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Andreassen R, Rangnes F, Sivertsen M, Chiang M, Tran M, Worren MM. Discovery of miRNAs and Their Corresponding miRNA Genes in Atlantic Cod (Gadus morhua): Use of Stable miRNAs as Reference Genes Reveals Subgroups of miRNAs That Are Highly Expressed in Particular Organs. PLoS One 2016; 11:e0153324. [PMID: 27128807 PMCID: PMC4851352 DOI: 10.1371/journal.pone.0153324] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 03/28/2016] [Indexed: 12/21/2022] Open
Abstract
Background Atlantic cod (Gadus morhua) is among the economically most important species in the northern Atlantic Ocean and a model species for studying development of the immune system in vertebrates. MicroRNAs (miRNAs) are an abundant class of small RNA molecules that regulate fundamental biological processes at the post-transcriptional level. Detailed knowledge about a species miRNA repertoire is necessary to study how the miRNA transcriptome modulate gene expression. We have therefore discovered and characterized mature miRNAs and their corresponding miRNA genes in Atlantic cod. We have also performed a validation study to identify suitable reference genes for RT-qPCR analysis of miRNA expression in Atlantic cod. Finally, we utilized the newly characterized miRNA repertoire and the dedicated RT-qPCR method to reveal miRNAs that are highly expressed in certain organs. Results The discovery analysis revealed 490 mature miRNAs (401 unique sequences) along with precursor sequences and genomic location of the miRNA genes. Twenty six of these were novel miRNA genes. Validation studies ranked gmo-miR-17-1—5p or the two-gene combination gmo-miR25-3p and gmo-miR210-5p as most suitable qPCR reference genes. Analysis by RT-qPCR revealed 45 miRNAs with significantly higher expression in tissues from one or a few organs. Comparisons to other vertebrates indicate that some of these miRNAs may regulate processes like growth, lipid metabolism, immune response to microbial infections and scar damage repair. Three teleost-specific and three novel Atlantic cod miRNAs were among the differentially expressed miRNAs. Conclusions The number of known mature miRNAs was considerably increased by our identification of miRNAs and miRNA genes in Atlantic cod. This will benefit further functional studies of miRNA expression using deep sequencing methods. The validation study showed that stable miRNAs are suitable reference genes for RT-qPCR analysis of miRNA expression. Applying RT-qPCR we have identified several miRNAs likely to have important regulatory functions in particular organs.
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Affiliation(s)
- Rune Andreassen
- Department of Pharmacy and Biomedical Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
- * E-mail:
| | - Fredrik Rangnes
- Department of Pharmacy and Biomedical Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
| | - Maria Sivertsen
- Department of Pharmacy and Biomedical Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
| | - Michelle Chiang
- Department of Pharmacy and Biomedical Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
| | - Michelle Tran
- Department of Pharmacy and Biomedical Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
| | - Merete Molton Worren
- Bioinformatics Core Facility, Institute for Medical Informatics, Oslo University Hospital, Oslo, Norway
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Vartia S, Villanueva-Cañas JL, Finarelli J, Farrell ED, Collins PC, Hughes GM, Carlsson JEL, Gauthier DT, McGinnity P, Cross TF, FitzGerald RD, Mirimin L, Crispie F, Cotter PD, Carlsson J. A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding. ROYAL SOCIETY OPEN SCIENCE 2016; 3:150565. [PMID: 26909185 PMCID: PMC4736940 DOI: 10.1098/rsos.150565] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/10/2015] [Indexed: 05/14/2023]
Abstract
This study examines the potential of next-generation sequencing based 'genotyping-by-sequencing' (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS of microsatellites, using individual combinatorial barcoding, is potentially faster and cheaper than current microsatellite approaches and offers better and more data.
