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

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