Occurrence of MHC I and MHC II genes in selected species of Osteichthyes (11, 13)
| Selected species of Osteichthyes | MHC I | MHC II | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Lineage | ||||||||||
| U | Z | S | L | P | D | |||||
Sublineage | ||||||||||
| – | Z1 | Z2 | Z3 | – | – | – | A | B | E | |
| Lungfish (subclass Dipnoi) | – | x – lineage Z; | – | – | – | – | – | – | ||
| Paddlefish (family Polyodontidae) | x | – | – | – | – | – | – | x | ||
| Sturgeon (family Acipenseridae) | x | x – lineage Z; | – | – | – | – | – | x | ||
| Spotted gar (Lepisosteus oculatus) | x | x – lineage Z; | 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 |
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. | – the constituents of the nomenclature of MHC class I and class II genes are listed in Tables 2 and 4; | – the constituents of the nomenclature of MHC class I and class II genes are listed in Tables 2 and 4; | ||
| 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 / – genes of the classical MHC molecules | ||
| 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, – genes of the classical MHC molecules | None | ||
| (b) | ||||
| Chr. | MHC I genes in humans | MHC II genes in humans | ||
| 6 | – genes of the classical MHC molecules | – genes of the classical MHC molecules | ||
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 | – genes of the classical MHC II molecule; | MhcOrla-DAA–DAB | |||||
| A | MhcSasa-DAA–DAB | ||||||
| Sasa | C | – pairs of Oryzias latipes genes with limited expression and low polymorphism, clustering in sublineage A (5) | MhcOrla-DCA–DCB | ||||
| (Salmo salar) | F | – pairs of Oryzias latipes genes with limited expression and low polymorphism, clustering in sublineage A (5) | MhcOrla-DFA–DFB | ||||
| Mhc | D | E | E | A (for chain α) | – 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; | MhcSasa-DEA–DEB | |
| Orla | B | B (for chain β) | DBA–DBB | MhcSasa-DBA–DBB | |||
| (Oryzias latipes) | C | DCA–DCB1/2 | MhcSasa-DCA–DCB1 | ||||
| D | DDA–DDB | MhcSasa-DDA–DDB | |||||
| DDA–DDB1/2 | MhcOrla-DDA–DDB1 | ||||||
| E | – 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; | MhcOrla-DEA–DEB |
Genes from selected MHC regions, identified in humans and fish (5, 13)
| Humans | Spotted gar | Atlantic salmon | Shared genes – selected genes shared by humans (MHC region sized ~ 4Mb) and Salmo salar (MHC I and MHC II), as well as by Danio rerio and Oryzias latipes (MHC I); | ||||
|---|---|---|---|---|---|---|---|
| MHC I | MHC II | MHC I | MHC II | MHC I | MHC II | MHC I | MHC II – genes occurring within sublineage E in Salmonidae |
| HLA-G | HLA-DRα | U (3 loci) | Eα (2 loci) | U – syntenic gene; | 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 | |||||||
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 – a gene of an MHC Ia molecule; | MhcSasa-UBA | |||||
| C | UCA1 – locus no.; | MhcSasa-UCA1, MhcSasa-UCA2 | |||||
| D | UDA1 | MhcSasa-UDA1 | |||||
| G | UGA | MhcSasa-UGA | |||||
| U | None | H | UHA1, UHA2 | MhcSasa-UHA1, MhcSasa-UHA2 | |||
| L | ULA | MhcSasa-ULA | |||||
| A | ZAAa | MhcSasa-ZAAa | |||||
| B | ZBAa, ZBAb | MhcSasa-ZBAa, MhcSasa-ZBAb | |||||
| Z | Z1 – sublineage Z1 with a typical sequence, isolated in, inter alia, Salmo salar; | C | ZCAa, ZCAb | MhcSasa-ZCAa, MhcSasa-ZCAb | |||
| D | ZDAa, ZDAb – pseudogenes | MhcSasa-ZDAa, MhcSasa-ZDAb – pseudogenes | |||||
| Mhc | Sasa | S | None | A | A (for chain α) | SAA, SAA – pseudogenes | MhcSasa-SAA, MhcSasa-SAA – pseudogenes |
| C | LCA, LCA – pseudogenes | MhcSasa-LCA, MhcSasa-LCA – pseudogenes | |||||
| D | LDA | MhcSasa-LDA | |||||
| F | LFA | MhcSasa-LFA | |||||
| G | LGA | MhcSasa-LGA | |||||
| H | LHA | MhcSasa-LHA | |||||
| L | None | I | LIA, LIA – pseudogenes | MhcSasa-LIA, LIA – pseudogenes | |||
| K | LKA – pseudogenes | MhcSasa-LKA – pseudogenes | |||||
| L | LLA – pseudogenes | MhcSasa-LLA – pseudogenes | |||||
| P | None | A | PAA – pseudogenes | MhcSasa-PAA – pseudogenes |