Et tu, Bryde’s

Bryde's (pronounced BROO-dus) whales are members of the baleen whale family. They are considered one of the "great whales," a group that also includes blue whales and humpback whales. They are named for Johan Bryde, a Norwegian who built the first whaling stations in South Africa in the early 20th century. [1]

The classification of Bryde’s whales remains unclear: the Bryde’s complex is currently thought to consist of several genetically distinct populations, so chances are with more research they might get promoted to species level! [2]

Bryde’s whales are vulnerable to many stressors and threats, including vessel strikes, ocean noise, and whaling. This is particularly true of the Gulf of Mexico Bryde’s whale subspecies (Balaenoptera edeni (GOMx subspecies)), also threatened by oil and gas activities, as well as oil spills and cleanup. Scientists believe that there are fewer than 100 GoM Bryde’s whales, making it one of the most endangered whales in the world!  [3, 4]

To help with ongoing research and conservation efforts, today we share a chromosome-length genome assembly generated from a Bryde’s whale sample collected in the Gulf of Mexico. This work was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03 issued by the National Marine Fisheries Service (NMFS) under the authority of the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The specimen used in this study was collected by NMFS Panama City Lab/Lydia Staggs and provided by the National Marine Mammal Tissue Bank, which is maintained by the National Institute of Standards and Technology (NIST) in the NIST Biorepository, and which is operated under the direction of NMFS with the collaboration of USGS, USFWS, MMS, and NIST through the Marine Mammal Health and Stranding Response Program.

Gulf of Mexico Bryde's whales are special to the Gulf of Mexico; they are not found anywhere else in the world. We don’t know a lot about them, but we do know they are the only year-round baleen whales that make their home in the Gulf. We hope that the new assembly will help with the ongoing efforts to explore genetic variation within the Bryde’s whale complex, improve our understanding of this enigmatic creature, while also providing the foundation for future bioanalytical techniques such as eDNA research!

This genome assembly was done de novo following the $1K workflow from (Dudchenko et al., 2018). Check out below the growing body of whole-genome alignments to see how the chromosomes from the new assembly relate to those of other cetaceans in the DNA Zoo collection: the beluga whale, the Pacific white-sided dolphin, the orca, the Indo-pacific dolphin and the bottlenose dolphin!

Whole-genome alignment plots between the new Bryde’s whale (Balaenoptera_edeni_HiC) genome assembly and other cetacean chromosome-length genome assemblies at the DNA Zoo: Indo-Pacific bottlenose dolphin (ASM322739v1_HiC), orca (Oorc_1.1_HiC), Atlantic bottlenose dolphin (NIST_Tur_tru_v1_HiC), Pacific white-sided dolphin (ASM367639v1_HiC) and the beluga whale (ASM228892v2_HiC).

UPD: In 2021, the Gulf of Mexico Bryde's whales have been identified as distinct species, Balaenoptera ricei. The assembly page has been correspondingly renamed and is now available at https://www.dnazoo.org/assemblies/Balaenoptera_ricei. Read more about rice's whales on NOAA Fisheries website.

Everything is possum

The western ringtail possum refers to a marsupial, a species of possum, Pseudocheirus occidentalis, found in a small area of Southwest Australia (including Perth where DNA Zoo Australia headquarters is located). Western ringtail possums are critically endangered [1] and could be wiped out in 20 years unless something is done to save the species [2].

In order to help with the species conservation, we, in collaboration with the Mallarino Lab at Princeton University, share a de novo genome assembly for the western ringtail possum, here. The sample for generating the necessary sequencing libraries (short insert-size DNA-Seq and Hi-C) was donated by the Australian Biological Tissue Collection at the South Australian Museum. Included in the share are the homology-based annotations for the species, courtesy MacManes Lab.

The western ringtail possum is a member of the Diprotodontia (meaning “two front teeth”) order, in the Phalangeriformes suborder (possums, gliders and cuscus). The other two suborders of Diprotodontia are: Vombatiformes (wombats and koalas) and Macropodiformes (kangaroos and wallabies).

DNA Zoo has generated chromosome-length genome assemblies in all three of the listed suborders: ground cuscus in Phalangeriformes, common wombat in Vombatiformes and tammar wallaby, western grey kangaroo, eastern grey kangaroo and red kangaroo in the Macropodiformes. See some whole-genome alignment plots below for an idea on how the chromosomes of different Diprotodontia species spanning the last 28MY of evolution relate to each other: a rather plastic karyotype despite the deceivingly similar chromosome count!

Whole-genome alignment plots between the new western ringtail possum genome assembly (Pseudocheirus_occidentalis_HiC, 2n=20), to other Diprotodontia genome assemblies in the DNA Zoo: the ground cuscus (pg-2k, 2n=14), common wombat (vu-2k, 2n=16), tammar wallaby (me-1k, 2n=16), western grey kangaroo (mf-2k, 2n=16), eastern grey kangaroo (mg-2k, 2n=16) and red kangaroo (mr-2k, 2n=20).

A cheeky genome

Chinese hamsters are rodents that originated in the deserts of northern China and Mongolia. They are popular as pets throughout the world [1].

For decades, quite a few biotech drugs are produced by putting a gene for a protein into cells derived from the ovary of a Chinese hamster (CHO cell line), which then produce the protein. The history of CHO cells dates back to the 1950s, when ovarian connective tissue was harvested from the Chinese hamster and derivative cells spontaneously became immortal (Tjio, 1958). Since then, the host cells remain poorly characterized.

To facilitate CHO cell research and development, the community now relies on published draft genomes for the CHO-K1 cell line and several draft assemblies for the parent Chinese hamster. Today we share a chromosome-length upgrade to the assembly for the Chinese hamster published by Rupp et al., 2018. In order to do the upgrade, we used primary cells from the T.C. Hsu Cryo-Zoo at the University of Texas MD Anderson Cancer Center. The cells have been stored all the way back in 1977!

In agreement with previously published data, the chromosome-length assembly yielded 11 chromosomes (a very low chromosome number for a mammal!). See below how these gigantic chromosomes relate to those of other closely related rodents in the Cricetidae family (hamsters, voles, lemmings and New World rats and mice) we’ve recently assembled in the DNA Zoo: the golden hamster Mesocricetus auratus, shared here, and the canyon mouse Peromyscus crinitus, here!

Whole-genome alignment plots for the Chinese hamster (CriGri-PICR_HiC), the golden hamster (MesAur1.0_HiC) and the canyon mouse (pecr10X_v2_HiC) genome assemblies.