Table 1
MHC class I and II gene loci in Atlantic salmon (5, 13) (a) against the background of the relevant data for humans (b)
| (a) | ||||
| Chr. | *MHC I genes in Salmo salar (Sasa) (MhcSasa-U… or Z, S, L, P…) | *MHC II genes in Salmo salar (Sasa) (MhcSasa-D…) | ||
| 2 | None | DCB1, DCA / DEA, DEB / DCB2 | ||
| 5 | None | DEAψ, DEBψ | ||
| 7 | PAAψ | None | ||
| 9 | SAA | None | ||
| 10 | LKAψ | None | ||
| 11 | LCA, LCAψ | None | ||
| 12 | LDA | DDA, DDB / **DAA, DAB1 | ||
| 13 | None | DBB, DBA | ||
| 14 | UDA1, UCA2 / UCA1, UGA / ZBAb, ZCAb, ZDAbψ | None | ||
| 20 | SAAψ | None | ||
| 21 | LIA / UHA1, UHA2 | None | ||
| 22 | None | DABψ | ||
| 25 | LIAψ / LLAψ | None | ||
| 26 | LFA, LGA, LHA | None | ||
| 27 | ULA, **UBA, ZAAa, ZBAa, ZCAa, ZDAa | None | ||
| (b) | ||||
| Chr. | MHC I genes in humans | MHC II genes in humans | ||
| 6 | **HLA-A, HLA-B, HLA-C HLA-E, HLA-F, HLA-G, MICA and MICB | **HLA-DP, HLA-DQ and HLA-DR HLA-DM and HLA-DO |
Chr. – chromosome no.; symbol ( / ) – divides genes with separate loci;
* – the constituents of the nomenclature of MHC class I and class II genes are listed in Tables 2 and 4;
Table 2
Constituents of the nomenclature of MHC class I genes (table cells with grey underlay) in fish on the example of Atlantic salmon (11, 13)
| MHC | Fish genus and species symbol | MHC class I gene lineage | MHC class I gene sublineage | Locus | Subclass | Gene | Full name / symbol of gene |
|---|---|---|---|---|---|---|---|
| B | UBA** | MhcSasa-UBA | |||||
| C | UCA1***, UCA2 | MhcSasa-UCA1, MhcSasa-UCA2 | |||||
| D | UDA1 | MhcSasa-UDA1 | |||||
| G | UGA | MhcSasa-UGA | |||||
| U | None | H | UHA1, UHA2 | MhcSasa-UHA1, MhcSasa-UHA2 | |||
| A | ZAAa | MhcSasa-ZAAa | |||||
| B | ZBAa, ZBAb | MhcSasa-ZBAa, MhcSasa-ZBAb | |||||
| Z | Z1* | C | ZCAa, ZCAb | MhcSasa-ZCAa, MhcSasa-ZCAb | |||
| C | LCA, LCAψ | MhcSasa-LCA, MhcSasa-LCAψ | |||||
| D | LDA | MhcSasa-LDA | |||||
| F | LFA | MhcSasa-LFA | |||||
| G | LGA | MhcSasa-LGA | |||||
| H | LHA | MhcSasa-LHA | |||||
| L | None | I | LIA, LIAψ | MhcSasa-LIA, LIAψ | |||
| K | LKAψ | MhcSasa-LKAψ | |||||
| P | None | A | PAAψ | MhcSasa-PAAψ |
Table 3
| Lungfish (subclass Dipnoi) | – | x* | – | – | – | – | – | – | ||
| Paddlefish (family Polyodontidae) | x | – | – | – | – | – | – | x | ||
| Sturgeon (family Acipenseridae) | x | x* | – | – | – | – | – | x | ||
| Spotted gar (Lepisosteus oculatus) | x | x* | 0 | x | x | x | x | |||
| Zebrafish (Danio rerio) | x | x | – | – | 0 | x | 0 | x | x | 0 |
| Carp (Cyprinus carpio) | x | x | – | x | – | – | – | x | – | x |
| Mexican tetra (Astyanax mexicanus) | x | x | x | – | x | x | x | – | – | – |
| Atlantic salmon (Salmo salar) | x | x | – | – | x | x | x | x | x | x |
| Medaka (Oryzias latipes) | x | x | – | – | 0 | 0 | 0 | x | x | 0 |
| Stickleback (Gasterosteus aculeatus) | x | x | – | – | 0 | 0 | 0 | x | x | 0 |
symbol ( – ) – lack of sufficient data to deduce that MHC genes of a specific lineage or sublineage are present or absent; 0 – lack of MHC genes of a specific lineage or sublineage; x – occurrence of MHC genes of a specific lineage or sublineage
