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Guðbrandsson J, Kapralova KH, Franzdóttir SR, Bergsveinsdóttir ÞM, Hafstað V, Jónsson ZO, Snorrason SS, Pálsson A. Extensive genetic differentiation between recently evolved sympatric Arctic charr morphs. Ecol Evol 2019; 9:10964-10983. [PMID: 31641448 PMCID: PMC6802010 DOI: 10.1002/ece3.5516] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/22/2022] Open
Abstract
The availability of diverse ecological niches can promote adaptation of trophic specializations and related traits, as has been repeatedly observed in evolutionary radiations of freshwater fish. The role of genetics, environment, and history in ecologically driven divergence and adaptation, can be studied on adaptive radiations or populations showing ecological polymorphism. Salmonids, especially the Salvelinus genus, are renowned for both phenotypic diversity and polymorphism. Arctic charr (Salvelinus alpinus) invaded Icelandic streams during the glacial retreat (about 10,000 years ago) and exhibits many instances of sympatric polymorphism. Particularly, well studied are the four morphs in Lake Þingvallavatn in Iceland. The small benthic (SB), large benthic (LB), planktivorous (PL), and piscivorous (PI) charr differ in many regards, including size, form, and life history traits. To investigate relatedness and genomic differentiation between morphs, we identified variable sites from RNA-sequencing data from three of those morphs and verified 22 variants in population samples. The data reveal genetic differences between the morphs, with the two benthic morphs being more similar and the PL-charr more genetically different. The markers with high differentiation map to all linkage groups, suggesting ancient and pervasive genetic separation of these three morphs. Furthermore, GO analyses suggest differences in collagen metabolism, odontogenesis, and sensory systems between PL-charr and the benthic morphs. Genotyping in population samples from all four morphs confirms the genetic separation and indicates that the PI-charr are less genetically distinct than the other three morphs. The genetic separation of the other three morphs indicates certain degree of reproductive isolation. The extent of gene flow between the morphs and the nature of reproductive barriers between them remain to be elucidated.
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Affiliation(s)
- Jóhannes Guðbrandsson
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Marine and Freshwater Research InstituteReykjavikIceland
| | - Kalina H. Kapralova
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
| | - Sigríður R. Franzdóttir
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Biomedical CenterUniversity of IcelandReykjavikIceland
| | | | - Völundur Hafstað
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
| | - Zophonías O. Jónsson
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Biomedical CenterUniversity of IcelandReykjavikIceland
| | | | - Arnar Pálsson
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Biomedical CenterUniversity of IcelandReykjavikIceland
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Guðbrandsson J, Franzdóttir SR, Kristjánsson BK, Ahi EP, Maier VH, Kapralova KH, Snorrason SS, Jónsson ZO, Pálsson A. Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs. PeerJ 2018; 6:e4345. [PMID: 29441236 PMCID: PMC5807978 DOI: 10.7717/peerj.4345] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/19/2018] [Indexed: 02/06/2023] Open
Abstract
Phenotypic differences between closely related taxa or populations can arise through genetic variation or be environmentally induced, leading to altered transcription of genes during development. Comparative developmental studies of closely related species or variable populations within species can help to elucidate the molecular mechanisms related to evolutionary divergence and speciation. Studies of Arctic charr (Salvelinus alpinus) and related salmonids have revealed considerable phenotypic variation among populations and in Arctic charr many cases of extensive variation within lakes (resource polymorphism) have been recorded. One example is the four Arctic charr morphs in the ∼10,000 year old Lake Thingvallavatn, which differ in numerous morphological and life history traits. We set out to investigate the molecular and developmental roots of this polymorphism by studying gene expression in embryos of three of the morphs reared in a common garden set-up. We performed RNA-sequencing, de-novo transcriptome assembly and compared gene expression among morphs during an important timeframe in early development, i.e., preceding the formation of key trophic structures. Expectedly, developmental time was the predominant explanatory variable. As the data were affected by some form of RNA-degradation even though all samples passed quality control testing, an estimate of 3'-bias was the second most common explanatory variable. Importantly, morph, both as an independent variable and as interaction with developmental time, affected the expression of numerous transcripts. Transcripts with morph effect, separated the three morphs at the expression level, with the two benthic morphs being more similar. However, Gene Ontology analyses did not reveal clear functional enrichment of transcripts between groups. Verification via qPCR confirmed differential expression of several genes between the morphs, including regulatory genes such as AT-Rich Interaction Domain 4A (arid4a) and translin (tsn). The data are consistent with a scenario where genetic divergence has contributed to differential expression of multiple genes and systems during early development of these sympatric Arctic charr morphs.
