No tapiring off on assemblies

The Baird's tapir (Tapirella bairdii) is a species of tapir native to Mexico, Central America and northwestern South America. It is the largest native land mammal in both Central and South America!

Baird's Tapir by Eric Kibly, [CC BY-SA 2.0], via flickr.com

These nocturnal vegetarians are wide-ranging and responsible for eating a lot of vegetation and dispersing seeds, making them “the gardeners of the forest.” Although their long, flexible snouts (which they can move in all directions) imply familial ties with the elephant, their closest relatives are actually the horse and rhinoceros families.

The Baird's tapir has a distinctive cream-colored marking on its face, throat, and tips of its ears, with a dark spot on each cheek, behind and below the eye. The rest of its hair is dark brown or grayish brown. Females are larger than males and body mass in adults can range from 150 to 400 kilograms.

According to the IUCN, the Baird's tapir is endangered. There are two main contributing factors in the decline of the species; poaching and habitat loss. Though in many areas the animal is only hunted by a few humans, any loss of life is a serious blow to the tapir population because their reproductive rate is so slow. In Mexico, Belize, Guatemala, Costa Rica, and Panama, hunting of the Baird's tapirs is illegal, but the laws protecting them are often unenforced. Furthermore, restrictions against hunting do not address the problem of deforestation. Therefore, many conservationists focus on environmental education and sustainable forestry to try to save the Baird's tapir and other rainforest species from extinction.

Prior to the beginning of the Lowland Tapir Conservation Initiative (LTCI), little was known about the health of their populations or the places where they lived. The Houston Zoo has provided funding and support for their wild tapir satellite-collar and camera-trapping studies across the region. From these studies, they have learned that the Pantanal is the most important stronghold for the species so the Houston Zoo is supporting LTCI’s work with Brazilian landowners, schools, and the media to increase public interest and understanding of tapirs and involving them in conservation efforts.

Today, we share the chromosome-length genome assembly for the Baird's tapir, Tapirus bairdii! The genome assembly scaffolded to (2n=80) chromosomes was generated using samples provided by Noah the tapir living at the Houston Zoo. Read more about Noah and his partner Moli in this blog post by the Houston Zoo. Recently they have welcomed their first baby. Cogratulations!

This is a $1K genome assembly, generated from a draft assembly with short-insert size Illumina reads [266,035,705 PE reads] and scaffolded to chromosome length genome with Hi-C [186,199,173 PE reads]. See our Methods page for more details on the procedure. Check the interactive map of the 40 chromosomes,(2n= 80), of the Baird's tapir below!

This is the third tapir species we've released here on the DNA Zoo. Check out the assembly pages for the South American tapir, T. terrestris (2n=80), and the Malayan tapir, T. indicus (2n=52).

We gratefully acknowledge 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

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.