Table 1.
Immune gene repertoire of broad-nosed pipefish, Syngnathus typhle. The immune gene repertoire is compared with cod [6]. The last column indicates how the transcript was identified, either via contig annotation, or via reciprocal best tBLASTx using teleost queries to the S. typhle database (see the electronic supplementary material, S1 and S2; see §2 for details). The results of the tBLASTx search are presented in the electronic supplementary materials, tables S5 and S6.
| gene abbreviation | pathway | pipefish, this study | cod | identification |
|---|---|---|---|---|
| MHC I | MHC I | yes | yes | contig annot |
| B2-microglobulin | MHC I | yes | yes | contig annot |
| TAP1 | MHC I | yes | yes | contig annot |
| TAP2 | MHC I | yes | yes | contig annot |
| Tapasin | MHC I | yes | yes | contig annot |
| PSME1 | MHC I | yes | yes | contig annot |
| PSME2 | MHC I | yes | yes | contig annot |
| PSME3 | MHC I | yes | yes | contig annot |
| PSMB1 | MHC I | yes | yes | contig annot |
| PSMB2 | MHC I | yes | yes | contig annot |
| PSMB3 | MHC I | yes | yes | contig annot |
| PSMB4 | MHC I | yes | yes | contig annot |
| PSMB5 | MHC I | yes | yes | contig annot |
| PSMB6 | MHC I | yes | yes | contig annot |
| PSMB7 | MHC I | yes | yes | contig annot |
| PSMB8 | MHC I | yes | yes | tBLASTx |
| PSMB9 | MHC I | yes | yes | tBLASTx |
| PSMB10 | MHC I | yes | yes | tBLASTx |
| GranzymeB | MHC I | yes | yes | contig annot |
| Perforin | MHC I | yes | yes | contig annot |
| FasL | MHC I | yes | yes | contig annot |
| Fas | MHC I | yes | yes | contig annot |
| Erap1 | MHC I | yes | yes | contig annot |
| Erap2 | MHC I | yes | yes | contig annot |
| Irap | MHC I | yes | yes | contig annot |
| UNC93B | MHC I | yes | yes | contig annot |
| RFXANK | MHC II | yes | yes | contig annot |
| RFXAP | MHC II | yes | yes | contig annot |
| RFX5 | MHC II | yes | yes | contig annot |
| RFX7 | MHC II | yes | yes | contig annot |
| CIITA | MHC II | no | yes | n.a. |
| MHC II alpha | MHC II | no | no | n.a. |
| MHC II beta | MHC II | no | no | n.a. |
| invariant chain | MHC II | not functional | no | contig annot |
| CD3e | T-cell receptors | yes | yes | contig annot |
| CD8a | T-cell receptors | yes | yes | contig annot |
| CD8b | T-cell receptors | no | yes | n.a. |
| CD4 | T-cell receptors | no | truncated | n.a. |
| CD3 zeta | T-cell receptors | yes | yes | contig annot |
| CD3g/d | T-cell receptors | yes | yes | contig annot |
| TCR alpha | T-cell receptors | yes | yes | contig annot |
| TCR beta | T-cell receptors | yes | yes | contig annot |
| TCR gamma | T-cell receptors | no | yes | n.a. |
| AIRE | T-cell receptors | yes | yes | tBLASTx |
| AICDA | T-cell receptors | yes | yes | contig annot |
| RAG1 | T-cell receptors | yes | yes | contig annot |
| RAG2 | T-cell receptors | yes | yes | tBLASTx |
| IL1B | interleukins and interferons | yes | yes | contig annot |
| IL6ST | interleukins and interferons | yes | yes | contig annot |
| IL8 | interleukins and interferons | yes | yes | contig annot |
| IL10 | interleukins and interferons | yes | yes | contig annot |
| IL12B | interleukins and interferons | yes | yes | tBLASTx |
| IL15 | interleukins and interferons | yes | yes | contig annot |
| IL17D | interleukins and interferons | yes | yes | contig annot |
| IL17A F1 | interleukins and interferons | yes | yes | tBLASTx |
| IL22 | interleukins and interferons | yes | yes | contig annot |
| IL2RG | interleukins and interferons | yes | yes | contig annot |
| IL2RB | Interleukins and interferons | yes | yes | contig annot |
| IL4RA | interleukins and interferons | yes | yes | contig annot |
| IL8RB-Like | interleukins and interferons | yes | yes | contig annot |
| IL12RB2 | interleukins and interferons | yes | yes | contig annot |
| IL17RA | interleukins and interferons | yes | yes | contig annot |
| IL17RD | interleukins and interferons | yes | yes | contig annot |
| FOXP3 | interleukins and interferons | yes | yes | tBLASTx |
| TNFa | interleukins and interferons | yes | yes | contig annot |
| TGFB | interleukins and interferons | yes | yes | contig annot |
| IFNG | interleukins and interferons | yes | yes | contig annot |
| IPS1 | interleukins and interferons | yes | yes | contig annot |
| IKKG | interleukins and interferons | yes | yes | contig annot |
| MYD88 | interleukins and interferons | yes | yes | contig annot |
| C1qT4 | complement cascade | yes | yes | tBLASTx |
| C1qT5 | complement cascade | yes | yes | contig annot |
| C3 | complement cascade | yes | yes | contig annot |
| C4 | complement cascade | yes | yes | tBLASTx |
| C5 | complement cascade | yes | yes | contig annot |
| C6 | complement cascade | yes | yes | contig annot |
| C7 | complement cascade | yes | yes | contig annot |
| C8 | complement cascade | yes | yes | contig annot |
| C9 | complement cascade | yes | yes | contig annot |
| IgM | B cells and APC's | yes | yes | contig annot |
| Igb | B cells and APC's | yes | yes | contig annot |
| IgD | B cells and APC's | yes | yes | contig annot |
| PTPRC | B cells and APC's | yes | yes | contig annot |
| CD79A | B cells and APC's | yes | yes | contig annot |
| CD79B | B cells and APC's | yes | yes | contig annot |
| CD226 | B cells and APC's | yes | yes | tBLASTx |
| CD40L | B cells and APC's | yes | yes | contig annot |
| CD40 | B cells and APC's | yes | yes | contig annot |
| BLNK | B cells and APC's | yes | yes | contig annot |
| IGBP1 | B cells and APC's | yes | yes | contig annot |
| CXCR2 | chemokines and receptors | yes | yes | contig annot |
| CXCR3 | chemokines and receptors | yes | yes | contig annot |
| CXCR4 | chemokines and receptors | yes | yes | contig annot |
| CCR5 | chemokines and receptors | yes | yes | contig annot |
| CCR6 | chemokines and receptors | yes | yes | contig annot |
| CCR7 | chemokines and receptors | yes | yes | contig annot |
| CCR9 | chemokines and receptors | yes | yes | contig annot |