Table 4
Constituents of the nomenclature of MHC class II genes (table cells with grey underlay) in fish on the example of Salmo salar and Oryzias latipes
| MHC | Fish genus and species symbol | MHC class II gene lineage | MHC class II gene sublineage | Locus | Subclass | Gene | Full name / symbol of gene |
|---|---|---|---|---|---|---|---|
| A | *DAA–DAB | MhcOrla-DAA–DAB | |||||
| E | **DEA–DEB | MhcOrla-DEA–DEB |
*** – pairs of Oryzias latipes genes with limited expression and low polymorphism, clustering in sublineage A (5)
*** – pairs of Oryzias latipes genes with limited expression and low polymorphism, clustering in sublineage A (5)
** – gene clustering based on the domain α1 sequence, according to Dijkstra et al. (5) and Grimholt (11), with preservation of sublineage E for sequences making up a cluster with DEA–DEB in Salmo salar and with creation of sublineage B with sequences forming a cluster with DEA–DEB in Oryzias latipes;
** – gene clustering based on the domain α1 sequence, according to Dijkstra et al. (5) and Grimholt (11), with preservation of sublineage E for sequences making up a cluster with DEA–DEB in Salmo salar and with creation of sublineage B with sequences forming a cluster with DEA–DEB in Oryzias latipes;
Table 5
| Humans | Spotted gar | Atlantic salmon | Shared genes** | ||||
|---|---|---|---|---|---|---|---|
| MHC I | MHC II | MHC I | MHC II | MHC I | MHC II | MHC I | MHC II*** |
| HLA-G | HLA-DRα | U (3 loci) | Eα (2 loci) | U* | Eα | PSMB8 | PBX2 |
| HLA-A | HLA-DRβ | P (3 loci) | Eβ (2 loci) | Eβ | TUBB | TAP1 | |
| HLA-E | HLA-DQα | L (2 loci) | A/Bα | FLOT1 | RGL2 | ||
| HLA-C | HLA-DQβ | u.s. | A/Bβ | TCF19 | PHF1 | ||
| HLA-B | HLA-DPα | u.s. α | TAP2 | BRD2 | |||
| HLA-DPβ | PSMB9 | SYNGAP-like | |||||
| HLA-DMα | BRD2 | ||||||
| HLA-DMβ | TAPBP | ||||||
| HLA-Doα | RXRB | ||||||
| HLA-Doβ | HSD17B8 | ||||||
| PSMB10 | |||||||
u.s. – undefined sequence; PSMB8 – protein-coding gene, proteasome subunit β type-8; TUBB – protein-coding gene, tubulin β-chain; FLOT1 – protein-coding gene, flotillin-1; TCF19 – protein-coding gene, transcription factor 19; TAP2 – protein-coding gene, antigen peptide transporter 2; PSMB9 – protein-coding gene, proteasome subunit β type-9; BRD2 – protein-coding gene, bromodomain-containing protein 2; TAPBP – protein-coding gene, TAP-associated glycoprotein, also known as tapasin; RXRB – gene, retinoid X reflex point β (RXR-β); HSD17B8 – enzyme, oestradiol 17 β-dehydrogenase 8; PSMB10 – protein coding gene, proteasome subunit β type-10; PBX2 – protein-coding gene, pre-B-cell leukaemia transcription factor 2; TAP1 – protein-coding gene, transporter associated with antigen processing 1; RGL2 – protein-coding gene, ral guanine nucleotide dissociation stimulator-like 2; PHF1 – protein-coding gene, PHD finger protein 1; SYNGAP-like – Ras GTPase-activating protein SynGap-like;