Big-ears to fill

Today, we release the chromosome-length assembly for the Rafinesque's big-eared bat (Corynorhinus rafinesquii). Also known as the southeastern big-eared bats, they are a species of vesper bats from the genus Corynorhinus which means "club-nosed". Their common name is no hyperbole, this species has ears over an inch long which is about 1/4th of their body length!

Corynorhinus rafinesquii, image via Jennifer Kindel (South Carolina Department of of Natural Resources)

Rafinesque's big-eared bat is a medium-sized bat with a length around 7.5–10 cm and a wingspan of 25–30 cm with two lumps on either side of its nose. The ears and face are a pinkish-brown color, while the forearm and wing membrane are dark brown. Like all bats in the southeastern United States, these are insectivorous, nocturnal, and locate food primarily by echolocation. They consume a wide range of insects, including mosquitoes, beetles, and flies, although moths make up 90% of the diet.

These bats have a social structure that keeps the males and females apart except during the breeding season in early fall. The females do not actually fertilize the egg until early spring. At that point the breeding females form an all-female maternal colony to raise their young. Each female will give birth to one pup per year. The pup is flightless until it is three weeks old. Within two months they are fully grown and can only be recognized as a young bat due to the color of their fur, which is darker than an adult bats’.

Video Description: C. rafinesquii taking flight in slow-motion. Video provided by Jennifer Kindel (SCDNR).

The U.S. Fish and Wildlife Service classifies this bat as a Candidate II Species of Concern, meaning it is on the watch list for the Endangered Species Act. Texas Parks and Wildlife Department lists the bat as a threatened species.

Population declines for this species could be related to a number of reasons. First of all, the Rafinesque’s depend on mature bottomland hardwood forests. Most forests in the southeast U.S. are all relatively young with few trees being over 50 years old. Secondly, their food source, insects, may possibly be contaminated with heavy metals or other forms of contaminants. Finally, with a female only producing one young per year, any loss of pups can drive the population to lower levels in just a few short years.

Measures should be taken to provide species-specific alternate roost structures before eviction, and structures that mimic large hollow trees such as large bat towers may be a suitable alternative for Rafinesque’s big-eared bats. Conservation measures include conserving old-growth forests and reestablishing corridors connecting suitable habitat (Clark 2000); protecting mature bottomland hardwood forests and recruitment of younger stages of high quality bottomland habitat for growth into future roost trees; and providing artificial roosts in areas of depleted roosting resources (Clark and Williams 1993).

Bat tower mimicking a hollow tree; image courtesy of Jennifer Kindel (SCDNR)

The $1K genome assembly scaffolded to 32 chromosomes with a contig n50 = 35 Kb and a scaffold n50 = 145 Mb.The draft assembly was generated from short-insert size Illumina reads [303,683,554 PE reads] and scaffolded to chromosome length genome with Hi-C [554,882,019 PE reads]. Check out the interactive JuiceBox.js session below and please see our Methods page for assembly procedure details!

We graciously thank Jennifer Kindel and Christy Greenwood the South Carolina Department of Natural Resources (SCDNR) and S.C. Department of Health and Environmental Control (DHEC) for help with coordinating the sample used to generate this assembly. We also thank the Pawsey Supercomputing Centre and DNA Zoo Australia team at the University of Western Australia for computational and analyses support for this genome assembly.

Blog post by Parwinder Kaur, with contributions from Ruqayya Khan and Jennifer Kindel

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.