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Affiliation(s)
- Salla Vartia
- Area 52 Research Group, University College Dublin, Belfield, Dublin, Republic of Ireland
- Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland
- Carna Research Station, Ryan Institute, National University of Ireland, Galway, Carna, Connemara, Republic of Ireland
| | - José L. Villanueva-Cañas
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - John Finarelli
- School of Biology and Environment Science, University College Dublin, Belfield, Dublin, Republic of Ireland
- Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland
| | - Edward D. Farrell
- Area 52 Research Group, University College Dublin, Belfield, Dublin, Republic of Ireland
- Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland
| | - Patrick C. Collins
- School of Biological Sciences, Queen’s University Belfast, Medical Biology Centre, Lisburn Road, Belfast, UK
| | - Graham M. Hughes
- School of Biology and Environment Science, University College Dublin, Belfield, Dublin, Republic of Ireland
- Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland
| | - Jeanette E. L. Carlsson
- Area 52 Research Group, University College Dublin, Belfield, Dublin, Republic of Ireland
- Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland
| | - David T. Gauthier
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
| | - Philip McGinnity
- Beaufort Fish Genetics Programme, School of Biological, Earth and Environmental Sciences/Aquaculture and Fisheries Development Centre, University College Cork, Distillery Fields, North Mall, Cork, Republic of Ireland
| | - Thomas F. Cross
- Beaufort Fish Genetics Programme, School of Biological, Earth and Environmental Sciences/Aquaculture and Fisheries Development Centre, University College Cork, Distillery Fields, North Mall, Cork, Republic of Ireland
| | - Richard D. FitzGerald
- Carna Research Station, Ryan Institute, National University of Ireland, Galway, Carna, Connemara, Republic of Ireland
| | - Luca Mirimin
- Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Dublin Road, Galway, Republic of Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Republic of Ireland
- Alimentary Pharmabiotic Centre, Cork, Republic of Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Republic of Ireland
- Alimentary Pharmabiotic Centre, Cork, Republic of Ireland
| | - Jens Carlsson
- Area 52 Research Group, University College Dublin, Belfield, Dublin, Republic of Ireland
- Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland
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Carlsson J, Gauthier DT, Carlsson JEL, Coughlan JP, Dillane E, Fitzgerald RD, Keating U, McGinnity P, Mirimin L, Cross TF. Rapid, economical single-nucleotide polymorphism and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod Gadus morhua. JOURNAL OF FISH BIOLOGY 2013; 82:944-958. [PMID: 23464553 DOI: 10.1111/jfb.12034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Accepted: 11/21/2012] [Indexed: 06/01/2023]
Abstract
By combining next-generation sequencing technology (454) and reduced representation library (RRL) construction, the rapid and economical isolation of over 25 000 potential single-nucleotide polymorphisms (SNP) and >6000 putative microsatellite loci from c. 2% of the genome of the non-model teleost, Atlantic cod Gadus morhua from the Celtic Sea, south of Ireland, was demonstrated. A small-scale validation of markers indicated that 80% (11 of 14) of SNP loci and 40% (6 of 15) of the microsatellite loci could be amplified and showed variability. The results clearly show that small-scale next-generation sequencing of RRL genomes is an economical and rapid approach for simultaneous SNP and microsatellite discovery that is applicable to any species. The low cost and relatively small investment in time allows for positive exploitation of ascertainment bias to design markers applicable to specific populations and study questions.
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Affiliation(s)
- J Carlsson
- Beaufort Genetics Research Programme, School of Biological, Earth and Environmental Sciences/Aquauculture and Fisheries Development Centre, University College Cork, Distillery Fields, North Mall, Cork, Ireland.
