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.

Introducing the T.C. Hsu Cryo-Zoo at the University of Texas MD Anderson Cancer Center

Tao-Chiuh (T.C.) Hsu, Ph.D. (17 April 1917 – 9 July 2003) was a Professor at the University of Texas MD Anderson Cancer Center, joining the institution in 1955. He was an internationally-recognized cytogeneticist, having discovered a technique using a hypotonic solution, that revolutionized chromosome preparations to determine karyotypes. He was President of the American Society for Cell Biology (1974). He has been called the "Father of modern cytogenetics".

During his tenure at MD Anderson, Dr. Hsu collected and cryo-archived fibroblasts derived from biopsies of numerous and diverse mammalian species. These specimens were collected from zoos, universities, and the wild from collaborators around the world. Fibroblasts derived from the biopsies were karyotyped and frozen for storage. The Cryo-Zoo represents a unique cell archive of genetic information.

Dr. Hsu said "If through my work children two centuries hence may be able to see extinct species live again, I feel that I will have left a worthwhile legacy."

The Cryo-Zoo is currently held by Drs. Asha Multani, Sen Pathak, and Richard Behringer in the Department of Genetics at the MD Anderson Cancer Center. More recently, Dr. Liesl Nel-Themaat and Arisa Furuta contributed to the organization and annotation of the Cryo-Zoo.

Today, we are excited to announce that the Cryo-Zoo is joining the DNA Zoo consortium. Working together, we are hoping to digitize the notebooks describing the Cryo-Zoo, grow the cells in larger numbers, make them available to the scientific community, and use them to accelerate comparative genomics and epigenomics.

Today’s assembly is an example of what we hope to achieve: we used fibroblasts first archived in the Cryo-Zoo in 1977, over half a century ago. You can read more about the Cryo-Zoo in a 1971 excerpt from the Time magazine!