On the shoulders of giants

With more than two meters from head to tail, the giant anteater (Myrmecophaga tridactyla) is the largest anteater species. Anteaters are most closely related to sloths within xenarthrans (Order Pilosa), which also include armadillos (Order Cingulata). As all xenarthrans, giant anteaters originated in South America and are widely distributed throughout the Neotropics from Southern Brazil to Honduras in Central America. Unlike other anteater species, giant anteaters are fully terrestrial and occupy a diversity of habitats from tropical moist forests, dry forests, savannas and open grasslands.

Giant anteater (Myrmecophaga tridactyla) by Mehgan Murphy, [CC BY 2.0], via flickr.com

Feeding exclusively on social insects, the giant anteater is the ultimate termites and ants eating machine in being able to ingest more than 30,000 insects from 80 different colonies in a single night! This highly specialized myrmecophagous diet has triggered the evolution of an arsenal of morphological adaptations to efficiently forage and digest such impressive amounts of insects. The giant anteater possesses powerful claws for breaking into ant and termite nests and an extremely elongated tongue (reaching 60 cm) coated with sticky saliva to catch the social insects. Being completely toothless, preys are ingested directly, predigested by saliva produced through enlarged salivary glands, and further process in a muscular stomach.

Male and female adult giant anteaters are solitary and only paired once every two years for a brief courtship period during the breeding season. They usually produce a single offspring that stays under maternal care with the female carrying the young on her back until it is able to walk, about two or three months after birth. Young remain with their mother until they are about one year old and become experienced enough to disperse.

From the conservation point of view, the giant anteater is currently classified as Vulnerable on the IUCN Red List of Threatened Species. Despite its wide geographical distribution, habitat loss is a major concern and represents a significant threat in many parts of its range. There have been many records of local extinctions in Central America (Guatemala and Belize) and in the southern parts of the distribution (Uruguay). In grasslands such as in Brazil, the species is particularly susceptible to fires and animals are sometimes killed on roads. It has been estimated that the giant anteater population has suffered an overall reduction in population size of more than 30% over the last 60 years (three generations).

Today, we share a chromosome-length assembly for the giant anteater. This is a Hi-C upgrade to a draft genome hybrid assembly generated by combining Nanopore long reads with Illumina short reads by Rémi Allio, Frédéric Delsuc and team at Centre National de la Recherche Scientifique (CNRS) and Université de Montpellier as part of the ConvergeAnt project (https://www.convergeant-project.com). The original sample used for the initial draft assembly comes from a captive individual born at Duisburg Zoo (Germany) in 2014 and who died at Cayenne Zoo (French Guiana) in 2018. This sample (M3023) is part of the JAGUARS collection curated by Benoit de Thoisy (Institut Pasteur de Cayenne and Kwata NGO, French Guiana). The sample for the Hi-C upgrade was donated by Rio soon after she was born at the Houston Zoo.

Check out the interactive contact map featuring 30 giant anteater chromosomes below. More data and links related to this assembly can be found on the corresponding assembly page!

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.