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Affiliation(s)
- Jóhannes Guðbrandsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Freshwater Division, Marine and Freshwater Research Institute, Reykjavík, Iceland
| | - Sigríður Rut Franzdóttir
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | | | - Ehsan Pashay Ahi
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Karl-Franzens-Universität, Graz, Austria
| | - Valerie Helene Maier
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | | | | | - Zophonías Oddur Jónsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | - Arnar Pálsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
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Spoelhof JP, Chester M, Rodriguez R, Geraci B, Heo K, Mavrodiev E, Soltis PS, Soltis DE. Karyotypic variation and pollen stainability in resynthesized allopolyploids Tragopogon miscellus and T. mirus. AMERICAN JOURNAL OF BOTANY 2017; 104:1484-1492. [PMID: 29885228 DOI: 10.3732/ajb.1700180] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/08/2017] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Polyploidy has extensively shaped the evolution of plants, but the early stages of polyploidy are still poorly understood. The neoallopolyploid species Tragopogon mirus and T. miscellus are both characterized by widespread karyotypic variation, including frequent aneuploidy and intergenomic translocations. Our study illuminates the origins and early impacts of this variation by addressing two questions: How quickly does karyotypic variation accumulate in Tragopogon allopolyploids following whole-genome duplication (WGD), and how does the fertility of resynthesized Tragopogon allopolyploids evolve shortly after WGD? METHODS We used genomic in situ hybridization and lactophenol-cotton blue staining to estimate the karyotypic variation and pollen stainability, respectively, of resynthesized T. mirus and T. miscellus during the first five generations after WGD. KEY RESULTS Widespread karyotypic variation developed quickly in synthetics and resembled that of naturally occurring T. mirus and T. miscellus by generation S4 . Pollen stainability in resynthesized allopolyploids was consistently lower than that of natural T. mirus and T. miscellus, as well as their respective diploid progenitor species. Logistic regression showed that mean pollen stainability increased slightly over four generations in resynthesized T. mirus but remained at equivalent levels in T. miscellus. CONCLUSIONS Our results clarify some of the changes that occur in T. mirus and T. miscellus immediately following their origin, most notably the rapid onset of karyotypic variation within these species immediately following WGD.
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Affiliation(s)
- Jonathan P Spoelhof
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Michael Chester
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
- Royal Botanic Gardens, Kew, Natural Capital and Plant Health Department, Richmond, Surrey TW9 3DS, UK
| | - Roseana Rodriguez
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Blake Geraci
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Kweon Heo
- Kangwon National University, Department of Applied Plant Sciences, Chuncheon 24341, Korea
| | - Evgeny Mavrodiev
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA
- Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
- Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
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A SNP Based Linkage Map of the Arctic Charr ( Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication. G3-GENES GENOMES GENETICS 2017; 7:543-556. [PMID: 27986793 PMCID: PMC5295600 DOI: 10.1534/g3.116.038026] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Diploidization, which follows whole genome duplication events, does not occur evenly across the genome. In salmonid fishes, certain pairs of homeologous chromosomes preserve tetraploid loci in higher frequencies toward the telomeres due to residual tetrasomic inheritance. Research suggests this occurs only in homeologous pairs where one chromosome arm has undergone a fusion event. We present a linkage map for Arctic charr (Salvelinus alpinus), a salmonid species with relatively fewer chromosome fusions. Genotype by sequencing identified 19,418 SNPs, and a linkage map consisting of 4508 markers was constructed from a subset of high quality SNPs and microsatellite markers that were used to anchor the new map to previous versions. Both male- and female-specific linkage maps contained the expected number of 39 linkage groups. The chromosome type associated with each linkage group was determined, and 10 stable metacentric chromosomes were identified, along with a chromosome polymorphism involving the sex chromosome AC04. Two instances of a weak form of pseudolinkage were detected in the telomeric regions of homeologous chromosome arms in both female and male linkage maps. Chromosome arm homologies within the Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) genomes were determined. Paralogous sequence variants (PSVs) were identified, and their comparative BLASTn hit locations showed that duplicate markers exist in higher numbers on seven pairs of homeologous arms, previously identified as preserving tetrasomy in salmonid species. Homeologous arm pairs where neither arm has been part of a fusion event in Arctic charr had fewer PSVs, suggesting faster diploidization rates in these regions.
