mechanisms that contribute to disease resistance or susceptibility to L. salmonis in salmon. Here, we utilize histochemistry and transcriptomics in a comparative infection model with susceptible (Atlantic, sockeye) and resistant (coho) salmon. At least three cell populations (MHIIβ+, IL1β+, TNFα+) were activated in coho salmon skin during L. salmonis infection. Locally elevated expression of several pro-inflammatory mediators (e.g. IL1β, IL8, TNFα, COX2, C/EBPβ), and tissue repair enzymes (MMP9, MMP13) were detected in susceptible and resistant species. However, responses specific to coho salmon (e.g. IL4, IL6, TGFβ) or responses shared among susceptible salmon (e.g. SAP, TRF, Cath in Atlantic and sockeye salmon) provide evidence for species-specific pathways contributing to resistance or susceptibility, respectively. Our results confirm the importance of an early pro-inflammatory TH1-type pathway as an initial host response during infection with Pacific sea lice, and demonstrate subsequent regulatory TH2-type processes as candidate defense mechanisms in the skin of resistant coho salmon.
Collapse
Affiliation(s)
- Laura M Braden
- Centre for Biomedical Research, Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Ben F Koop
- Centre for Biomedical Research, Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Simon R M Jones
- Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, British Columbia V9T 6N7, Canada.
| |
Collapse
|
47
|
Sutherland BJG, Poley JD, Igboeli OO, Jantzen JR, Fast MD, Koop BF, Jones SRM. Transcriptomic responses to emamectin benzoate in Pacific and Atlantic Canada salmon lice Lepeophtheirus salmonis with differing levels of drug resistance. Evol Appl 2014; 8:133-48. [PMID: 25685190 PMCID: PMC4319862 DOI: 10.1111/eva.12237] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/16/2014] [Indexed: 01/10/2023] Open
Abstract
Salmon lice Lepeophtheirus salmonis are an ecologically and economically important parasite of wild and farmed salmon. In Scotland, Norway, and Eastern Canada, L. salmonis have developed resistance to emamectin benzoate (EMB), one of the few parasiticides available for salmon lice. Drug resistance mechanisms can be complex, potentially differing among populations and involving multiple genes with additive effects (i.e., polygenic resistance). Indicators of resistance development may enable early detection and countermeasures to avoid the spread of resistance. Here, we collect sensitive Pacific L. salmonis and sensitive and resistant Atlantic L. salmonis from salmon farms, propagate in laboratory (F1), expose to EMB in bioassays, and evaluate either baseline (Atlantic only) or induced transcriptomic differences between populations. In all populations, induced responses were minor and a cellular stress response was not identified. Pacific lice did not upregulate any genes in response to EMB, but downregulated degradative enzymes and transport proteins at 50 ppb EMB. Baseline differences between sensitive and now resistant Atlantic lice were much greater than responses to exposures. All resistant lice overexpressed degradative enzymes, and resistant males, the most resistant group, overexpressed collagenases to the greatest extent. These results indicate an accumulation of baseline expression differences related to resistance.
Collapse
Affiliation(s)
- Ben J G Sutherland
- Centre for Biomedical Research, Department of Biology, University of Victoria Victoria, BC, Canada ; Institut de Biologie Intégrative et des Systèmes (IBIS), Département de biologie, Université Laval Québec, QC, Canada
| | - Jordan D Poley
- Hoplite Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island Charlottetown, PEI, Canada
| | - Okechukwu O Igboeli
- Hoplite Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island Charlottetown, PEI, Canada
| | - Johanna R Jantzen
- Centre for Biomedical Research, Department of Biology, University of Victoria Victoria, BC, Canada
| | - Mark D Fast
- Hoplite Lab, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island Charlottetown, PEI, Canada
| | - Ben F Koop
- Centre for Biomedical Research, Department of Biology, University of Victoria Victoria, BC, Canada
| | | |
Collapse
|
48
|
Sun B, Greiner-Tollersrud L, Koop BF, Robertsen B. Atlantic salmon possesses two clusters of type I interferon receptor genes on different chromosomes, which allows for a larger repertoire of interferon receptors than in zebrafish and mammals. Dev Comp Immunol 2014; 47:275-86. [PMID: 25149134 DOI: 10.1016/j.dci.2014.08.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/13/2014] [Accepted: 08/14/2014] [Indexed: 06/03/2023]
Abstract
Mammalian type I interferons (IFNs) signal through a receptor composed of the IFNAR1 and IFNAR2 chains. In zebrafish two-cysteine IFNs utilize a receptor composed of CRFB1 and CRFB5, while four-cysteine IFNs signal through a receptor formed by CRFB2 and CRFB5. In the present work two CRFB clusters were identified in different chromosomes of Atlantic salmon. Genes of three CRFB5s, one CRFB1, one CRFB2 and the novel CRFB5x were identified, cloned and studied functionally. All CRFBs were expressed in 10 different organs, but the relative expression of CRFBs varied. Mx-reporter assay was used to study which CRFBs might be involved in receptors for salmon IFNa, IFNb and IFNc. The results of Mx-reporter assays suggest that IFNa signals through a receptor composed of CRFB1a as the long chain and either CRFB5a, CRFB5b or CRFB5c as the short chain; IFNc signals through a receptor with CRFB5a or CRFB5c as the short chain while IFNb may signal through a receptor with CRFB5x as a short chain. Taken together, the present work demonstrates that Atlantic salmon has a more diverse repertoire of type I IFN receptors compared to zebrafish or mammals.
