Assembly squirrules

The unstriped ground squirrel (Xerus rutilus) is a small rodent endemic to East Africa. Xerus derives from the Greek word 'xeros' meaning 'dry' which refers to the natural habitat of the unstriped ground squirrel, and rutilus is a Latin word that means 'golden-red' referencing the coat hue.

Unstriped ground squirrel by Roger Smith, [CC BY-NC 2.0], via flickr.com

The lack of longitudinal stripes makes these squirrels unique and different from other African ground squirrels. X. rutilus is relatively heavy-bodied with an average length of 225.8mm and weight of 420g. Their pelage is bristly and coarse, varying from pale tan to red-brown in colour with a conspicuous white eye ring. Populations in drier areas tend to consist of paler coloration (1).


They are diurnal, burrow-dwelling inhabitants of arid and semi-arid regions. Burrow systems are isolated from one another and typically have two to six entrances. Emergence above ground is late in relation to the sunrise, and is followed by sunbasking and grooming prior to leaving the area to forage. Their diet consists of fruits, seeds, herbaceous material, and insects (1).


Unstriped ground squirrels are non-territorial and have large, overlapping home ranges. Individuals with shared home ranges form linear dominance hierarchies, with males exhibiting dominance over females for access to food (1).


Today we share a $1K chromosome-length assembly for the unstriped ground squirrel. The draft assembly was generated by the DNA Zoo team from short insert-size PCR-free DNA-Seq data using w2rap-contigger (Clavijo et al. 2017), see (Dudchenko et al., 2018) for details.


The above draft was scaffolded to 19 chromosomes with Hi-C data generated by DNA Zoo labs using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details.


We gratefully acknowledge T.C. Hsu Cryo-Zoo at the University of Texas MD Anderson Cancer Center for providing the sample for this work. The work was supported by resources provided by DNA Zoo, Aiden lab, Baylor College of Medicine (BCM), DNA Zoo Australia, The University of Western Australia (UWA). We acknowledge the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia for contributing computational resources to help with this assembly.


The following people contributed: Ashling Charles, Ruqayya Khan, Olga Dudchenko, David Weisz, Asha Multani, Sen Pathak, Richard Behringer, Parwinder Kaur, and Erez Aiden.


Citations

O’Shea, Thomas J. "Xerus rutilus." Mammalian Species 370 (1991): 1-5.