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McKinney GJ, Waples RK, Seeb LW, Seeb JE. Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping-by-sequencing data from natural populations. Mol Ecol Resour 2016; 17:656-669. [DOI: 10.1111/1755-0998.12613] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 10/06/2016] [Accepted: 10/10/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Garrett J. McKinney
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street, Box 355020 Seattle WA 98195-5020 USA
| | - Ryan K. Waples
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street, Box 355020 Seattle WA 98195-5020 USA
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street, Box 355020 Seattle WA 98195-5020 USA
| | - James E. Seeb
- School of Aquatic and Fishery Sciences; University of Washington; 1122 NE Boat Street, Box 355020 Seattle WA 98195-5020 USA
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Kutyrev I, Cleveland B, Leeds T, Wiens GD. Proinflammatory cytokine and cytokine receptor gene expression kinetics following challenge with Flavobacterium psychrophilum in resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss). FISH & SHELLFISH IMMUNOLOGY 2016; 58:542-553. [PMID: 27693200 DOI: 10.1016/j.fsi.2016.09.053] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 09/22/2016] [Accepted: 09/26/2016] [Indexed: 06/06/2023]
Abstract
Flavobacterium psychrophilum (Fp) is the causative agent of bacterial cold water disease (BCWD) which causes appreciable economic losses in rainbow trout aquaculture. We previously reported development of a genetic line, designated ARS-Fp-R that exhibits higher survival relative to a susceptible line, designated ARS-Fp-S, following either laboratory or natural on-farm challenge. The objectives of this study were to determine the temporal kinetics of gene expression between experimentally-challenged ARS-Fp-R and ARS-Fp-S fish and the correlation between gene expression and pathogen load. We developed a GeXP multiplex RT-PCR assay to simultaneously examine expression of immune-relevant genes, concentrating on tumor necrosis factor and interleukin-1 ligand/receptor systems and acute phase response genes. Spleen tissue was sampled at 6 h, 24 h, 48 h and 144 h post-challenge and pathogen load quantified by qPCR. Transcript abundance of cytokine genes tnfa1, tnfa2, tnfa3, il1b1, il1b2, il11a; acute phase response genes saa and drtp1; and putative cytokine receptors il1r1-like-b, il1r2, tnfrsf1a, tnfrsf9, tnfrsf1a-like-b increased following challenge while the transcript abundance of il1r-like-1 and tnfrsf1a-like-a decreased compared to PBS-injected line-matched control fish. Principal component analysis identified transcript levels of genes il1r-like-1 and tnfrsf1a-like-a as exhibiting differential expression between genetic lines. In summary, Fp i.p. injection challenge elicited a proinflammatory cytokine gene expression response in the spleen, with ARS-Fp-R line fish exhibiting modestly higher basal expression levels of several putative cytokine receptors. This study furthers the understanding of the immune response following Fp challenge and differences in gene expression associated with selective breeding for disease resistance.
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Affiliation(s)
- Ivan Kutyrev
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, USDA, 11861 Leetown Rd, Kearneysville, WV 25430, USA; Institute of General and Experimental Biology, Siberian Branch of Russian Academy of Sciences, Sakhyanovoi St., 6, 670047 Ulan-Ude, Russia.
| | - Beth Cleveland
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, USDA, 11861 Leetown Rd, Kearneysville, WV 25430, USA
| | - Timothy Leeds
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, USDA, 11861 Leetown Rd, Kearneysville, WV 25430, USA
| | - Gregory D Wiens
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, USDA, 11861 Leetown Rd, Kearneysville, WV 25430, USA.
