Comparative Genomics Identifies Candidate Genes for Infectious Salmon Anemia (ISA) Resistance in Atlantic Salmon (Salmo salar)

Marine Biotechnology

Volumn 13, Issue 2, 2011, Pages 232-241

  Li, Jieying ^a   Boroevich, Keith A ^a   Koop, Ben F ^b   Davidson, William S ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

^b UNIVERSITY OF VICTORIA   (Canada)

Author keywords

Atlantic salmon; Comparative genomics; Disease resistance; Infectious salmon anemia

Indexed keywords

ATLANTIC SALMON; BACTERIAL ARTIFICIAL CHROMOSOMES; BIOLOGICAL FUNCTIONS; CANDIDATE GENES; CHROMOSOME WALKING; COMPARATIVE GENOMICS; CONSERVED SYNTENY; CONTIGS; DIFFERENTIAL EXPRESSIONS; DISEASE RESISTANCE; GENETIC MAP; INFECTIOUS SALMON ANEMIA; LINKAGE GROUPS; MICROSATELLITE MARKERS; QUANTITATIVE TRAIT LOCUS; SALMO SALAR; SEQUENCE DATABASE;

CHROMOSOMES; DISEASES; VIRUSES;

GENE EXPRESSION;

FISH PROTEIN;

CHROMOSOME; DISEASE RESISTANCE; DISEASE SPREAD; GENETIC MARKER; GENOMICS; INFECTIOUS DISEASE; SALMONID; SALMONID CULTURE; VIRUS;

ANIMAL; ANIMAL DISEASE; AQUACULTURE; ARTICLE; ATLANTIC SALMON; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME WALKING; COMPARATIVE STUDY; FISH DISEASE; GENETICS; GENOMICS; IMMUNOLOGY; INNATE IMMUNITY; METABOLISM; MICROARRAY ANALYSIS; ORTHOMYXOVIRUS; ORTHOMYXOVIRUS INFECTION; VIROLOGY;

ANIMALS; AQUACULTURE; CHROMOSOME WALKING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; FISH DISEASES; FISH PROTEINS; GENOMICS; IMMUNITY, INNATE; ISAVIRUS; MICROARRAY ANALYSIS; ORTHOMYXOVIRIDAE INFECTIONS; SALMO SALAR;

CHILE;

BACTERIA (MICROORGANISMS); HUMAN IMMUNODEFICIENCY VIRUS; INFECTIOUS SALMON ANEMIA VIRUS; ORYZIAS; ORYZIINAE; SALMO SALAR; TETRAODON;

EID: 79955528926     PISSN: 14362228     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10126-010-9284-0     Document Type: Article

References (58)

