A rare carnivorous bat genome

Trachops cirrhosus, known as the fringe-lipped bat or the frog-eating bat, is a member of the New World leaf-nosed bats, Phyllostomidae. This species is the only member of its genus and is one of the only carnivorous bat species in the Americas, feeding on primarily insects alongside lizards, frogs, and even fruits and seeds. Fringe-lipped bats detect their prey using their keen hearing; they listen for frog calls to hunt frogs, and listen for rustling noises in vegetation and leaf litter to find lizards and large insects. These bats are distributed from southern Mexico to southern Brazil and roost in trees and caves. This species is listed as an IUCN Least Concern.

Photo of Trachops cirrhosus in Belize by Sherri and Brock Fenton

Today, we release the first chromosome-length assembly for Trachops cirrhosus. This is a $1K-model genome assembly, with a contig n50 = 60 Kb and a scaffold n50 = 124 Mb. (For more details on our assembly procedure, please see our Methods page.) The liver sample used for in situ Hi-C preparation (AMNH-AMCC-225240) came from a male individual of Trachops cirrhosis collected on the 26th of April, 2017 at the Ka’Kabish Archaeological Reserve in Orange Walk District, Belize (17.81531 N, 88.73057 W). Capture and export of this specimen were licensed under Belize Forest Department permits WL/2/1/17(16), WL/2/1/17(19), and WL/2/7/17(21). The voucher specimen and data for this sample are archived at the American Museum of Natural History under catalog number AMNH-Mammalogy-279525. We graciously thank Nancy Simmons (AMNH Department of Mammalogy), Svetlana Katanova (AMNH Ambrose Monell Cryo Collection), and Daniel Becker (University of Oklahoma) for access to this sample.

This is the third phyllostomid bat species released on dnazoo.org (see Seba's short-tailed bat [Carollia perspicillata] and the Jamaican fruit bat [Artibeus jamaicensis]) and the 15th bat species overall!

Check out the 15 chromosomes of the fringe-lipped bat in the interactive JuiceBox.js session below, and follow the assembly page link for more data.

Species and perches

The Eastern Yellow Robin (EYR) is a small insectivorous passerine bird native to eastern Australia, their distinctive piping call is one of the first to be heard in the morning chorus, often beginning before light. They are relatively unafraid of humans, often seen perched sideways on tree trunks in a range of habitats from dry woodland to rainforest. They are mostly perch-and-pounce predators, grabbing invertebrates and some other small animals such as lizards out of leaf litter on the ground.

Photo Description: Eastern Yellow Robin (Eopsaltria australis) - Inland lineage. Photo Credits and acknowledgements – Geoff Park

Eastern yellow robins have distribution spanning thousands of kilometres along north-south axis and across a large range of climates. Southern birds have an olive rump, different from the brighter yellow of northern birds. Surprisingly, there is a major genetic distinction perpendicular to this geographic colour variation. Genetically the species appears to be split approximately into ‘inland’ and ‘coastal’ forms (respectively red and blue dots on the map shown below), thought to be caused by two ecologically relevant adaptive sweeps in the mitochondrial genome (mitochondria are the powerhouses of cells which bear their own small genome) [1, 2].

Inland and coastal Eastern Yellow Robins seem not to interbreed freely where they occur side-by-side at a limited number of special locations. There is particular resistance to exchange of genomic material between the lineages in the part of the genome harbouring the greatest density of nuclear-encoded mitochondrial genes. This ‘mitonuclear cluster’ has been implicated in environmental adaptation by mitonuclear co-evolution in EYR [3]. This genomic region was subsequently found to be sex-linked, associated with a fusion between an autosome (that is, a chromosome found in two copies in both sexes) and a sex chromosome forming a ‘neo-sex chromosome’ [4]. The species may be on its way to becoming two species, suited to different environments and conferring different metabolisms [5].

From Morales et al, 2017

Such wildlife species that have genomic variation distributed heterogeneously through environmental and geographic space are excellent models for studying evolutionary processes under natural conditions. To support ongoing scientific efforts, DNA Zoo has been working with Paul Sunnucks, Alexandra Pavlova and Gabriel Low at Monash University to obtain chromosome-length genome assemblies for one inland- and one coastal-lineage female EYRs. The coastal-lineage chromosome length was released by DNA Zoo in 2020 and today we release the inland-lineage assembly.

The inland-lineage chromosome-length assembly is based on a draft assembly published by Gan et al 2019 [4]. This draft was scaffolded with 98,992,919 PE Hi-C reads generated by DNA Zoo labs using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details.