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7
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Ahi EP, Steinhäuser SS, Pálsson A, Franzdóttir SR, Snorrason SS, Maier VH, Jónsson ZO. Differential expression of the aryl hydrocarbon receptor pathway associates with craniofacial polymorphism in sympatric Arctic charr. EvoDevo 2015; 6:27. [PMID: 26388986 PMCID: PMC4574265 DOI: 10.1186/s13227-015-0022-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/04/2015] [Indexed: 12/03/2022] Open
Abstract
Background The developmental basis of craniofacial morphology hinges on interactions of numerous signalling systems. Extensive craniofacial variation in the polymorphic Arctic charr, a member of the salmonid family, from Lake Thingvallavatn (Iceland), offers opportunities to find and study such signalling pathways and their key regulators, thereby shedding light on the developmental pathways, and the genetics of trophic divergence. Results To identify genes involved in the craniofacial differences between benthic and limnetic Arctic charr, we used transcriptome data from different morphs, spanning early development, together with data on craniofacial expression patterns and skeletogenesis in model vertebrate species. Out of 20 genes identified, 7 showed lower gene expression in benthic than in limnetic charr morphs. We had previously identified a conserved gene network involved in extracellular matrix (ECM) organization and skeletogenesis, showing higher expression in developing craniofacial elements of benthic than in limnetic Arctic charr morphs. The present study adds a second set of genes constituting an expanded gene network with strong, benthic–limnetic differential expression. To identify putative upstream regulators, we performed knowledge-based motif enrichment analyses on the regulatory sequences of the identified genes which yielded potential binding sites for a set of known transcription factors (TFs). Of the 8 TFs that we examined using qPCR, two (Ahr2b and Ap2) were found to be differentially expressed between benthic and limnetic charr. Expression analysis of several known AhR targets indicated higher activity of the AhR pathway during craniofacial development in benthic charr morphotypes. Conclusion These results suggest a key role of the aryl hydrocarbon receptor (AhR) pathway in the observed craniofacial differences between distinct charr morphotypes. Electronic supplementary material The online version of this article (doi:10.1186/s13227-015-0022-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland
| | - Sophie S Steinhäuser
- Biomedical Center, University of Iceland, Vatnsmýrarvegur 16, 101 Reykjavik, Iceland
| | - Arnar Pálsson
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland ; Biomedical Center, University of Iceland, Vatnsmýrarvegur 16, 101 Reykjavik, Iceland
| | - Sigrídur Rut Franzdóttir
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland
| | - Sigurdur S Snorrason
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland
| | - Valerie H Maier
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland ; Biomedical Center, University of Iceland, Vatnsmýrarvegur 16, 101 Reykjavik, Iceland
| | - Zophonías O Jónsson
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavik, Iceland ; Biomedical Center, University of Iceland, Vatnsmýrarvegur 16, 101 Reykjavik, Iceland
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8
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Gudbrandsson J, Ahi EP, Franzdottir SR, Kapralova KH, Kristjansson BK, Steinhaeuser SS, Maier VH, Johannesson IM, Snorrason SS, Jonsson ZO, Palsson A. The developmental transcriptome of contrasting Arctic charr (Salvelinus alpinus) morphs. F1000Res 2015; 4:136. [PMID: 27635217 PMCID: PMC5007756 DOI: 10.12688/f1000research.6402.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/10/2024] Open
Abstract
Species and populations with parallel evolution of specific traits can help illuminate how predictable adaptations and divergence are at the molecular and developmental level. Following the last glacial period, dwarfism and specialized bottom feeding morphology evolved rapidly in several landlocked Arctic charrSalvelinus alpinuspopulations in Iceland. To study the genetic divergence between small benthic morphs and limnetic morphs, we conducted RNA-sequencing charr embryos at four stages in early development. We studied two stocks with contrasting morphologies: the small benthic (SB) charr from Lake Thingvallavatn and Holar aquaculture (AC) charr.The data reveal significant differences in expression of several biological pathways during charr development. There was also an expression difference between SB- and AC-charr in genes involved in energy metabolism and blood coagulation genes. We confirmed differing expression of five genes in whole embryos with qPCR, includinglysozymeandnatterin-likewhich was previously identified as a fish-toxin of a lectin family that may be a putative immunopeptide. We also verified differential expression of 7 genes in the developing head that associated consistently with benthic v.s.limnetic morphology (studied in 4 morphs). Comparison of single nucleotide polymorphism (SNP) frequencies reveals extensive genetic differentiation between the SB and AC-charr (~1300 with more than 50% frequency difference). Curiously, three derived alleles in the otherwise conserved 12s and 16s mitochondrial ribosomal RNA genes are found in benthic charr.The data implicate multiple genes and molecular pathways in divergence of small benthic charr and/or the response of aquaculture charr to domestication. Functional, genetic and population genetic studies on more freshwater and anadromous populations are needed to confirm the specific loci and mutations relating to specific ecological traits in Arctic charr.