1. Adzhubei AA, Vlasov AV, Hagen-Larsen H, Ruden TA, Laerdahl JK, Høyheim B (2007) Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource. BMC Genomics 8: 209.
2. Akira S, Uematsu S, Takeuchi O (2006) Pathogen recognition and innate immunity. Cell 124: 783-801.
3. Allendorf FW, Thorgaard GH (1984) Tetraploidy and the evolution of salmonids fishes. In: Turner BJ (ed) Evolutionary genetics of fishes. Plenum Press, New York, pp 55-93.
4. Beutler B, Eidenschenk C, Crozat K, Imler J-L, Takeuchi O, Hoffmann JA, Akira S (2007) Genetic analysis of resistance to viral infection. Nature Rev Immunol 7: 753-766.
5. Boroevich KA, Lubieniecki KP, Chow W, de Jong P, Schein J, Field M, Moore R, de Boer JG, Koop BF, Davidson WS (2008) Physical mapping and BAC-end sequence analysis of Atlantic salmon BAC libraries. In: W282: large-insert DNA libraries and their applications. Plant & Animal Genomes XVI Conference (W282), San Diego, CA, 12-16 Jan 2008.
6. Danzmann RG, Davidson EA, Ferguson MM, Gharbi K, Koop BF, Hoyheim B, Lien S, Lubieniecki KP, Moghadam HK, Park J, Phillips RB, Davidson WS (2008) Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon). BMC Genomics 9: 557.
7. de Boer JG, Yazawa R, Davidson WS, Koop BF (2007) Bursts and horiozontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids. BMC Genomics 8: 422.
8. Diebold SS, Tsuneyasu K, Hemmi H, Akira S, Reis e Sousa C (2004) Innate antiviral responses by means of TLR7-mediated recognition of single-stranded RNA. Science 303: 1529-1531.
9. Dumoutier L, Leemans C, Lejeune D, Kotenko SV, Renauld J-C (2001) Stat activation by IL-19, IL-20 and mda-7 through IL-20 receptors of two types. J Immunol 167: 3545-3549.
10. Eliassen TM, Froystad MK, Dannevig BH, Jankowska M, Brech A, Falk K, Romoren K, Gjoen T (2000) Initial events in infectious salmon anemia virus infection: evidence for the requirement of a low-pH step. J Virol 74: 218-227.
11. Falk K, Namork E, Rimstad E, Mjaaland S, Dannevig BH (1997) Characterization of infectious salmon anemia virus, an orthomyxo-like virus isolated from Atlantic salmon (Salmo salar L.). J Virol 71: 9016-9023.
12. Falk K, Aspehaug V, Vlasak R, Endresen C (2004) Identification and characterization of viral structural proteins of infectious salmon anemia virus. J Virol 78: 3063-3071.
13. Gale MJ, Korth MJ, Tang NM, Tan SL, Hopkins DA, Dever TE, Polyak SJ, Gretch DR, Katze MG (1997) Evidence that hepatitis C virus resistance to interferon is mediated through repression of the PKR protein kinase by the nonstructural 5A protein. Virology 230: 217-227.
14. Gjoen HM, Refstie T, Ulla O, Gjerde B (1997) Genetic correlations between survival of Atlantic salmon in challenge and field tests. Aquaculture 158: 277-288.
15. Godoy MG, Aedo A, Kibenge MJ, Groman DB, Yason CV, Grothusen H, Lisperguer A, Calbucura M, Avendanio F, Imilan M, Jarpa M, Kibenge FS (2008) First detection, isolation and molecular characterization of infectious salmon anemia virus associated with clinical disease in farmed Atlantic salmon (Salmo salar) in Chile. BMC Vet Res 4: 28.
16. Gross JB, Protas M, Conrad M, Scheid PE, Vidal O, Jeffrey WR, Borowsky R, Tabin CJ (2008) Synteny and candidate gene prediction using an anchored linkage map of Astyanax mexicanus. Proc Natl Acad Sci USA 105: 20106-20111.
17. Haller O, Staeheli P, Kochs G (2007) Interferon-induced Mx proteins in antiviral host defense. Biochemie 89: 812-818.
18. Hayashi F, Smith KD, Ozinsky A, Hawn TR, Yi EC, Godltt DR, Eng JK, Akira S, Underhill DM, Anderem A (2001) The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5. Nature 410: 1099-1103.
19. Heeney JL, Dalgleish AG, Weiss RA (2006) Origin of HIV and the evolution of resistance to AIDS. Science 313: 462-466.
20. Heil F, Hemmi H, Hochrein H, Ampenberger F, Kirschning C, Akira S, Lipford G, Wagner H, Bauer S (2004) Species-specific recognition of single-stranded RNA via Toll-like receptor 7 and 8. Science 303: 1526-1529.
