Fisheries Science

, Volume 83, Issue 3, pp 433–446 | Cite as

Genomic structure, polymorphism, and expression analysis of the spotted scat Scatophagus argus major histocompatibility complex class I alpha gene

  • Xiaobing Wang
  • Yanmei Liu
  • Zhizhi Liu
  • Tianrui Zhang
  • Qiang Li
  • Junbin Zhang
Original Article Aquaculture


The complete complementary DNA (cDNA) sequence of the major histocompatibility complex (MHC) class I α gene in Scatophagus argus was obtained by homology-based cloning and rapid amplification of cDNA ends polymerase chain reaction (PCR. The intron sequences, polymorphism, and tissue expression of this gene were then analyzed. The gene cDNA sequence is 2020 base pairs (bp) in length, including a 86-bp 5′-untranslated region (UTR), 866-bp 3′-UTR and 1068-bp open reading frame. It contains seven exons and six introns, of which there are two types of the fourth intron with respective lengths of 655 and 691 bp; it also has microsatellite (T)n fragments, and the sixth intron has a separate 3′-UTR. From 42 individuals, 20 alleles of the class I α-chain gene were identified, called here “Scar-UA*0101–Scar-UA*2001,” which demonstrate high polymorphism. Reverse transcription-PCR analysis shows its expression in ten tissues, with high expression levels in the liver, spleen, and kidney, and low levels of expression in the stomach, intestines, and muscle. A tree depicting the molecular relationships built using the neighbor-joining method shows that Scatophagus argus has a close genetic relationship to Perciformes fish such as Sparus aurata, Dicentrarchus labrax, and a more distant relationship to salmonid and cyprinid fishes, amphibians, birds, and mammals.


Tissue expression Amplification Complementary DNA Intron Karyocyte Exon MHC 



This study was supported by grants from the Natural Science Foundation of China (41176109). The authors would like to thank the two anonymous reviewers for their very useful comments and remarks.

Author contributions

Z. Z. L. and J. B. Z. conceived and designed the experiments, and polished the manuscript. X. B. W. and Y. M. L. performed some of the experiments, analyzed the data and wrote the manuscript. T. R. Z. performed the RNA expression experiment of the MHC class I gene. Q. L. helped collect the samples of the spotted scat.


