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Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome

By Jong S Leong, Stuart G Jantzen, Kristian R von Schalburg, Glenn A Cooper, Amber M Messmer, Nancy Y Liao, Sarah Munro, Richard Moore, Robert A Holt, Steven JM Jones, William S Davidson and Ben F Koop
Topics: Research Article
Publisher: BioMed Central
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Provided by: PubMed Central

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  1. (2003). A: Asymmetric sequence divergence of duplicate genes. Genome Res
  2. (1999). A: CAP3: A DNA sequence assembly program. Genome Res
  3. (2000). Adaptive diversification within a large family of recently duplicated, placentally expressed genes. P Natl Acad Sci USA
  4. (2003). AG: RevTrans: multiple alignment of coding DNA from aligned amino acid sequences.
  5. Animal Genome Size Database.
  6. (1998). Apweiler R: The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res
  7. (2006). Avise JC: Phylogenetic conservation of chromosome numbers in Actinopterygiian fishes. Genetica
  8. (2005). B: A physical map of the genome of Atlantic salmon, Salmo salar. Genomics
  9. (2003). Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the "Protacanthopterygii". Mol Phylogenet Evol
  10. (1998). Base-calling of automated sequencer traces using PHRED. I. Accuracy assessment. Genome Res
  11. (1998). Base-calling of automated sequencer traces using PHRED. II. Error probabilities. Genome Res
  12. (2007). BF: Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids.
  13. (2004). BF: Development and application of a salmonid EST database and cDNA microarray: Data mining and interspecific hybridization characteristics. Genome Res
  14. (2008). BF: Effects of diesel on survival, growth, and gene expression in rainbow trout (Oncorhynchus mykiss) fry. Environ Sci Technol
  15. (2005). BF: Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray.
  16. (2008). BF: Functional adaptive diversity of the Atlantic salmon T-cell receptor gamma locus. Mol Immunol
  17. (2007). BF: Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon (Salmo salar). BMC Genomics
  18. (2008). BF: Isolation, characterization and comparison of Atlantic and Chinook salmon growth hormone 1 and 2. BMC Genomics
  19. (2008). BJ: Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization.
  20. (2008). Chourrout D: Differential evolution of the 13 Atlantic salmon Hox clusters. Mol Biol Evol
  21. (1999). Cunningham EP: Microsatellite genetic variation between and within farmed and wild Atlantic salmon (Salmo salar) populations. Aquaculture
  22. (2005). de: Modeling gene and genome duplications in eukaryotes. P Natl Acad Sci USA
  23. Documentation for PHRAP.
  24. (2004). Duplication and divergence: The evolution of new genes and old ideas. Annu Rev Genet
  25. (2003). E: Atlantic salmon Salmo salar L., brown trout Salmo trutta L. and Arctic charr Salvelinus alpinus (L.): a review of aspects of their life histories. Ecol Freshw Fish
  26. (2000). Ecological determinants and temporal stability of the within-river population structure in Atlantic salmon (Salmo salar L.). Mol Ecol
  27. (2005). Environmental and dietary influences on highly unsaturated fatty acid biosynthesis and expression of fatty acyl desaturase and elongase genes in liver of Atlantic salmon (Salmo salar). Biochimica et Biophysica Acta-molecular and Cell Biology of Lipids
  28. (2000). Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol
  29. (1970). Evolution by gene duplication
  30. Fishes of the world. 4th edition.
  31. (2003). Fitness reduction and potential extinction of wild populations of Atlantic salmon, Salmo salar, as a result of interactions with escaped farm salmon. P Roy Soc BBiol Sci
  32. (2006). Gjoen T: Expression of MHC class I pathway genes in response to infectious salmon anaemia virus in Atlantic salmon (Salmo salar L.) cells. Fish Shellfish Immun
  33. (2001). Good genes as heterozygosity': the major histocompatibility complex and mate choice in Atlantic salmon (Salmo salar). P Roy Soc B-Biol Sci
  34. (2008). Grimholt U: Multiple expressed MHC class II loci in salmonids; details of one non-classical region in Atlantic salmon (Salmo salar).
