Birds Ig

Specific in Birds

Until 2024/5/23, the only annotated bird in IMGT is Chicken. According to the IMGT, chicken heavy chain gene has only 1 functional V gene , 3 functional D genes, and 1 J gene. This is hugely difference from human or other mammals.

Birds have three classes of antibody: IgM (the only class in all vertebrates), IgY, and IgA. Not been directly determined but inferred from size estimates of the intact molecules of IgM and IgA, they could form polypeptide chains^[1]. In addition, ducks have a smaller form of IgY, called IgY (ΔFc).

• IgM is the only class of antibody that is found in all vertebrate. IgM is larger than that of a true tetrameric IgM, such as occurs in teleost fish^[2] and thus both are likely to be pentameric.
• IgY is the major low-molecular weight form of antibody found circulating in birds, where it has sometimes been referred to as IgG. An IgY-like molecule is likely to have been the evolutionary precursor of both IgG and IgE immunoglobulins^[3][4].

Chicken

The first avian genomic MHC map was the chicken minimal and essential one on chromosome 16. This map, spanning 92 kb and harboring 19 genes, was then extended to be 242 kb containing 46 genes^[5][6].

Chicken (Gallus gallus) IGH locus on chromosome 31

• The chicken (Gallus gallus) IGH locus is on chromosome 31. The orientation of the locus is reverse (REV).
• The chicken (Gallus gallus) IGH locus spans 116 kilobases (kb), from 10 kb upstream of the most 5’ gene in the locus, IGHV1-83 §, to 10 kb downstream of the most 3’ gene in the locus, IGHJ (F). The Locus representation encompasses 120 kb.
• The chicken (Gallus gallus) IGH locus consists of 94 IGHV genes belonging to 1 IGHV subgroup, 4 IGHD belonging to 1 IGHD set, 1 IGHJ gene belonging to 1 IGHJ set and 3 IGHC genes.
• The IGHV genes span 97 kilobases (kb), the IGHD genes span 7251 bases (b) and the IGHJ gene span 12 kilobases (kb).
  source: Imgt

https://www.imgt.org/ligmdb/view?id=IMGT000014

The generation of antibody binding-site diversity is very well understood for the chicken:

• Parvari R, Avivi A, Lentner F, Ziv E, Tel-Or S, Burstein Y, et al. Chicken immunoglobulin gamma-heavy chains: limited VH gene repertoire, combinatorial diversification by D gene segments and evolution of the heavy chain locus. EMBO J. 1988;7:739–44.
• Reynaud CA, Anquez V, Dahan A, Weill JC. A single rearrangement event generates most of the chicken immunoglobulin light chain diversity. Cell. 1985;40:283–91.
• Reynaud CA, Anquez V, Grimal H, Weill JC. A hyperconversion mechanism generates the chicken light chain preimmune repertoire. Cell. 1987;48:379–88.
• Reynaud CA, Dahan A, Anquez V, Weill JC. Somatic hyperconversion diversifies the single Vh gene of the chicken with a high incidence in the D region. Cell. 1989;59:171–83.

Duck

The newest Duck genome is available at BMC: Jiaxiang Hu, et al; 2024^[7]. The old one ZJU1.0^[8] has (GCF_015476345.1) 33 chromosomes (not included sexual and mitochondira). For the SKLA1.0 (GCA_037218355.1), it covers 40 chromosomes (included in Z chromosome). For the ZJU1.0, they used 115 SMRT cells were sequenced with PacBio RS II. In SJKA1.0, they integrated Nanopore, Bionano, and Hi-C data. It also contains a complete genomic map of the MHC.

In E. W´ojcik and E. Smalec’s work in 2017^[9], they described 1-13 autosomes. In there karyotyping analysis result, the got about 84 dots for Anas platyrhynchos.

© E. W´ojcik; 2017

Anseriform birds (ducks and their relatives) are the closest relatives of the chickens which was well understood and be studied.

Ducks have the same hematopoietic tissues as chickens, including bone marrow, gut associated lymphoid tissue, spleen, thymus and the Bursa of Fabricius, a specialized organ for B lymphoid development. However, there is one notable difference. Ducks have lymph nodes, which are completely absent in chickens^[10].

1. a single functional rearrangement of the variable (V) region, like chicken.
2. generate diversity through gene conversion from a pool of pseudogenes.
3. V region element and the pseudogenes appear to consist of a single gene family (The same as the Chicken)
4. Further analysis of 26 heavy chain joining (JH) and 27 light chain JL segments shows there is use of a single J segment in ducks.
   From: Lundqvist M L, et al.^[1:1]

The overwhelming evidence is that all birds express only a single class of immunoglobulin light (L) chain^[11][12] most closely related to the λ chain of the mammals ^[13][14]. The suggestion of additional classes of L chain in the birds ^[15] has not been substantiated at the amino acid sequence or genetic level.

Duck IgY

Ducks IgY:

• secreted form
• a receptor form with a hydrophobic membrane-spanning C-terminus
• truncated form termed IgY(ΔFc)

Difference and similarities in other species:

• No truncated form: Chickens express only the full-length and membrane-receptor forms of IgY^[3:1].
• Has truncated form: A small form of IgY (5.7S) is produced by some species of turtles^[16].