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Bowman S, Hubert S, Higgins B, Stone C, Kimball J, Borza T, Bussey JT, Simpson G, Kozera C, Curtis BA, Hall JR, Hori TS, Feng CY, Rise M, Booman M, Gamperl AK, Trippel E, Symonds J, Johnson SC, Rise ML. An integrated approach to gene discovery and marker development in Atlantic cod (Gadus morhua). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:242-255. [PMID: 20396923 PMCID: PMC3084941 DOI: 10.1007/s10126-010-9285-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Accepted: 03/04/2010] [Indexed: 05/29/2023]
Abstract
Atlantic cod is a species that has been overexploited by the capture fishery. Programs to domesticate this species are underway in several countries, including Canada, to provide an alternative route for production. Selective breeding programs have been successfully applied in the domestication of other species, with genomics-based approaches used to augment conventional methods of animal production in recent years. Genomics tools, such as gene sequences and sets of variable markers, also have the potential to enhance and accelerate selective breeding programs in aquaculture, and to provide better monitoring tools to ensure that wild cod populations are well managed. We describe the generation of significant genomics resources for Atlantic cod through an integrated genomics/selective breeding approach. These include 158,877 expressed sequence tags (ESTs), a set of annotated putative transcripts and several thousand single nucleotide polymorphism markers that were developed from, and have been shown to be highly variable in, fish enrolled in two selective breeding programs. Our EST collection was generated from various tissues and life cycle stages. In some cases, tissues from which libraries were generated were isolated from fish exposed to stressors, including elevated temperature, or antigen stimulation (bacterial and viral) to enrich for transcripts that are involved in these response pathways. The genomics resources described here support the developing aquaculture industry, enabling the application of molecular markers within selective breeding programs. Marker sets should also find widespread application in fisheries management.
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Affiliation(s)
- Sharen Bowman
- The Atlantic Genome Centre, NRC Institute for Marine Biosciences, 1411 Oxford Street, Halifax, NS, B3H 3Z1, Canada.
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Hubert S, Higgins B, Borza T, Bowman S. Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua). BMC Genomics 2010; 11:191. [PMID: 20307277 PMCID: PMC2846918 DOI: 10.1186/1471-2164-11-191] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Accepted: 03/22/2010] [Indexed: 01/24/2023] Open
Abstract
Background Atlantic cod (Gadus morhua) is a species with increasing economic significance for the aquaculture industry. The genetic improvement of cod will play a critical role in achieving successful large-scale aquaculture. While many microsatellite markers have been developed in cod, the number of single nucleotide polymorphisms (SNPs) is currently limited. Here we report the identification of SNPs from sequence data generated by a large-scale expressed sequence tag (EST) program, focusing on fish originating from Canadian waters. Results A total of 97976 ESTs were assembled to generate 13448 contigs. We detected 4753 SNPs that met our selection criteria (depth of coverage ≥ 4 reads; minor allele frequency > 25%). 3072 SNPs were selected for testing. The percentage of successful assays was 75%, with 2291 SNPs amplifying correctly. Of these, 607 (26%) SNPs were monomorphic for all populations tested. In total, 64 (4%) of SNPs are likely to represent duplicated genes or highly similar members of gene families, rather than alternative alleles of the same gene, since they showed a high frequency of heterozygosity. The remaining polymorphic SNPs (1620) were categorised as validated SNPs. The mean minor allele frequency of the validated loci was 0.258 (± 0.141). Of the 1514 contigs from which validated SNPs were selected, 31% have a significant blast hit. For the SNPs predicted to occur in coding regions (141), we determined that 36% (51) are non-synonymous. Many loci (1033 SNPs; 64%) are polymorphic in all populations tested. However a small number of SNPs (184) that are polymorphic in the Western Atlantic were monomorphic in fish tested from three European populations. A preliminary linkage map has been constructed with 23 major linkage groups and 924 mapped SNPs. Conclusions These SNPs represent powerful tools to accelerate the genetic improvement of cod aquaculture. They have been used to build a genetic linkage map that can be applied to quantitative trait locus (QTL) discovery. Since these SNPs were generated from ESTs, they are linked to specific genes. Genes that map within QTL intervals can be prioritized for testing to determine whether they contribute to observed phenotypes.
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Affiliation(s)
- Sophie Hubert
- The Atlantic Genome Centre, Halifax, NS B3H3Z1, Canada
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