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9
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Gudbrandsson J, Ahi EP, Franzdottir SR, Kapralova KH, Kristjansson BK, Steinhaeuser SS, Maier VH, Johannesson IM, Snorrason SS, Jonsson ZO, Palsson A. The developmental transcriptome of contrasting Arctic charr ( Salvelinus alpinus) morphs. F1000Res 2015; 4:136. [PMID: 27635217 PMCID: PMC5007756 DOI: 10.12688/f1000research.6402.2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/05/2016] [Indexed: 12/23/2022] Open
Abstract
Species and populations with parallel evolution of specific traits can help illuminate how predictable adaptations and divergence are at the molecular and developmental level. Following the last glacial period, dwarfism and specialized bottom feeding morphology evolved rapidly in several landlocked Arctic charr
Salvelinus alpinus populations in Iceland. To study the genetic divergence between small benthic morphs and limnetic morphs, we conducted RNA-sequencing charr embryos at four stages in early development. We studied two stocks with contrasting morphologies: the small benthic (SB) charr from Lake Thingvallavatn and Holar aquaculture (AC) charr. The data reveal significant differences in expression of several biological pathways during charr development. There was also an expression difference between SB- and AC-charr in genes involved in energy metabolism and blood coagulation genes. We confirmed differing expression of five genes in whole embryos with qPCR, including
lysozyme and
natterin-like which was previously identified as a fish-toxin of a lectin family that may be a putative immunopeptide. We also verified differential expression of 7 genes in the developing head that associated consistently with benthic v.s.limnetic morphology (studied in 4 morphs). Comparison of single nucleotide polymorphism (SNP) frequencies reveals extensive genetic differentiation between the SB and AC-charr (~1300 with more than 50% frequency difference). Curiously, three derived alleles in the otherwise conserved 12s and 16s mitochondrial ribosomal RNA genes are found in benthic charr. The data implicate multiple genes and molecular pathways in divergence of small benthic charr and/or the response of aquaculture charr to domestication. Functional, genetic and population genetic studies on more freshwater and anadromous populations are needed to confirm the specific loci and mutations relating to specific ecological traits in Arctic charr.
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Affiliation(s)
- Johannes Gudbrandsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Ehsan P Ahi
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Sigridur R Franzdottir
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Kalina H Kapralova
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | | | - S Sophie Steinhaeuser
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Valerie H Maier
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Isak M Johannesson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Sigurdur S Snorrason
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Zophonias O Jonsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Arnar Palsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
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10
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Hu G, Lin C, He M, Wong AOL. Neurokinin B and reproductive functions: "KNDy neuron" model in mammals and the emerging story in fish. Gen Comp Endocrinol 2014; 208:94-108. [PMID: 25172151 DOI: 10.1016/j.ygcen.2014.08.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 08/12/2014] [Accepted: 08/14/2014] [Indexed: 12/13/2022]
Abstract
In mammals, neurokinin B (NKB), the gene product of the tachykinin family member TAC3, is known to be a key regulator for episodic release of luteinizing hormone (LH). Its regulatory actions are mediated by a subpopulation of kisspeptin neurons within the arcuate nucleus with co-expression of NKB and dynorphin A (commonly called the "KNDy neurons"). By forming an "autosynaptic feedback loop" within the hypothalamus, the KNDy neurons can modulate gonadotropin-releasing hormone (GnRH) pulsatility and subsequent LH release in the pituitary. NKB regulation of LH secretion has been recently demonstrated in zebrafish, suggesting that the reproductive functions of NKB may be conserved from fish to mammals. Interestingly, the TAC3 genes in fish not only encode the mature peptide of NKB but also a novel tachykinin-like peptide, namely NKB-related peptide (or neurokinin F). Recent studies in zebrafish also reveal that the neuroanatomy of TAC3/kisspeptin system within the fish brain is quite different from that of mammals. In this article, the current ideas of "KNDy neuron" model for GnRH regulation and steroid feedback, other reproductive functions of NKB including its local actions in the gonad and placenta, the revised model of tachykinin evolution from invertebrates to vertebrates, as well as the emerging story of the two TAC3 gene products in fish, NKB and NKB-related peptide, will be reviewed with stress on the areas with interesting questions for future investigations.
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Affiliation(s)
- Guangfu Hu
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Chengyuan Lin
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Mulan He
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Anderson O L Wong
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
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11
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Jiang Y, Xu P, Liu Z. Generation of physical map contig-specific sequences. Front Genet 2014; 5:243. [PMID: 25101119 PMCID: PMC4105628 DOI: 10.3389/fgene.2014.00243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 07/07/2014] [Indexed: 12/13/2022] Open
Abstract
Rapid advances of the next-generation sequencing technologies have allowed whole genome sequencing of many species. However, with the current sequencing technologies, the whole genome sequence assemblies often fall in short in one of the four quality measurements: accuracy, contiguity, connectivity, and completeness. In particular, small-sized contigs and scaffolds limit the applicability of whole genome sequences for genetic analysis. To enhance the quality of whole genome sequence assemblies, particularly the scaffolding capabilities, additional genomic resources are required. Among these, sequences derived from known physical locations offer great powers for scaffolding. In this mini-review, we will describe the principles, procedures and applications of physical-map-derived sequences, with the focus on physical map contig-specific sequences.
