Table 1.
Evolution of the ZF in PRDM9 orthologs with different domain architectures. PRDM9 orthologs for which an empirical comparison dataset is available are ordered by their domain structures: from the top, we present cases of complete PRDM9 orthologs with KRAB-SSXRD-SET domains; partial orthologs putatively lacking KRAB or SSXRD domains or partial orthologs lacking both; then those containing only the SET domain. A row is shaded green if the ZF is in the top 5% most rapidly evolving C2H2 ZF in the species, as summarized by the proportion of amino-acid diversity at DNA-binding sites, and is blue if it is ranked first. A complete PRDM9 ortholog from dolphins (Balaenoptera acuforostrata scammoni) is shaded in gray because there is no amino acid diversity between ZFs of the tandem array. The empirical rank is also shown, as are the number of PRDM9 orthologs identified in the species. Asterisks indicate PRDM9 orthologs known to play a role in directing recombination. For PRDM9 genes from teleost fish, under major group, we additionally indicate whether or not the gene is a PRDM9α or PRDM9β gene.
| Organism | Major group | PRDM9 structure | Proportion AA diversity at DNA-binding sites |
Rank | Number of PRDM9 genes from species |
Number of ZF genes evaluated from species |
|---|---|---|---|---|---|---|
| Balaenoptera acutorostrata scammoni | placental | KRAB-SSXRD-SET | NA | NA | 1 | 272 |
| Bison bison bison | placental | KRAB-SSXRD-SET | 0.667 | 1 | 1 | 285 |
| Bos taurus* (chr1) | placental | KRAB-SSXRD-SET | 0.684 | 1 | 3 | 313 |
| Bos taurus (chrX) | placental | KRAB-SSXRD-SET | 0.414 | 6 | 3 | 313 |
| Bos taurus* (chrX) | placental | KRAB-SSXRD-SET | 0.414 | 7 | 3 | 313 |
| Bubalus bubalis | placental | KRAB-SSXRD-SET | 0.667 | 1 | 1 | 268 |
| Chelonia mydas | turtle | KRAB-SSXRD-SET | 0.414 | 11 | 1 | 235 |
| Chlorocebus sabaeus | placental | KRAB-SSXRD-SET | 0.500 | 1 | 1 | 344 |
| Chrysemys picta bellii | turtle | KRAB-SSXRD-SET | 0.478 | 1 | 1 | 308 |
| Cricetulus griseus | placental | KRAB-SSXRD-SET | 0.781 | 3 | 1 | 259 |
| Dasypus novemcinctus | placental | KRAB-SSXRD-SET | 0.614 | 1 | 1 | 289 |
| Dipodomys ordii | placental | KRAB-SSXRD-SET | 0.567 | 1 | 1 | 194 |
| Esox lucius | teleost fish (α) | KRAB-SSXRD-SET | 0.455 | 1 | 4 | 234 |
| Fukomys damarensis | placental | KRAB-SSXRD-SET | 0.430 | 3 | 1 | 227 |
| Homo sapiens* | placental | KRAB-SSXRD-SET | 0.687 | 1 | 1 | 357 |
| Latimeria chalumnae | coelacanth | KRAB-SSXRD-SET | 0.545 | 2 | 1 | 227 |
| Loxodonta africana | placental | KRAB-SSXRD-SET | 0.617 | 1 | 1 | 381 |
| Macaca fascicularis | placental | KRAB-SSXRD-SET | 0.680 | 1 | 1 | 364 |
