Dama gazelle

The dama gazelle (Nanger dama) is the largest of the gazelles. They are 160 to 170 centimeters long, 90 to 120 centimeters tall and weigh 50 to 85 kilograms. Dama gazelles’ horns are S-shaped and, for males, can grow to 20 to 40 centimeters long. Males are noticeably larger than females, and their horns are much longer.

Dama gazelle by Valerie, [CC BY-NC-ND 2.0], via flickr.com

Dama gazelles inhabit the foothills, plateaus and steppes of the Sahara and Sahel of North Africa. They are highly social, diurnal animals. Their social organization largely depends on the season. During the dry season, groups migrate from the Sahara to the more mesic Sahel, where they occur as solitary animals or in small groups. Other times, they gather in mixed groups of 10 to 20 individuals, including a dominant male.

Members of the herd spend their days moving about in search of edible vegetation and water sources. Dama gazelles are quite drought tolerant and mostly obtain water from the various shrubs and coarse desert grasses they consume. When the rainy season arrives, these animals migrate to the Sahara, where they gather in large herds.

Dama gazelles were once numerous across a range that spanned from Morocco to Senegal in the west to Sudan in the east. The number of dama gazelles began to significantly decline in the 1950s due to overhunting and habitat loss. By 1980, these animals had disappeared from many areas of their range, but were found to be abundant in some local regions. In 2001, studies were conducted that showed that the total number of remaining dama gazelles was extremely small and the range very fragmented. In addition to hunting and habitat loss, increasing aridity due to gradual climate change may also affect the long-term survival of the species in the wild.

The dama gazelle is categorized as a critically endangered species by the International Union for Conservation of Nature. Only about 2,600 individuals remain in the world. Most dama gazelles are maintained and managed in ex situ herds within zoos, reserves and private ranches in Europe, the Middle East and the United States.

Given dama gazelles’ small population size, maintaining genetically diverse populations and avoiding inbreeding are top priorities for conservationists. Animals from ex situ populations can be reintroduced to reserves in the Sahelian and Saharan regions and help establish resilient populations across their former range.

Today, we are delighted to share the chromosome-length assembly representing one of the three subspecies of the dama gazelle, the addra gazelle (Nanger dama ruficollis). The draft contig-based assembly was produced with 10X Genomics linked-read sequencing and assembled using Supernova version 2.0. The genetic material used to generate the contig-based assembly and the Hi-C data for chromosome-length scaffolding was collected from a male addra gazelle belonging to an ex situ herd managed at the Smithsonian Conservation Biology Institute in Front Royal, Virginia, USA. In conjunction with international collaborators, we are using this assembly to investigate a number of questions related to the conservation genomics of this unique gazelle. Check out the interactive Hi-C contact map of the assembled chromosomes below!

The Smithsonian Conservation Biology Institute (SCBI) spearheads research programs at its headquarters in Virginia, the Smithsonian’s National Zoo in Washington, D.C., and at field research stations and training sites worldwide. SCBI scientists tackle some of today’s most complex conservation challenges by applying and sharing what they learn about animal behavior and reproduction, ecology, genetics, migration and conservation sustainability. Findings from these studies provide critical data for the management of populations in human care and valuable insights for the conservation and management of wild populations.

This update was written by Pasha Dobrynin, Budhan Pukazhenthi and Klaus-Peter Koepfli of the Smithsonian Conservation Biology Institute.

Western Australia’s faunal emblem - Numbat

Have no fear, the numbat is here! Today we announce the release of the first chromosome-length genome assembly for one of Australia’s most prized native marsupials.

Australian numbat (Myrmecobius fasciatus) boasts a beautifully coloured reddish-brown fur coat, laced with white stripes that contrast with the salt and pepper fur presiding from their tail to slightly past their rear feet. Glossy black eyes located in front of their two cupped ears are tied together with the numbat’s perfectly pointed black noise, making for an intriguing yet eye catching complexion. With their dazzling looks it’s easy to see why numbats are one of Australia’s most prized possessions.

Photo Description: Numbat (Myrmecobius fasciatus). Photo credits: Perth Zoo, CC BY-SA 3.0, via Creative Commons

Numbats can be found in most of the 'lower half' of Australia. They are known to be solitary and territorial, occupying up to 1.5 square kilometres of land per individual, for same-sex animals. It’s common for male and female territories to overlap, and the two sexes may move even closer together during their mating season lasting from February to March.

Originating from the Dasyuromorphia, the order comprising most of the Australian carnivorous marsupials, these cute creatures feast exclusively on termites. Fussy eaters you might say! Consuming up to 20 000 per day, numbats are strictly diurnal, which means they are only active during the day and their activity levels are closely linked to those of termites [3].

The numbat was on the verge of extinction during the late 20th century. Extensive conservation efforts as well as government and community intervention led to a gradually increasing population of numbats. Still, with less than 1000 numbats left in the wild, the species is listed as ‘endangered’ on the Red List of the International Union for the Conservation of Nature and Natural Resources. The main threat to numbats is predation by introduced predators – foxes and cats. This threat of predation is exacerbated by other factors including habitat loss and fragmentation from land clearing, which also makes numbats more vulnerable to birds of prey such as wedge-tailed eagles and falcons.

The genome assembly shared today was generated using the sample provided by Perth Zoo which was used to generate a draft assembly with short-insert size Illumina reads [404,932,803 PE reads] and scaffolded to a chromosome-length genome with Hi-C [662,932,607 PE reads]. See our Methods page for more detail on the assembly procedure. Check the interactive map of the 7 numbat chromosomes below!

The termite-eating numbat is one of the thylacine’s closest living relatives, sharing a common ancestor ~35 million years ago. Both these enigmatic creatures have stripes, but that’s not where the similarity ends – as much as 95 per cent of their DNA may be identical [1].

Check out below how the chromosomes in the new assembly align with those of another close relative of the thylacine, the Tasmanian devil. It appears that the chromosomes have been very stable across Dasyuromorphia, with both species exhibiting the 2n=14 karyotype and one-to-one correspondence between the chromosomes, with just a few tentative inversions.

Whole genome alignment plot between the Numbat and the Tasmanian devil. Numbat genome assembly: Myrmecobius_fasciatus_HiC, Tasmanian devil genome assembly: Devil_ref_v7.0_HiC, a DNA Zoo upgrade from (Murchison et al., 2012).

This work was enabled by resources provided by DNA Zoo Australia, The University of Western Australia (UWA) and DNA Zoo, Aiden Lab at Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.

SRA catchup for 275 genome assemblies

Hey everyone! With the latest release we've hit the 275 assemblies mark, which means it's time to do some raw sequencing data upload to NCBI Sequence Read Archive!

The new data have now been uploaded under BioProject accession PRJNA512907, with legume data from a recently published paper available under BioProject accession PRJNA679437. Overall, the uploaded data cover Hi-C data for 281 species and WGS data for 91 spanning 569 experiments and 34,565,252,649,062 bases!

We thank Illumina, Macrogen, Novogen, the Broad Institute and Baylor College of Medicine GARP core for their help with the data production!

As always, we share the data without restrictions: see our data usage policy here.

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P.S.: Check out the celebratory card from a junior DNA Zoo Australia member marking the occasion, below!