21. Hellebo A, Vilas U, Falk K, Balzac R (2004) Infectious salmon anemia virus specifically binds and hydrolyzes 4-O-acetylated sialic acids. J Virol 78: 3055-3062.
22. Jaillon O, Aury JM, Brunet F et al (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431: 946-957.
23. Johnstone KA, Lubieniecki KP, Chow W, Phillips RB, Koop BF, Davidson WS (2008) Genomic organization and characterization of two vomeronasal 1 receptor-like genes (ora1 and ora2) in Atlantic salmon Salmo salar. Mar Genomics 1: 23-31.
24. Jørgensen SM, Hetland DL, Press CM, Grimholt U, Gjøen T (2007) Effect of early infectious salmon anemia virus (ISAV) infection on expression of MHC pathway genes and type I and II interferon in Atlantic salmon (Salmo salar) tissues. Fish Shellfish Immunol 23: 576-588.
25. Jørgensen SM, Afanasyev S, Krasnov A (2008) Gene expression analyses in Atlantic salmon challenged with infectious salmon anemia virus reveal differences between individuals with early, intermediate and late mortality. BMC Genomics 9: 179.
26. Kibenge FSB, Munir K, Kibenge MJT, Joseph T, Moneke E (2004) Infectious salmon anemia virus: causative agent, pathogenesis and immunity. Anim Health Res Rev 5: 65-78.
27. Kiling Ø, Brundtland MI, Robertsen B (2007) Infectious salmon anemia virus is a powerful inducer of key genes of the type I interferon system of Atlantic salmon, but is not inhibited by interferon. Fish Shellfish Immunol 23: 378-389.
28. Koop BF, von Schalburg KR, Leong J, Walker N, Lieph R, Cooper GA, Robb A, Beetz-Sargent M, Holt RA, Moore R, Brahmbhatt S, Rosner J, Rexroad CE III, McGowan CR, Davidson WS (2008) A salmonid EST genomic study: genes, duplications, phylogeny and microarrays. BMC Genomics 9: 545.
29. Krossoy B, Devold M, Sanders L, Knappskog PM, Aspehaug V, Falk K, Nylund A, Koumans S, Endresen C, Biering E (2001) Cloning and identification of the infectious salmon anemia haemagglutinin. J Gen Virol 82: 1757-1765.
30. Li Q, Verma IA (2002) NF-κβ regulation and the immune system. Nat Rev Immunol 2: 725-734.
31. Lorenz S, Brenna-Hansen S, Moen T, Roseth A, Davidson WS, Omholt SW, Lien S (2009) BAC-based upgrading and physical integration of a genetic SNP map in Atlantic salmon. Anim Genet 41: 48-54. doi: 10. 1111/j. 1365-2052. 2009. 01963. x.
32. MacDonald A, Harris M (2004) Hepatitis C virus NS5A: tales of a promiscuous protein. J Gen Virol 85: 2485-2502.
33. McBeath AJA, Snow M, Secombes CJ, Ellis AE, Collet B (2007) Expression kinetics of interferon and interferon-induced genes in Atlantic salmon (Salmo salar) following infection with infectious pancreatic necrosis virus and infectious salmon anaemia virus. Fish Shellfish Immunol 22: 230-241.
34. Moen T, Fjalestad KT, Munck H, Gomez-Raya L (2004a) A multi-stage testing strategy for detection of quantitative trait loci affecting disease resistance in Atlantic salmon. Genetics 167: 851-858.
35. Moen T, Hoyheim B, Munck H, Gomez-Raya L (2004b) A linkage map of Atlantic salmon (Salmo salar) reveals an uncommonly large difference in recombination rate between the sexes. Anim Genet 35: 81-92.
36. Moen T, Sonesson AK, Hayes B, Lien S, Munck H, Meuwissen THE (2007) Mapping of a quantitative trait locus for resistance against infectious salmon anemia in Atlantic salmon (Salmo salar): comparing survival analysis with analysis on affected/resistant data. BMC Genet 8: 53.
37. Moen T, Hayes B, Baranski M, Berg PR, Kjoglum S, Koop BF, Davidson WS, Omholt SW, Lien S (2008) A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers. BMC Genomics 9: 223.
38. Ng SH, Artieri CG, Bosdet IE, Chiu R, Danzmann RG, Davidson WS, Ferguson MM, Fjell CD, Hoyheim B, Jones SJ, de Jong PJ, Koop BF, Krzywinski MI, Lubieniecki K, Marra MA, Mitchell LA, Mathewson C, Osoegawa K, Parisotto SE, Phillips RB, Rise ML, von Schalburg KR, Schein JE, Shin H, Siddigui A, Thorsen J, Wye N, Yang G, Zhu B (2005) A physical map of the genome of Atlantic salmon, Salmo salar. Genomics 86: 396-404.