Duck immune response inept:

• lacking: precipitation, agglutination, complement fixation and opsonization^[17][18] (related the lacks an Fc region).

Duck IgA

IgA has been described to date only in mammals and birds

• secretions of the gut, respiratory and reproductive tracts, as well as in tears, bile and (in mammals) the milk

• IgA of mammals is typically a dimer.

• Duck IGH:

  1. a single family of VH sequences
  2. a single expressed JH element
  3. JH is immediately downstream of a D segment

• Duck IGL:

  1. there are few functional coding VL and JL elements in the germline
  2. diversification most likely arises in large measure from gene conversion events from an extensive suite of germline VL-related sequences; (Genomic Southern blot analysis showed that there is a large family of germline VL-related sequences in the mallard duck^[11:1])
  3. It is not known whether there is a single functional V and J element in the duck L chain locus, however, that is the simplest explanation of the results.
  4. muscovy duck were at least two functional VL genes^[19].
  5. a single family of VL sequences

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1. Lundqvist M L, Middleton D L, Radford C, et al. Immunoglobulins of the non-galliform birds: antibody expression and repertoire in the duck[J]. Developmental & Comparative Immunology, 2006, 30(1-2): 93-100. ↩︎ ↩︎

2. Leslie GA, Clem LW. Phylogeny of immunoglobulin structure and function. 3. Immunoglobulins of the chicken. J Exp Med. 1969;130:1337–52. ↩︎

3. Parvari R, Avivi A, Lentner F, Ziv E, Tel-Or S, Burstein Y, et al. Chicken immunoglobulin gamma-heavy chains: limited VH gene repertoire, combinatorial diversification by D gene segments and evolution of the heavy chain locus. EMBO J. 1988;7:739–44. ↩︎ ↩︎

4. Magor KE, Higgins DA, Middleton DL, Warr GW. One gene encodes the heavy chains for three different forms of IgY in the duck. J Immonol. 1994;153:5549–55. ↩︎

5. Kaufman J, Milne S, Göbel TW, Walker BA, Jacob JP, Auffray C, et al. The chicken B locus is a minimal essential major histocompatibility complex. Nature. 1999;401:923–5. ↩︎

6. Shiina T, Briles WE, Goto RM, Hosomichi K, Yanagiya K, Shimizu S, et al. Extended gene map reveals tripartite motif, C-type lectin, and Ig superfamily type genes within a subregion of the chicken MHC-B affecting infectious disease. J Immunol. 2007;178:7162–72. ↩︎

7. Hu J, Song L, Ning M, et al. A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families[J]. BMC biology, 2024, 22(1): 31. ↩︎

8. Li J, Zhang J, Liu J, et al. A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals[J]. Gigascience, 2021, 10(1): giaa142. ↩︎

9. Wójcik E, Smalec E. Constitutive heterochromatin in chromosomes of duck hybrids and goose hybrids[J]. Poultry Science, 2017, 96(1): 18-26.
   ↩︎

10. Flajnik MF, Miller KM, Du Pasquier L. Evolution of the immune system. In: Paul WE, editor. Fundamental immunology. 5th ed. Philadelphia: Lippincott Williams and Wilkins; 2003. p. 519–70. ↩︎

11. Magor KE, Higgins DA, Middleton DL, Warr GW. cDNA sequence and organization of the immunoglobulin light chain gene of the duck, Anas platyrhynchos. Dev Comp Immunol. 1994;18:523–31. ↩︎ ↩︎

12. Reynaud CA, Dahan A, Weill JC. Complete sequence of a chicken lambda light chain immunoglobulin derived from the nucleotide sequence of its mRNA. Proc Natl Acad Sci USA. 1983;80:4099–103. ↩︎

13. Grant JA, Sanders B, Hood L. Partial amino acid sequences of chicken and turkey immunoglobulin light chains. Homology with mammalian lambda chains. Biochemistry. 1971;10:3123–32. ↩︎

14. Kubo RT, Rosenblum IY, Benedict AA. The unblocked N-terminal sequence of chicken IgG lambda-like light chains. J Immunol. 1970;105:534–6. ↩︎

15. Leslie GA. Evidence for a second avian light chain isotype. Immunochemistry. 1977;14:149–51. ↩︎

16. Leslie GA, Clem LW. Phylogeny of immunoglobulin structure and function, VI. 17S, 7.5S and 5.7S anti-DNP of the turtle, Pseudamys scripta. J Immunol. 1972;108:1656–64. ↩︎

17. Grey HM. Duck immunoglobulins. II. Biologic and immunochemical studies. J Imunol. 1967;98:820–6. ↩︎

18. Humphrey BD, Calvert CC, Klasing KC. The ratio of full length IgY to truncated IgY in immune complexes affects macrophage phagocytosis and the acute phase response of mallard ducks (Anas platyrhynchos) Dev Comp Immunol. 2004;28:665–72. ↩︎

19. McCormack WT, Carlson LM, Tjoelker LW, Thompson CB. Evolutionary comparison of the avian IgL locus: combinatorial diversity plays a role in the generation of the antibody repertoire in some avian species. Int Immunol. 1989;1:332–41. ↩︎