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Affiliation(s)
- Yanliang Jiang
- Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences Beijing, China
| | - Peng Xu
- Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences Beijing, China
| | - Zhanjiang Liu
- Aquatic Genomics Unit, The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University AL, USA
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12
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Lopes-Marques M, Cunha I, Reis-Henriques MA, Santos MM, Castro LFC. Diversity and history of the long-chain acyl-CoA synthetase (Acsl) gene family in vertebrates. BMC Evol Biol 2013; 13:271. [PMID: 24330521 PMCID: PMC3890633 DOI: 10.1186/1471-2148-13-271] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 12/04/2013] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Fatty acids, a considerable fraction of lipid molecules, participate in fundamental physiological processes. They undergo activation into their corresponding CoA esters for oxidation or esterification into complex lipids (e.g. triglycerides, phospholipids and cholesterol esters), a process that is carried out by acyl-CoA synthases (ACS). Here we analyze the evolution of the gene family encoding for the long-chain acyl-CoA synthetases (Acsl) in vertebrates. RESULTS By means of phylogenetics and comparative genomics we show that genome duplications (2R) generated the diversity of Acsl genes in extant vertebrate lineages. In the vertebrate ancestor two separate genes originated the current Acsl1/5/6 and the Acsl3/4 gene families, and the extra gene duplicates in teleosts are a consequence of the teleost specific third round of genome duplication (3R). Moreover, the diversity of Acsl family members is broader than anticipated. Our strategy uncovered a novel uncharacterized Acsl-like gene found in teleosts, spotted gar, coelacanth and possibly lamprey, which we designate Acsl2. The detailed analysis of the Acsl2 teleost gene locus strongly supports the conclusion that it corresponds to a retained 2R paralogue, lost in tetrapods. CONCLUSIONS We provide here the first evolutionary analysis of the Acsl gene family in vertebrates, showing the specific contribution of 2R/3R to the diversity of this gene family. We find also that the division of ACSL enzymes into two groups predates at least the emergence of deuterostomes. Our study indicates that genome duplications significantly contributed to the elaboration of fatty acid activation metabolism in vertebrates.
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Affiliation(s)
| | | | | | | | - L Filipe C Castro
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, CIMAR Associate Laboratory, UPorto, University of Porto, Porto, Portugal.
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13
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Christensen KA, Brunelli JP, Lambert MJ, DeKoning J, Phillips RB, Thorgaard GH. Identification of single nucleotide polymorphisms from the transcriptome of an organism with a whole genome duplication. BMC Bioinformatics 2013; 14:325. [PMID: 24237905 PMCID: PMC3840595 DOI: 10.1186/1471-2105-14-325] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 11/12/2013] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The common ancestor of salmonid fishes, including rainbow trout (Oncorhynchus mykiss), experienced a whole genome duplication between 20 and 100 million years ago, and many of the duplicated genes have been retained in the trout genome. This retention complicates efforts to detect allelic variation in salmonid fishes. Specifically, single nucleotide polymorphism (SNP) detection is problematic because nucleotide variation can be found between the duplicate copies (paralogs) of a gene as well as between alleles. RESULTS We present a method of differentiating between allelic and paralogous (gene copy) sequence variants, allowing identification of SNPs in organisms with multiple copies of a gene or set of genes. The basic strategy is to: 1) identify windows of unique cDNA sequences with homology to each other, 2) compare these unique cDNAs if they are not shared between individuals (i.e. the cDNA is homozygous in one individual and homozygous for another cDNA in the other individual), and 3) give a "SNP score" value between zero and one to each candidate sequence variant based on six criteria. Using this strategy we were able to detect about seven thousand potential SNPs from the transcriptomes of several clonal lines of rainbow trout. When directly compared to a pre-validated set of SNPs in polyploid wheat, we were also able to estimate the false-positive rate of this strategy as 0 to 28% depending on parameters used. CONCLUSIONS This strategy has an advantage over traditional techniques of SNP identification because another dimension of sequencing information is utilized. This method is especially well suited for identifying SNPs in polyploids, both outbred and inbred, but would tend to be conservative for diploid organisms.