39. Nomura N, Zhao M-J, Nagase T, Maekawa T, Ishizaki R, Tabata S, Ishii S (1991) HIV-EP2, a new member of the gene family encoding the human immunodeficiency virus type 1 enhancer binding protein. J Biol Chem 266: 8590-8594.
40. Phillips RB, Keatley KA, Morasch MR, Ventura AB, Lubieniecki KP, Koop BF, Danzmann RG, Davidson WS (2009) 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). BMC Genet 10: 46.
41. Quinn NL, Levenkova N, Chow W, Bouffard P, Boroevich KA, Knight JR, Jarvie TP, Lubieniecki KP, Desany BA, Koop BF, Harkins TT, Davidson WS (2008) Assessing the feasibility of GS FLX pyrosequencing for sequencing the Atlantic salmon genome. BMC Genomics 9: 404.
42. Rimstad E, Mjaaland S (2002) Infectious salmon anemia virus: an orthomyxovirus causing an emerging infection in Atlantic salmon. APMIS 110: 273-282.
43. Rise ML, von Schalburg KR, Brown GD, Devlin RH, Mawer MA, Kuipers N, Busby M, Beetz-Sargent M, Alberto R, Gibbs AR, Hunt P, Shukin R, Zeznik JA, Nelson C, Jones SRM, Smailus DE, Jones SJM, Schein JE, Marra MA, Butterfield YSN, Stott JM, Ng SH, Davidson WS, Koop BF (2004) Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Res 14: 478-490.
44. Robertsen B (2008) Expression of interferon and interferon-induced genes in salmonids in response to virus infection, interferon-inducing compounds and vaccination. Fish Shellfish Immunol 25: 351-357.
45. Rychlik W, Rhoads RE (1989) A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acids Res 17: 8543-8551.
46. Sarropoulou E, Nousdili D, Magoulas A, Kotoulas G (2008) Linking the genomes of nonmodel teleosts through comparative genomics. Mar Biotechnol 10: 227-233.
47. Schiøtz BL, Jørgensen SM, Rexroad C, Gjøen T, Krasnov A (2008) Transcriptomic analysis of responses to infectious salmon anemia virus infection in macrophage-like cells. Virus Res 136: 65-74.
48. Srivastava B, Blazejewska P, Heßmann M, Bruder D, Geffers R, Mauel S, Gruber AD, Schughart K (2009) Host genetic background strongly influences the response to influenza A virus infections. PLoS ONE 4(3): e4857.
49. Tailor CSD, Lavillette D, Marin M, Kabat D (2003) Cell surface receptors for gammaretroviruses. Curr Top Microbiol Immunol 281: 29-106.
50. Takeda K, Kaisho S, Akira S (2003) Toll-like receptors. Annu Rev Immunol 21: 335-376.
51. Thorsen J, Zhu B, Frengen E, Osoegawa K, de Jong PJ, Koop BF, Davidson WS, Hoyheim B (2005) A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects. BMC Genomics 6: 50.
52. Thorud K, Djupvik HO (1988) Infectious anemia in Atlantic salmon (Salmo salar L.). Bull Eur Assoc Fish Pathol 8: 109-111.
53. Tsoi S, Park KC, Kay HH, O'Brien TJ, Podor E, Sun G, Duglas SE, Brown LL, Johnson SC (2007) Identification of a transcript encoding a soluble form of toll-like receptor 5 (TLR5) in Atlantic salmon during Aeromonas salmonicida infection. Vet Immunol Immunopathol 109: 183-187.
54. Van't Veer LJ, Lutz PM, Isselbacher KJ, Bernards R (1992) Structure and expression of major histocompatibility complex-binding protein 2, a 275-kDa zinc finger protein that binds to an enhancer of major histocompatibility complex clas I genes. Proc Natl Acad Sci USA 89: 8971-8975.
55. von Schalburg KR, Rise ML, Cooper GA, Brown GD, Gibbs RA, Nelson CC, Davidson WS, Koop BF (2008) Fish and chips: various methodologies demonstrate the utility of a 16, 000-gene salmonid microarray. BMC Genomics 6: 126-144.
56. Workenhe ST, Kibenge MJ, Wright GM, Wadowska DW, Groman DB, Kibenge FS (2008) Infectious salmon anemia virus replication and induction of alpha feron in Atlantic salmon erythrocytes. Virol J 5: 36.
57. Workenhe ST, Hori TS, Rise ML, Kibenge MJ, Kibenge FS (2009) Infectious salmon anemia virus (ISAV) isolates induce distinct gene expression responses in the Atlantic salmon macrophage/dendritic-like cell line TO assessed using genomic techniques. Mol Immunol 46: 2955-2974.
58. Yang Q, Cheng J, Liu Y, Hong Y, Wang JJ, Zhang SJ (2004) Cloning and identification of NS5ATP2 gene and its spliced variant transactivated by hepatitis C virus non-structural protein 5A. World J Gastroenterol 10: 1735-1739.