| Macaca mulatta | placental | KRAB-SSXRD-SET | 0.645 | 1 | 1 | 366 |
| Marmota marmota marmota | placental | KRAB-SSXRD-SET | 0.483 | 1 | 1 | 277 |
| Microcebus murinus | placental | KRAB-SSXRD-SET | 1.000 | 1 | 1 | 326 |
| Mus musculus* | placental | KRAB-SSXRD-SET | 0.910 | 1 | 1 | 224 |
| Nannospalax galili | placental | KRAB-SSXRD-SET | 1.000 | 1 | 1 | 307 |
| Octodon degus | placental | KRAB-SSXRD-SET | 0.333 | 5 | 3 | 227 |
| Octodon degus | placental | KRAB-SSXRD-SET | 0.331 | 6 | 3 | 227 |
| Ovis aries | placental | KRAB-SSXRD-SET | 0.615 | 1 | 2 | 252 |
| Ovis aries | placental | KRAB-SSXRD-SET | 0.398 | 4 | 2 | 252 |
| Ovis aries musimon | placental | KRAB-SSXRD-SET | 0.353 | 12 | 1 | 285 |
| Papio anubis | placental | KRAB-SSXRD-SET | 0.585 | 1 | 1 | 404 |
| Pelodiscus sinensis | turtle | KRAB-SSXRD-SET | 0.692 | 1 | 1 | 221 |
| Peromyscus maniculatus bairdii | placental | KRAB-SSXRD-SET | 1.000 | 1 | 1 | 243 |
| Protobothrops mucrosquamatus | squamata | KRAB-SSXRD-SET | 0.462 | 5 | 1 | 195 |
| Python bivittatus | squamata | KRAB-SSXRD-SET | 0.571 | 1 | 1 | 206 |
| Rattus norvegicus | placental | KRAB-SSXRD-SET | 0.570 | 1 | 1 | 255 |
| Rousettus aegyptiacus | placental | KRAB-SSXRD-SET | 0.742 | 1 | 1 | 258 |
| Salmo salar | teleost fish (α) | KRAB-SSXRD-SET | 0.538 | 9 | 4 | 510 |
| Salmo salar | teleost fish (α) | KRAB-SSXRD-SET | 0.500 | 11 | 4 | 510 |
| Sus scrofa | placental | KRAB-SSXRD-SET | 0.542 | 1 | 1 | 248 |
| Thamnophis sirtalis | squamata | KRAB-SSXRD-SET | 0.459 | 3 | 1 | 179 |
| Tupaia chinensis | placental | KRAB-SSXRD-SET | 1.000 | 1 | 1 | 249 |
| Tursiops truncatus | placental | KRAB-SSXRD-SET | 0.939 | 1 | 1 | 233 |
| Myotis lucifugus | placental | SSXRD-SET | 0.524 | 1 | 2 | 308 |
| Myotis lucifugus | placental | SSXRD-SET | 0.310 | 68 | 2 | 308 |
| Octodon degus | placental | SSXRD-SET | 0.282 | 46 | 3 | 227 |
| Sarcophilus harrisii | marsupial | SSXRD-SET | 0.224 | 277 | 2 | 344 |
| Callorhinchus millii | cartilaginous fish | KRAB-SET | 0.314 | 6 | 1 | 63 |
| Astyanax mexicanus | teleost fish (α) | SET | 0.258 | 60 | 2 | 158 |
| Astyanax mexicanus | teleost fish (β) | SET | 0.167 | 152 | 2 | 158 |
| Clupea harengus | teleost fish (α) | SET | 0.279 | 6 | 4 | 118 |
| Clupea harengus | teleost fish (α) | SET | 0.278 | 7 | 4 | 118 |
| Clupea harengus | teleost fish (α) | SET | 0.274 | 10 | 4 | 118 |
| Clupea harengus | teleost fish (β) | SET | 0.158 | 114 | 4 | 118 |
| Cynoglossus semilaevis | teleost fish (β) | SET | 0.182 | 80 | 1 | 107 |
| Danio rerio | teleost fish (β) | SET | 0.179 | 345 | 1 | 367 |
| Esox lucius | teleost fish (α) | SET | 0.295 | 32 | 4 | 234 |