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Affiliation(s)
- Kris A Christensen
- School of Molecular Biosciences, Washington State University, Pullman WA 99164-4660, USA
- Center for Reproductive Biology, Washington State University, Pullman WA 99164-7520, USA
| | - Joseph P Brunelli
- School of Biological Sciences, Washington State University, Pullman WA 99164-4236, USA
- Center for Reproductive Biology, Washington State University, Pullman WA 99164-7520, USA
| | - Matthew J Lambert
- School of Biological Sciences, Washington State University, Vancouver, 14204 NE Salmon Creek Ave, Vancouver WA 98686-9600, USA
- Center for Reproductive Biology, Washington State University, Pullman WA 99164-7520, USA
| | - Jenefer DeKoning
- School of Biological Sciences, Washington State University, Vancouver, 14204 NE Salmon Creek Ave, Vancouver WA 98686-9600, USA
- Center for Reproductive Biology, Washington State University, Pullman WA 99164-7520, USA
| | - Ruth B Phillips
- School of Biological Sciences, Washington State University, Vancouver, 14204 NE Salmon Creek Ave, Vancouver WA 98686-9600, USA
- Center for Reproductive Biology, Washington State University, Pullman WA 99164-7520, USA
| | - Gary H Thorgaard
- School of Biological Sciences, Washington State University, Pullman WA 99164-4236, USA
- Center for Reproductive Biology, Washington State University, Pullman WA 99164-7520, USA
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14
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Jiang Y, Ninwichian P, Liu S, Zhang J, Kucuktas H, Sun F, Kaltenboeck L, Sun L, Bao L, Liu Z. Generation of physical map contig-specific sequences useful for whole genome sequence scaffolding. PLoS One 2013; 8:e78872. [PMID: 24205335 PMCID: PMC3811975 DOI: 10.1371/journal.pone.0078872] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 09/16/2013] [Indexed: 11/29/2022] Open
Abstract
Along with the rapid advances of the nextgen sequencing technologies, more and more species are added to the list of organisms whose whole genomes are sequenced. However, the assembled draft genome of many organisms consists of numerous small contigs, due to the short length of the reads generated by nextgen sequencing platforms. In order to improve the assembly and bring the genome contigs together, more genome resources are needed. In this study, we developed a strategy to generate a valuable genome resource, physical map contig-specific sequences, which are randomly distributed genome sequences in each physical contig. Two-dimensional tagging method was used to create specific tags for 1,824 physical contigs, in which the cost was dramatically reduced. A total of 94,111,841 100-bp reads and 315,277 assembled contigs are identified containing physical map contig-specific tags. The physical map contig-specific sequences along with the currently available BAC end sequences were then used to anchor the catfish draft genome contigs. A total of 156,457 genome contigs (~79% of whole genome sequencing assembly) were anchored and grouped into 1,824 pools, in which 16,680 unique genes were annotated. The physical map contig-specific sequences are valuable resources to link physical map, genetic linkage map and draft whole genome sequences, consequently have the capability to improve the whole genome sequences assembly and scaffolding, and improve the genome-wide comparative analysis as well. The strategy developed in this study could also be adopted in other species whose whole genome assembly is still facing a challenge.
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Affiliation(s)
- Yanliang Jiang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Parichart Ninwichian
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Jiaren Zhang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Huseyin Kucuktas
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Fanyue Sun
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Ludmilla Kaltenboeck
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Luyang Sun
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Lisui Bao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
- * E-mail:
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15
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Nguyen M, Yang E, Neelkantan N, Mikhaylova A, Arnold R, Poudel MK, Stewart AM, Kalueff AV. Developing 'integrative' zebrafish models of behavioral and metabolic disorders. Behav Brain Res 2013; 256:172-87. [PMID: 23948218 DOI: 10.1016/j.bbr.2013.08.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 07/31/2013] [Accepted: 08/03/2013] [Indexed: 02/09/2023]
Abstract
Recently, the pathophysiological overlap between metabolic and mental disorders has received increased recognition. Zebrafish (Danio rerio) are rapidly becoming a popular model organism for translational biomedical research due to their genetic tractability, low cost, quick reproductive cycle, and ease of behavioral, pharmacological or genetic manipulation. High homology to mammalian physiology and the availability of well-developed assays also make the zebrafish an attractive organism for studying human disorders. Zebrafish neurobehavioral and endocrine phenotypes show promise for the use of zebrafish in studies of stress, obesity and related behavioral and metabolic disorders. Here, we discuss the parallels between zebrafish and other model species in stress and obesity physiology, as well as outline the available zebrafish models of weight gain, metabolic deficits, feeding, stress, anxiety and related behavioral disorders. Overall, zebrafish demonstrate a strong potential for modeling human behavioral and metabolic disorders, and their comorbidity.