This work was enabled by wildlife authorities including the Victorian Department of Environment, Land, Water and Planning, Parks Victoria, and the Australian Bird and Bat Banding Scheme. The research has been supported by the Holsworth Wildlife Endowment Fund, Australian Research Council grants DP180102359 and DP210102275, and Monash University.

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

Citations

1. Morales, H., P. Sunnucks, L. Joseph, and A. Pavlova. (2017). Perpendicular axes of differentiation generated by mitochondrial introgression. Molecular Ecology 26:3241–3255.

2. Morales HE, Pavlova A, Joseph L, Sunnucks P (2015) Positive and purifying selection in mitochondrial genomes of a bird with mitonuclear discordance. Molecular Ecology 24, 2820–2837.

3. Sunnucks P, Morales HE, Lamb AM, Pavlova A, Greening C (2017). Integrative Approaches for Studying Mitochondrial and Nuclear Genome Co-evolution in Oxidative Phosphorylation. Frontiers in Genetics 8:25. doi:10.3389/fgene.2017.00025

4. Gan HM, Falk S, Moraleś HE, Austin CM, Sunnucks P, Pavlova A. Genomic evidence of neo-sex chromosomes in the eastern yellow robin. Gigascience. 2019;8(12):giz131. doi:10.1093/gigascience/giz131

5. Morales HE, Pavlova A, Amos JN, Major R, Kilian A, Greening C and Sunnucks P (2018) Concordant divergence of mitogenomes and a mitonuclear gene cluster in bird lineages inhabiting different climates. Nature Ecology & Evolution 2, 1258–1267.

Pouchies against ouchies

Southern giant pouched rats (Cricetomys ansorgei), referred to as “Pouchies” due to the fact that they are only distantly related to conventional rats, are very large rodents best known for their powerful olfactory senses conferring the ability to reliably detect underground explosives such as TNT. In fact, this species is currently being trained and employed as biodetectors used to clear abandoned landmine fields in the wake of armed conflict.

Southern giant pouched rat, photo by Ehren Bentz [CC]

Notably, in 2020, a Southern giant pouched rat became the first rodent to be awarded the PDSA Gold medal for animal bravery from the British organization the ‘People's Dispensary for Sick Animals’. During his career, ‘Magawa’ (internationally known as the ‘Hero rat’) was responsible for the detection and subsequent removal of at least 71 landmines, as well as dozens of other unexploded ordinance items from extremely dangerous abandoned mine fields in Cambodia. Further, this species’ utility as biodetectors may extend beyond explosives, as they are also able to detect subtle chemical signals indicative of Tuberculosis infection – a condition which is often cryptic and difficult to diagnose.

In addition to their impressive chemosensory prowess, Pouchies also exhibit a unique and interesting reproductive physiology. Similar to some other rodents, females are born lacking a vaginal opening, which typically appears as they reach sexual maturity. In Pouchies, this non-reproductive condition often uniquely persists for years into adulthood, and is even reversible, with adult females exhibiting vaginal openings completely covered by an area of skin, sometimes even after having previously given birth to a litter of pups. The mechanisms governing these unusually plastic reproductive developmental timelines appear to be, at least in part, mediated by pheromonal signals. Pheromonal communication is an important aspect of life for these interesting animals, enabling them to detect subtle differences in chemical social signals used to advertise sex, physiological state, and reproductive status through nothing more than urine.

Today, we release the chromosome-length assembly for the Southern giant pouched rats. This genome assembly was produced by Dr. Ehren Bentz and Dr. Alexander Ophir in the Psychology department at Cornell University in collaboration with DNA Zoo. Whole genome sequencing was performed by the University of Georgia Genomics and Bioinformatics Core using Pacific Biosciences continuous long read sequencing. Reads were error corrected and assembled using Canu (Koren et al., 2017), and contigs were anchored to scaffolds using in situ Hi-C sequencing (Rao, Huntley et al., 2014), 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). The resulting chromosome-level scaffolds were then polished with PacBio long reads using Racon (Vaser, Sović et al., 2017). Check out the interactive JuiceBox.js session exploring the 40 chromosomes below!

The pouched rat’s extremely acute chemosensory abilities, as well as its unique reproductive physiology and social behaviors, provide a powerful, novel model for investigating olfactory communication, reproductive physiology, and development in an exotic rodent species with tremendous potential. This chromosome-length genome assembly surely constitutes an invaluable resource facilitating the development of the Pouched rat as both a research model and as a biodetector.

Funding for this work was provided by the Army Research Office and the National Science Foundation.