  1. 1.
    Hashimoto K, Nakanishi T, Kurosawa Y (1990) Isolation of carp genes encoding major histocompatibility complex antigens. J Proc Natl Acad Sci USA 87(17):6863–6867CrossRefGoogle Scholar
  2. 2.
    Sültmann H, Mayer WE, Figueroa F, O’HUigin C, Klein J (1994) Organization of MHC class II B genes in the zebrafish (Brachydanio rerio). Genomics 23(1):1–14CrossRefPubMedGoogle Scholar
  3. 3.
    Hansen JD, Strassburger P, Thorgaard GH, Young WP, Du Pasquier L (1999) Expression, linkage, and polymorphism of MHC-related genes in rainbow trout, Oncorhynchus mykiss. J Immunol 163:774–786PubMedGoogle Scholar
  4. 4.
    Fujiki K, Booman M, Dixon E, Dixon B (2001) Cloning and characterization of cDNA clones encoding membrane bound and potentially secreted major histocompatibility class I receptors from walleye (Stizostedion vitreum). Immunogenetics 53:760–769CrossRefPubMedGoogle Scholar
  5. 5.
    Xu TJ, Chen SL, Ji XS, Sha ZX (2009) Molecular cloning, genomic structure, polymorphism and expression analysis of major histocompatibility complex class II A and II B genes of half-smooth tongue sole (Cynoglossus semilaevis). Fish Shellfish Immunol 27(2):192–201CrossRefPubMedGoogle Scholar
  6. 6.
    Yu SH, Ao JQ, Chen XH (2010) Molecular characterization and expression analysis of MHC class alpha and beta genes in large yellow croaker (Pseudosciaena crocea). Mol Biol Rep 37:1295–1307CrossRefPubMedGoogle Scholar
  7. 7.
    Pang JC, Gao FY, Lu MX, Ye X, Zhu HP, Ke XL (2013) Major histocompatibility complex class II A and II B genes of Nile tilapia (Oreochromis niloticus): genomic structure, molecular polymorphism and expression patterns. Fish Shellfish Immunol 34(2):486–496CrossRefPubMedGoogle Scholar
  8. 8.
    Bardach JE, Ryther JH, McLarney WO (1974) The farming and husbandry of freshwater and marine organisms. Aquaculture 3(2):208–209CrossRefGoogle Scholar
  9. 9.
    Barry TP, Fast AW (1992) Biology of the spotted scat (Scatophagus argus) in the Philippines. Fish Sci 5(3):163–179Google Scholar
  10. 10.
    Lin ZB, Ma QT, Chen KL (1998) Freshwater aquaculture test summary of spotted scat (Scatophagus argus). Fish Sci Technol 4(16–17):23Google Scholar
  11. 11.
    Zhang BJ, Liang RJ, Mao DN, Zhang BH (1999) The growth characteristic of spotted scat (Scatophagus argus) with salt water pond domestication. Mod Fish Inf 14(10):8–15Google Scholar
  12. 12.
    Lan GB, Yan B, Liao SM, Luo Y, Xie RC (2005) Biology research and review of spotted scat (Scatophagus argus). Fish Sci 24:39–41Google Scholar
  13. 13.
    Sivan G, Venketesvaran K, Radhakrishnan CK (2007) Biological and biochemical properties of Scatophagus argus venom. Toxicon 50:563–571CrossRefPubMedGoogle Scholar
  14. 14.
    Wu B, Zhang MZ, Deng SP, Shi SL, Li GL, Zhu CH (2014) Morphological variance analysis of spotted scat (Scatophagus argus) male and female individuals. J Shanghai Ocean Univ 23(1):64–69Google Scholar
  15. 15.
    Sivan G, Venketesvaran K, Radhakrishnan CK (2010) Characterization of biological activity of Scatophagus argus venom. Toxicon 56:914–925CrossRefPubMedGoogle Scholar
  16. 16.
    Zhang MZ, Deng SP, Zhu CH, Li GL (2013) The influence of temperature on the ovaries of spotted scat (Scatophagus argus). Chin Fish Sci 20:599–606Google Scholar
  17. 17.
    Cui D, Liu ZW, Liu NX, Zhang YY, Zhang JB (2013) Gonad development and organization structure observation of spotted scat (Scatophagus argus). J Fish China 37:696–704CrossRefGoogle Scholar
  18. 18.
    Liu HF, Mu XJ, Gui L, Su ML, Li H, Zhang G, Liu ZH, Zhang JB (2014) Characterization and gonadal expression of FOXL2 relative to Cyp19a2 genes in spotted scat Scatophagus argus. Gene 61(1):6–14CrossRefGoogle Scholar
  19. 19.
    Cai ZP, Wang Y, Hu JW, Zhang JB, Lin YG (2010) Breeding biology and induced spawning test of spotted scat (Scatophagus argus). J Trop Oceanogr 29(5):180–185Google Scholar
  20. 20.
    Mu XJ, Su ML, Gui L, Liang XM, Zhang PP, Hu P, Liu ZH, Zhang JB (2014) Comparative renal gene expression in response to abrupt hypoosmotic shock in spotted scat (Scatophagus argus). Gen Comp Endocrinol 215(1):25–35PubMedGoogle Scholar
  21. 21.
    Zhang QH, Ma WY, Chen B, Liu ZZ, Xu HD, Zhang QY, Wang XB, Jia L (2016) Research on Aremonas hydrophila-caused bacteria disease in spotted scat (Scatophagus argus). J Fish China 4(40):634–643Google Scholar
  22. 22.
    Klein J, Bontrop RE, Dawkins RL, Erlich HA, Gyllensten UB, Heise ER, Jones PP, Parham P, Wakeland EK, Watkins DI (1990) Nomenclature for the major histocompatibility complexes of different species: a proposal. Immunogenetics 31(4):217–219CrossRefPubMedGoogle Scholar
  23. 23.
    Anmarkrud JA, Johnsen A (2010) Ancestral polymorphism in exon 2 of blue throat (Luscinia svecica) MHC class II B genes. J Evol Biol 23(6):1206–1217CrossRefPubMedGoogle Scholar
  24. 24.
    Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98Google Scholar
  25. 25.
    Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25(24):4876–4882CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Petersen TN, Brunak S, Heijne G, Nielsen H (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8(10):785–786CrossRefPubMedGoogle Scholar
  27. 27.
    Chen YJ, Yu P, Luo JC, Jiang Y (2003) Secreted protein prediction system combining CJ-SPHMM, TMHMM and PSORT. Mamm Genome 14(12):859–865CrossRefPubMedGoogle Scholar
  28. 28.
    Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism date. Bioinformatics 25(11):1451–1452CrossRefPubMedGoogle Scholar
  29. 29.
    Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA 4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24(8):1596–1599CrossRefPubMedGoogle Scholar
  30. 30.
    Sommer S (2005) The importance of immune gene variability (MHC) in evolutionary ecology and conservation. Front Zool 2(1):16–34CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Grimholt U, Drablos F, Jorgensen S, Høyheim B, Stet RJ (2002) The major histocompatibility class I locus in Atlantic salmon (Salmo salar L.): polymorphism, linkage analysis and protein modelling. Immunogenetics 54:570–581CrossRefPubMedGoogle Scholar
  32. 32.
    Xu TJ, Chen SL (2011) Molecular cloning, genomic structure and expression analysis of major histocompatibility complex class I α gene of half-smooth tongue sole (Cynoglossus semilaevis). Fish Physiol Biochem 37:85–90CrossRefPubMedGoogle Scholar
  33. 33.
    Srisapoome P, Ohira T, Hirono I, Aoki T (2004) Cloning, characterization and expression of cDNA containing major histocompatibility complex class I, II α and II β genes of Japanese flounder (Paralichthys olivaceus). Fish Sci 70:264–276CrossRefGoogle Scholar
  34. 34.
    Stet RJ, Vries B, Mudde K, Hermsen T, Heerwaarden J, Shum BP (2002) Unique haplotypes of co-segregating major histocompatibility complex class II A and class II B alleles in Atlantic salmon (Salmo salar) give rise to diverse class II genotypes. Immunogenetics 54:320–331CrossRefPubMedGoogle Scholar
  35. 35.
    Rakus KL, Wiegertjes GF, Adamek M, Bekh V, Stet RJM, Irnazarow I (2008) Application of PCR-RF-SSCP to study major histocompatibillity class II B polymorphism in common carp (Cyprinus carpio L.). Fish Shellfish Immunol 24(6):734–744CrossRefPubMedGoogle Scholar
  36. 36.
    Aoyagi K, Dijkstra JM, Xia C, Denda I, Ototake M, Hashimoto K, Nakanishi T (2002) Classical MHC class I genes composed of highly divergent sequence lineages share a single locus in rainbow trout (Oncorhynchus mykiss). J Immunol 168:260–273CrossRefPubMedGoogle Scholar
  37. 37.
    Li JP, Gao FY, Lu MX, Cao JM, Zhu HP, Ke XL, Liu ZG (2014) Molecular identification, polymorphism, and expression analysis of major histocompatibility complex class I α genes of Nile tilapia (Oreochromis niloticus). J Fish China 6:1134–1145Google Scholar
  38. 38.
    Xia C, Xu GX, Lin CY, Hu TJ, Yan RQ, Gao FG (2004) Molecular cloning and polymorphism of major histocompatibility complex class I genes from grass carp (Ctenophangodon idellus). Prog Nat Sci 1:51–59Google Scholar
  39. 39.
    Li TM, Zhou FN, Cui ZF, Ji XS, Wang H (2013) Cloning and polymorphism analysis of major histocompatibility complex class I A genes of tilapia nilotica (Oreochromis niloticus). J Shandong Univ (Nat Sci) 48(11):14–22Google Scholar
  40. 40.
    Pargam P, Ohat T (1996) Population biology of antigen presentation by MHC class I molecules. Science 272:67–74CrossRefGoogle Scholar
  41. 41.
    Zhang YX, Chen SL (2006) Molecular identification, polymorphism, and expression analysis of major histocompatibility complex class II A and B genes of turbot (Scophthalmus maximus). Mar Biotechnol 8(6):611–623CrossRefPubMedGoogle Scholar
  42. 42.
    Xu TJ, Chen SL, Zhang YX (2010) MHC class II A gene polymorphism and its association with resistance/susceptibility to Hbrio anguillarum in Japanese flounder (Paralichthys olivaceus). Dev Comp Immunol 34:1042–1050CrossRefPubMedGoogle Scholar
  43. 43.
    Miller KM, Withler RE, Beacham TD (1997) Molecular evolution at MHC genes in two populations of chinook salmon Oncorhynchus tshawytscha. Mol Ecol 6:937–954CrossRefPubMedGoogle Scholar
  44. 44.
    Yang TY, Hao HF, Jia ZhH, Chen WH, Xia C (2006) Characterisation of grass carp (Ctenopharyngodon idellus) MHC class I domain lineages. Fish Shellfish Immunol 21:583–591CrossRefPubMedGoogle Scholar
  45. 45.
    Choi W, Lee EY, Choi TJ (2006) Cloning and sequence analysis of the beta2-microglobulin transcript from flounder Paralichthys olivaceous. Mol Immunol 43:1565–1572CrossRefPubMedGoogle Scholar
  46. 46.
    Antao AB, Gregory Chinchar V, McConnell TJ, Miller NW, William Clem L, Wilson MR (1999) MHC class I genes of the channel catfish: sequence analysis and expression. Immunogenetics 49:303–311CrossRefPubMedGoogle Scholar

Copyright information

© Japanese Society of Fisheries Science 2017

Authors and Affiliations

  1. 1.Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of EducationShanghai Ocean UniversityShanghaiChina
  2. 2.Central LaboratoryShanghai Xuhui Central HospitalShanghaiChina

Personalised recommendations