Allelic diversity of the PRDM9 coding minisatellite in minke whales

The PRDM9 protein controls the reshuffling of parental genomes in most metazoans. During meiosis the PRDM9 protein recognizes and binds specific target motifs via its zinc-finger array, which is encoded by a hypervariable minisatellite. To date, PRDM9 diversity has been little studied outside humans, wild mice and some domesticated species where evolutionary constraints may have been relaxed.

Here we explore the structure and variability of PRDM9 in samples of the minke whales from the Atlantic, Pacific and Southern Oceans. We show that minke whales possess all the features characteristic of organisms with PRDM9-directed recombination initiation, including complete KRAB, SSXRD and SET domains and a rapidly evolving array of C₂H₂-type-Zincfingers (ZnF). We uncovered eighteen novel PRDM9 variants and evidence of rapid evolution, particularly of DNA-recognizing positions that evolve under positive selection.

At different geographical scales, we observed extensive PRDM9 diversity in Antarctic minke whales (Balaenoptera bonarensis), that conversely lack observable population differentiation in mitochondrial DNA and microsatellites. In contrast, a single PRDM9 variant is shared between all Common Minke whales and even across subspecies boundaries of North Atlantic (B. a. acutorostrata) and North Pacific (B. a. scammoni) minke whale, which do show clear population differentiation.

PRDM9 variation of whales predicts distinct recombination initiation landscapes genome wide, which has possible consequences for speciation.