Reference genome assembly of the false killer whale ( <i>Pseudorca crassidens</i> )
High-quality genomic resources are essential tools for conservation and management actions. We present a chromosome-level genome assembly for the false killer whale (Pseudorca crassidens, Owen, 1846), a large globicephaline delphinid found in tropical and subtropical waters. The final genome assembly is 2.7 Gb, with a scaffold N50 of 110.1 Mb, organized into 21 autosomes plus X and Y sex chromosomes. BUSCO scores were 97%, with low levels of duplicated and fragmented annotations. Repetitive elements were a larger proportion of the genome relative to most previously published cetacean genomes. Using this reference, we compared trends in historical demography and genome-wide heterozygosity in two North Pacific populations of false killer whales using short-read data mapped to the reference genome. Modeling of historical demography in these two populations indicate similar fluctuations in effective population size over time, reflecting shared ancestry until ~100-200 kya. Genome-wide heterozygosity levels were moderate relative to other cetaceans. The new genomic resources can facilitate further research on comparative genomics and can serve as a reference for other globicephaline cetaceans that currently lack chromosome-level genome assemblies.
Authors
- Jacquelyn Mountcastle (ORCID: https://orcid.org/0000-0003-1078-4905)
- Phillip A. Morin (ORCID: https://orcid.org/0000-0002-3279-1519)
- Giulio Formenti (ORCID: https://orcid.org/0000-0002-7554-5991)
- MS Springer
- Erich D. Jarvis (ORCID: https://orcid.org/0000-0001-8931-5049)
- Jennifer Balacco (ORCID: https://orcid.org/0000-0001-7102-1632)
- Linelle Ann L. Abueg (ORCID: https://orcid.org/0000-0002-6879-3954)
- Keith M. Hernandez (ORCID: https://orcid.org/0000-0001-9847-1158)
- Matthew T. Schmitz (ORCID: https://orcid.org/0000-0002-6177-8161)
- Nadolina Brajuka (ORCID: https://orcid.org/0009-0008-6639-8791)
- Olivier Fédrigo (ORCID: https://orcid.org/0000-0002-6450-7551)
- Robin William Baird (ORCID: https://orcid.org/0000-0002-9419-6336)
- Karen K. Martien (ORCID: https://orcid.org/0000-0002-1732-8729)
- Tatiana Tilley (ORCID: https://orcid.org/0009-0001-9277-7743)
- John Gatesy
Institutions
- University of California, Riverside (US)
- NOAA National Marine Fisheries Service (US)
- American Museum of Natural History (US)
- Howard Hughes Medical Institute (US)
- University of California, San Francisco (US)
- NOAA National Marine Fisheries Service Southwest Fisheries Science Center (US)
- Allen Institute (US)
- Cascadia Research Collective (US)
- Rockefeller University (US)
Publication Details
- Journal
- Journal of Heredity
- Published
- 2026-04-14
- DOI
- https://doi.org/10.1093/jhered/esag031
- Primary Topic
- Marine animal studies overview
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Science Foundation
- Howard Hughes Medical Institute