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.

Tail of a dunnart

Dunnarts are small nocturnal mouse-sized marsupials endemic to Australia. Nineteen different species are found in habitats ranging from tropical savanna grasslands to desert sandhills and dense forests of Australia’s southeast and southwest. The fat-tailed dunnart (Sminthopsis crassicaudata) belongs to the Dasyuridae family, which also includes the little red kaluta, quolls, and the Tasmanian devil.

Photo Description: Fat-tailed Dunnart (Sminthopsis crassicaudata) Photo Credits: Photograph by Bernard Dupont licensed under CC BY-SA 2.0 [Source link: https://search.creativecommons.org/photos/4dc501a3-5501-49c3-aa3d-6c7cef71a635]

Dunnarts sleep during the day in cup-shaped nests of dried grass and leaves in fallen hollow logs or in clumps of grass, sedges and grasstrees. Their diet includes insects such as beetles, spiders, small reptiles, and amphibians. They store fat reserves in their carrot-shaped tail for times of food shortage.

The fat-tailed dunnart can survive in extreme, semi-arid environments. One of the survival techniques that it uses is daily torpor. It lowers its body temperature and metabolic rate [1] in order to reduce energy expenditure. Torpor is unaffected by alterations in photoperiod but is greatly affected by environmental conditions.

The main threats to the dunnart are habitat fragmentation, inappropriate fire regimes, and feral predators. While once common throughout Southwest Australia these diminutive marsupials are near threatened in Victoria and now confined to ‘islands’ of remnant vegetation, the result of large-scale clearing for agriculture.

The majority of its remaining habitat is privately-owned bush remnants. Dunnarts are known to be able to recolonise burnt areas readily as they are adapted to mid-successional complexes of vegetation. However, a single fire can potentially wipe out an entire population.

DNA Zoo joined forces with Prof Andrew Pask and Dr Stephen Frankenberg from University of Melbourne, Australia to deliver a much required genomic resource: a chromosome-length genome assembly for the fat-tailed dunnart. The assembly is based on the draft provided by the University of Melbourne team, led by Prof Andrew Pask. The effort has been supported by an ARC grant (DP160103683) to Pask and Frankenberg and Oz Mammals Genomics initiative, a Bioplatforms Australia framework initiative, building genomic resources for conservation through a thorough understanding of the evolution of Australia’s unique mammals that are now under threat, through climate, disease or habitat modifications.

This draft assembly was scaffolded with 548,133,068 PE Hi-C reads 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! The Hi-C work was supported by resources provided by DNA Zoo Australia, The University of Western Australia and DNA Zoo, Aiden Lab at Baylor College of Medicine with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government, the Government of Western Australia.

The following people contributed to the Hi-C chromosome-length upgrade of the project: Erez Aiden, Olga Dudchenko, Ashling Charles & Parwinder Kaur.

Citations

1. Warnecke, Lisa; James Turner; Fritz Geiser (2008). "Torpor and basking in a small arid zone marsupial". Naturwissenschaften. 95 (1): 73–78. doi:10.1007/s00114-007-0293-4.

DNA Zoo & collaborators manuscript appears today in Science

Today we share some exciting news: a new paper is out today in the Science journal by DNA Zoo and collaborators!

In the manuscript, titled "3D genomics across the tree of life reveals condensin II as a determinant of architecture type" we use the DNA Zoo data to explore the nuclear architecture for 27 species across the eukaryotic tree of life.

27 species examined in the new manuscript. Left to right, top to bottom: common mushroom, Arctic lamprey, moss animal, lancelet, Chinese muntjac, ground peanut, fruit fly, brownbanded bamboo shark, Indian muntjac, red piranha, sea urchin, chicken, stony coral, sea squirt, human, wheat, southern house mosquito, tammar wallaby, waterbear, baker's yeast, yellow fever mosquito, python, sea gooseberry, African clawed frog, roundworm, California sea hare and the Oriental liver fluke. Illustrations by Adam Fotos @ adamfotos.com

We show that all of the chromosomal architectures observed across the species fall into one of just two types: those chromosome territory-like (with chromosomes occupying distinct nuclear subvolumes) and those Rabl-like (resembling the arrangement observed during cell division, with centromeres and/or telomeres clustered and chromosomes often "folded" along the telomere-to-centromere axis). We show that Rabl-like architecture in species is often associated with disruption of condensin II, a protein known to be responsible for lengthwise compaction of chromosomes.

We perform an experiment (led by our colleagues Claire Hoencamp and Benjamin Rowland at the Netherlands Cancer Institute) to disrupt condensin II in human cells. This transforms a territorial chromosome architecture typical of human cells into Rabl. We follow up with some physical simulations, led by our collaborators Sumitabha Brahmachari and José Onuchic at the Center for Theoretical Biological Physics at Rice University, suggesting that condensin II disruption results in long and floppy chromosomes that cannot generate mechanical tensions enough to disrupt the Rabl arrangement "inherited" from cell division. Read more about this in the manuscript and in the joint Baylor College of Medicine and Rice University press release.

As part of the effort described in the manuscript, we publish 17 new chromosome-length genome assemblies. We include the links to the assembly pages for those previously published and those shared today below.

We also generate chromosome-length haploblocks for 7 non-human species using a new Hi-C-based phaser, now part of 3D-DNA. The phaser uses a list of deduplicated Hi-C contacts, as generated by the Juicer pipeline (Durand, Shamim et al., 2016), to phase variants encoded in a vcf (variant call format) file. It plays well with prephased data, e.g. from linked reads, long reads or population data, and generates phasing contact maps to validate the results that can be further polished in Juicebox Assembly Tools. So, JBAT can now not only help with genome assembly, but also assists with phasing!

We explore the coverage requirements for whole chromosome phasing, and show that Hi-C based phasing works in most species, including human. However, we show that in species where the homologs are not separate during interphase, like Drosophila melanogaster, this method cannot be used. This highlights how the principles of genome assembly can vary across different complex eukaryotes.

We will write about the phasing piece separately, and in the meantime, please stay tuned for a few blog posts highlighting some of the newly shared genome assemblies in the next week or so!

• Tammar wallaby (Macropus eugenii)

• Burmese python (Python bivittatus)

• Red piranha (Pygocentrus nattereri)

• Bamboo shark (Chiloscyllium punctatum)

• Arctic lamprey (Lethenteron camtschaticum)

• Sea squirt (Ciona intestinalis-robusta)

• European lancelet (Branchiostoma lanceolatum)

• Sea urchin (Strongylocentrotus purpuratus)

• Tardigrade (Hypsibius dujardini)

• Oriental liver fluke (Clonorchis sinensis)

• California sea hare (Aplysia californica)

• Moss animal (Cristatella mucedo)

• Stony coral (Acropora millepora)

• Sea gooseberry (Pleurobrachia bachei)

• Common mushroom (Agaricus bisporus)

• Chinese muntjac (Muntiacus reevesi)

• Indian muntjac (Muntiacus muntjak)