Assembly whale done

Updated: Oct 26

Pygmy sperm whales (Kogia breviceps) are named after a waxy substance known as spermaceti found in their heads. It is this oil sac that helps the whales focus sound.

Pygmy sperm whale (Kogia breviceps); Rescued in accordance with NOAA's Marine Mammal Health and Stranding Response Program MMHSRP Permit #18786-04

Pygmy sperm whales are found in temperate and tropical seas worldwide but are most commonly found off coasts and along continental shelves. These mammals are often confused with their closest relatives known as dwarf sperm whales (Kogia sima). In fact, they were not distinguished as separate species until 1966. [1]

These gentle creatures are often seen either alone or in small groups of six to eleven individuals. They spend little time at the water’s surface, only when the sea and weather conditions are very calm, and almost never approach vessels. When spotted, they are usually swimming slowly or lying still (behavior commonly referred to as “logging”). While they do have a blowhole, they do not have a visible blow at the surface.


Pygmy sperm whales do not face the threat of direct hunting, but are affected by entanglement in nets and ingestion of marine pollution. As the species avoid vessels and planes, scientists rarely see pygmy sperm whales at sea. This makes it difficult to estimate their population size or current population trends. [2]


Today, we share a chromosome-length genome assembly for the pygmy sperm whale based on a draft published by the Zoonomia Project (Genereux et al., 2021). The draft was scaffolded to 21 chromosomes using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details. The interactive contact map of the pygmy sperm whale’s chromosomes is included below:

We gratefully acknowledge SeaWorld for providing the sample for this work and special thanks to Lexi Mena for help with the photo and sample coordination. As always, we thank the Pawsey Supercomputing Centre and DNA Zoo Australia team at the University of Western Australia for computational and analyses support of the upgrade.


Blog by: Ashling Charles and Parwinder Kaur