  35. (2006). Guiguen Y: Generation of a large scale repertoire of Expressed Sequence Tags (ESTs) from normalised rainbow trout cDNA libraries.
  36. (2000). Haedrich RL: Relationships among fat weight, body weight, water weight, and condition factors in wild Atlantic salmon parr. T Am Fish Soc
  37. (2006). Hemre GI, Mommsen TP: Carbohydrates in fish nutrition: digestion and absorption in postlarval stages. Aquacult Nutr
  38. (2007). Høyheim B: Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource.
  39. (2009). In silico evidence for functional specialization after genome duplication in yeast.
  40. (2002). Investigation of selected persistent organic pollutants in farmed Atlantic salmon (Salmo salar), salmon aquaculture feed, and fish oil components of the feed. Environ Sci Technol
  41. (2006). KH: Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species. Mol Biol Evol
  42. (2006). L: Parallelism in gene transcription among sympatric lake whitefish (Coregonus clupeaformis Mitchill) ecotypes. Mol Ecol
  43. (2003). L: The effects of 4-nonylphenol and atrazine on Atlantic salmon (Salmo salar L) smolts. Aquaculture
  44. (1999). Le Bail PY: Does light have an influence on fish growth? Aquaculture
  45. (1997). Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res
  46. (1996). Liuni S: Databases of mRNA untranslated regions for metazoa. Computers Chem
  47. (1998). MEB: Life history variation and growth rate thresholds for maturity in Atlantic salmon, Salmo salar.
  48. (2003). MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years?
  49. (2004). Ortí G: Esociform phylogeny. Copeia
  50. (2008). Ortí G: Optimal Data Partitioning and a Test Case for RayFinned Fishes (Actinopterygii) Based on Ten Nuclear Loci. Syst Biol
  51. (2002). Pesole G: Untranslated regions of mRNAs.
  52. (2001). Population structure of Atlantic salmon (Salmo salar L.): a range-wide perspective from microsatellite DNA variation. Mol Ecol
  53. (1999). Preservation of duplicate genes by complementary, degenerative mutations. Genetics
  54. (2001). Ráb P: Chromosome evolution in the Salmonidae (Pisces): an update. Biol Res
  55. (2001). Replacement of fish oil with rapeseed oil in diets of Atlantic salmon (Salmo salar) affects tissue lipid compositions and hepatocyte fatty acid metabolism.
  56. (2003). RJM: MHC polymorphism and disease resistance in Atlantic salmon (Salmo salar); facing pathogens with single expressed major histocompatibility class I and class II loci. Immunogenetics
  57. (2007). Rokhsar DS: Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis.
  58. (2003). Sequence analysis of a rainbow trout cDNA library and creation of a gene index. Cytogenet Genome Res
  59. (2006). Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. Genome Res
  60. (1998). Stefansson SO: Effects of temperature and salinity on osmoregulation and growth of Atlantic salmon (Salmo salar L.) smolts in seawater. Aquaculture
  61. (1994). The evolution of functionally novel proteins after gene duplication. P Roy Soc B-Biol Sci
  62. (2000). The Gene Ontology Consortium: Gene ontology: tool for the unification of biology.
  63. Thorgaard GH: Tetraploidy and the evolution of salmonid fishes.
  64. (1994). TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res
  65. (1993). Tolstoshev CM: dbEST - database for "expressed sequence tags".
  66. (1999). Vijayan MM Moon TW: Cortisol in teleosts: dynamics, mechanisms of action, and metabolic regulation. Rev Fish Biol Fisher
  67. (2002). Vision TJ, Gaut BS: Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Mol Biol Evol
  68. (2008). WS: A salmonid EST genomic study: genes, duplications, phylogeny and microarrays.
  69. (2009). WS: Assignment of Atlantic salmon (Salmo salar) linkage groups to specific chromosomes: Conservation of large syntenic blocks corresponding to whole chromosome arms in rainbow trout (Oncorhynchus mykiss).
  70. (2008). WS: Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon).
  71. (1980). Yasunaga T: Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application.