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Affiliation(s)
- Michael Nguyen
- Department of Biomedical Engineering, University of Virginia, 415 Lane Road, Charlottesville, VA 22908, USA; Thomas Jefferson High School for Science and Technology, 6560 Braddock Road, Alexandria, VA 22312, USA
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16
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Shedko SV, Miroshnichenko IL, Nemkova GA. Phylogeny of salmonids (salmoniformes: Salmonidae) and its molecular dating: Analysis of mtDNA data. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413060112] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Engelund MB, Chauvigné F, Christensen BM, Finn RN, Cerdà J, Madsen SS. Differential expression and novel permeability properties of three aquaporin 8 paralogs from seawater-challenged Atlantic salmon smolts. J Exp Biol 2013; 216:3873-85. [DOI: 10.1242/jeb.087890] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Summary
Aquaporins may facilitate transepithelial water absorption in the intestine of seawater (SW) acclimated fish. Here we have characterized three full-length aqp8 paralogs from Atlantic salmon (Salmo salar). Bayesian inference revealed that each paralog is a representative of the three major classes of aqp8aa, aqp8ab and aqp8b genes found in other teleosts. The permeability properties were studied by heterologous expression in Xenopus laevis oocytes, and the expression levels examined by qPCR, immunofluorescence and immunoelectron microscopy, and immunoblotting of membrane fractions from intestines of SW challenged smolts. All three Aqp8 paralogs were permeable to water and urea, whereas Aqp8ab and -8b were, surprisingly, also permeable to glycerol. The mRNA tissue distribution of each paralog was distinct although some tissues, such as the intestine showed redundant expression of more than one paralog. Immunofluorescence microscopy localized Aqp8aa(1+2) to intracellular compartments of the liver and intestine, and Aqp8ab and Aqp8b to apical plasma membrane domains of the intestinal epithelium, with Aqp8b also in goblet cells. In a control experiment with rainbow trout, immunoelectron microscopy confirmed abundant labeling of Aqp8ab and -8b at apical plasma membranes of enterocytes in the middle intestine and also in subapical vesicular structures. During SW-challenge, Aqp8ab showed significantly increased levels of protein expression in plasma membrane enriched fractions of the intestine. These data indicate that the Atlantic salmon Aqp8 paralogs have neofunctionalized on a transcriptional as well as on a functional level, and that Aqp8ab may play a central role in the intestinal transcellular uptake of water during SW acclimation.
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Affiliation(s)
| | - François Chauvigné
- Institut de Recerca i Tecnologia Agroalimentàries - Institut de Ciències del Mar, CSIC
| | | | | | - Joan Cerdà
- Institut de Recerca i Tecnologia Agroalimentàries - Institut de Ciències del Mar, CSIC
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18
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Lu J, Peatman E, Tang H, Lewis J, Liu Z. Profiling of gene duplication patterns of sequenced teleost genomes: evidence for rapid lineage-specific genome expansion mediated by recent tandem duplications. BMC Genomics 2012; 13:246. [PMID: 22702965 PMCID: PMC3464592 DOI: 10.1186/1471-2164-13-246] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 06/15/2012] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Gene duplication has had a major impact on genome evolution. Localized (or tandem) duplication resulting from unequal crossing over and whole genome duplication are believed to be the two dominant mechanisms contributing to vertebrate genome evolution. While much scrutiny has been directed toward discerning patterns indicative of whole-genome duplication events in teleost species, less attention has been paid to the continuous nature of gene duplications and their impact on the size, gene content, functional diversity, and overall architecture of teleost genomes. RESULTS Here, using a Markov clustering algorithm directed approach we catalogue and analyze patterns of gene duplication in the four model teleost species with chromosomal coordinates: zebrafish, medaka, stickleback, and Tetraodon. Our analyses based on set size, duplication type, synonymous substitution rate (Ks), and gene ontology emphasize shared and lineage-specific patterns of genome evolution via gene duplication. Most strikingly, our analyses highlight the extraordinary duplication and retention rate of recent duplicates in zebrafish and their likely role in the structural and functional expansion of the zebrafish genome. We find that the zebrafish genome is remarkable in its large number of duplicated genes, small duplicate set size, biased Ks distribution toward minimal mutational divergence, and proportion of tandem and intra-chromosomal duplicates when compared with the other teleost model genomes. The observed gene duplication patterns have played significant roles in shaping the architecture of teleost genomes and appear to have contributed to the recent functional diversification and divergence of important physiological processes in zebrafish. CONCLUSIONS We have analyzed gene duplication patterns and duplication types among the available teleost genomes and found that a large number of genes were tandemly and intrachromosomally duplicated, suggesting their origin of independent and continuous duplication. This is particularly true for the zebrafish genome. Further analysis of the duplicated gene sets indicated that a significant portion of duplicated genes in the zebrafish genome were of recent, lineage-specific duplication events. Most strikingly, a subset of duplicated genes is enriched among the recently duplicated genes involved in immune or sensory response pathways. Such findings demonstrated the significance of continuous gene duplication as well as that of whole genome duplication in the course of genome evolution.
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Affiliation(s)
- Jianguo Lu
- Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA
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