Collapse
Affiliation(s)
- Baojian Sun
- Norwegian College of Fishery Science, University of Tromsø, 9037 Tromsø, Norway
| | | | - Ben F Koop
- Centre for Biomedical Research, Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, Canada
| | - Børre Robertsen
- Norwegian College of Fishery Science, University of Tromsø, 9037 Tromsø, Norway.
| |
Collapse
|
49
|
Rondeau EB, Minkley DR, Leong JS, Messmer AM, Jantzen JR, von Schalburg KR, Lemon C, Bird NH, Koop BF. The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei. PLoS One 2014; 9:e102089. [PMID: 25069045 PMCID: PMC4113312 DOI: 10.1371/journal.pone.0102089] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 06/14/2014] [Indexed: 11/19/2022] Open
Abstract
The northern pike is the most frequently studied member of the Esociformes, the closest order to the diverse and economically important Salmoniformes. The ancestor of all salmonids purportedly experienced a whole-genome duplication (WGD) event, making salmonid species ideal for studying the early impacts of genome duplication while complicating their use in wider analyses of teleost evolution. Studies suggest that the Esociformes diverged from the salmonid lineage prior to the WGD, supporting the use of northern pike as a pre-duplication outgroup. Here we present the first genome assembly, reference transcriptome and linkage map for northern pike, and evaluate the suitability of this species to provide a representative pre-duplication genome for future studies of salmonid and teleost evolution. The northern pike genome sequence is composed of 94,267 contigs (N50 = 16,909 bp) contained in 5,688 scaffolds (N50 = 700,535 bp); the total scaffolded genome size is 878 million bases. Multiple lines of evidence suggest that over 96% of the protein-coding genome is present in the genome assembly. The reference transcriptome was constructed from 13 tissues and contains 38,696 transcripts, which are accompanied by normalized expression data in all tissues. Gene-prediction analysis produced a total of 19,601 northern pike-specific gene models. The first-generation linkage map identifies 25 linkage groups, in agreement with northern pike's diploid karyotype of 2N = 50, and facilitates the placement of 46% of assembled bases onto linkage groups. Analyses reveal a high degree of conserved synteny between northern pike and other model teleost genomes. While conservation of gene order is limited to smaller syntenic blocks, the wider conservation of genome organization implies the northern pike exhibits a suitable approximation of a non-duplicated Protacanthopterygiian genome. This dataset will facilitate future studies of esocid biology and empower ongoing examinations of the Atlantic salmon and rainbow trout genomes by facilitating their comparison with other major teleost groups.
Collapse
Affiliation(s)
- Eric B. Rondeau
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
| | - David R. Minkley
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
| | - Jong S. Leong
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
| | - Amber M. Messmer
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
| | - Johanna R. Jantzen
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
| | - Kristian R. von Schalburg
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
| | - Craig Lemon
- The Charles O. Hayford Hackettstown State Fish Hatchery, Hackettstown, New Jersey, United States of America
| | - Nathan H. Bird
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
| | - Ben F. Koop
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada
- * E-mail:
| |
Collapse
|
50
|
Sutherland BJG, Hanson KC, Jantzen JR, Koop BF, Smith CT. Divergent immunity and energetic programs in the gills of migratory and resident Oncorhynchus mykiss. Mol Ecol 2014; 23:1952-64. [PMID: 24612010 DOI: 10.1111/mec.12713] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 03/04/2014] [Accepted: 03/05/2014] [Indexed: 12/24/2022]
Abstract
Divergent life history strategies occur in steelhead or rainbow trout Oncorhynchus mykiss, and many populations produce both migrant (anadromous fish that move to the ocean after rearing) and resident (do not migrate and remain in fresh water) individuals. Mechanisms leading to each type are only partially understood; while the general tendency of a population is heritable, individual tendency may be plastic, influenced by local environment. Steelhead hatchery programmes aim to mitigate losses in wild stocks by producing trout that will migrate to the ocean and not compete with wild trout for limited freshwater resources. To increase our understanding of gill function in these migratory or resident phenotypes, here we compare gill transcriptome profiles of hatchery-released fish either at the release site (residents) or five river kilometres downstream while still in full fresh water (migrants). To test whether any of these genes can be used as predictive markers for smoltification, we compared these genes between migrant-like and undifferentiated trout while still in the hatchery in a common environment (prerelease). Results confirmed the gradual process of smoltification, and the importance of energetics, gill remodelling and ion transport capacity for migrants. Additionally, residents overexpressed transcripts involved in antiviral defences, potentially for immune surveillance via dendritic cells in the gills. The best smoltification marker candidate was protein s100a4, expression of which was highly correlated with Na(+) , K(+) ATPase (NKA) activity and smolt-like morphology in pre- and postrelease trout gills.
Collapse
Affiliation(s)
- Ben J G Sutherland
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia, V8W 3N5, Canada
| | | | | | | | | |
Collapse
|