| Esox lucius | teleost fish (β) | SET | 0.192 | 176 | 4 | 234 |
| Esox lucius | teleost fish (β) | SET | 0.192 | 177 | 4 | 234 |
| Fundulus heteroclitus | teleost fish (β) | SET | 0.189 | 158 | 1 | 206 |
| Haplochromis burtoni | teleost fish (β) | SET | 0.180 | 148 | 1 | 168 |
| Ictalurus punctatus | teleost fish (α) | SET | 0.320 | 14 | 8 | 140 |
| Ictalurus punctatus | teleost fish (α) | SET | 0.319 | 15 | 8 | 140 |
| Ictalurus punctatus | teleost fish (α) | SET | 0.306 | 24 | 8 | 140 |
| Ictalurus punctatus | teleost fish (α) | SET | 0.303 | 25 | 8 | 140 |
| Ictalurus punctatus | teleost fish (α) | SET | 0.286 | 33 | 8 | 140 |
| Ictalurus punctatus | teleost fish (α) | SET | 0.276 | 39 | 8 | 140 |
| Ictalurus punctatus | teleost fish (α) | SET | 0.253 | 55 | 8 | 140 |
| Ictalurus punctatus | teleost fish (β) | SET | 0.179 | 127 | 8 | 140 |
| Larimichthys crocea | teleost fish (β) | SET | 0.192 | 70 | 1 | 115 |
| Lepisosteus oculatus | holostei fish | SET | 0.223 | 48 | 1 | 106 |
| Maylandia zebra | teleost fish (β) | SET | 0.173 | 161 | 1 | 176 |
| Neolamprologus brichardi | teleost fish (β) | SET | 0.173 | 141 | 1 | 152 |
| Nothobranchius furzeri | teleost fish (β) | SET | 0.180 | 245 | 1 | 266 |
| Notothenia coriiceps | teleost fish (β) | SET | 0.167 | 83 | 1 | 87 |
| Oreochromis niloticus | teleost fish (β) | SET | 0.173 | 173 | 1 | 190 |
| Oryzias latipes | teleost fish (β) | SET | 0.213 | 104 | 1 | 191 |
| Otolemur garnettii | placental | SET | 0.266 | 121 | 1 | 285 |
| Poecilia formosa | teleost fish (β) | SET | 0.191 | 184 | 1 | 242 |
| Poecilia latipinna | teleost fish (β) | SET | 0.191 | 175 | 1 | 235 |
| Poecilia mexicana | teleost fish (β) | SET | 0.191 | 187 | 1 | 244 |
| Poecilia reticulata | teleost fish (β) | SET | 0.191 | 162 | 1 | 212 |
| Pundamilia nyererei | teleost fish (β) | SET | 0.173 | 134 | 1 | 147 |
| Pygocentrus nattereri | teleost fish (α) | SET | 0.331 | 12 | 2 | 142 |
| Pygocentrus nattereri | teleost fish (β) | SET | 0.179 | 124 | 2 | 142 |
| Salmo salar | teleost fish (β) | SET | 0.188 | 411 | 4 | 510 |
| Salmo salar | teleost fish (β) | SET | 0.180 | 454 | 4 | 510 |
| Sinocyclocheilus anshuiensis | teleost fish (β) | SET | 0.185 | 224 | 2 | 284 |
| Sinocyclocheilus anshuiensis | teleost fish (β) | SET | 0.185 | 225 | 2 | 284 |
| Sinocyclocheilus grahami | teleost fish (β) | SET | 0.185 | 211 | 1 | 271 |
| Sinocyclocheilus rhinocerous | teleost fish (β) | SET | 0.185 | 208 | 2 | 269 |
| Sinocyclocheilus rhinocerous | teleost fish (β) | SET | 0.185 | 209 | 2 | 269 |
| Takifugu rubripes | teleost fish (β) | SET | 0.188 | 66 | 1 | 98 |
| Xiphophorus maculatus | teleost fish (β) | SET | 0.191 | 117 | 1 | 158 |