Banding together

Unlike most other mongoose species, the banded mongoose, Mungos mungo, are social and prefer to band together. They live in groups of 10-20 individuals but may live in communities as large as 40 mongooses. As they are also smaller in size than other mongoose species, these groups may provide more protection. When a group of banded mongooses are approached by a predator, they group together to try and create the appearance of a larger, singular animal to intimidate the threat [1].

Banded mongoose by Cloudtail, [CC BY-NC-ND 2.0], via flickr.com

Today, we release the chromosome-length assembly for the banded mongoose, Mungos mungo! This is another $1K genome assembly, with contig n50 = 61 Kb and scaffold n50 = 129 Mb. We'd like to thank Fupi, a female banded mongoose from the Houston Zoo for donating the sample used to generate is assembly! Check out the interactive JuiceBox.js session below:

If you're interested in more assemblies from the Herpestidae family, check out our chromosome-length upgrade for the meerkat, Suricata suricatta. As always, we recommend subscribing to our mailing list below to keep up to date on our latest releases! Check back weekly for more chromosome-length genomes.

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’.

https://video.wixstatic.com/video/776026_1417abb8dd70406f9a70645f2c23fb36/720p/mp4/file.mp4

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