Superb starling assembly

Superb starlings (Lamprotornis superbus) really are as impressive as their name suggests. Their shimmering, iridescent green and blue plumage makes them hard to miss on the African savanna.

Superb starling, photo by Dustin Rubenstein, Columbia University [CC]

Yet, what really makes them stand out from other birds is their complex social system. Superb starlings are plural cooperative breeders that form some of the largest and most complicated social groups of any bird in the world. Read more about superb starlings in the Natural History article The Secret Lives of Starlings!

Today we release the chromosome-length genome assembly for the superb starling. This genome assembly is an upgrade of CU_Lasu_v1 assembly from the recent paper by Dustin Rubenstein and coauthors (Rubenstein et al. 2021). The paper uses functional genomics to explore the developmental basis of iridescent plumage in superb starlings, which produce both iridescent blue and non-iridescent red feathers.

We thank SeaWorld for their help with the Hi-C sample used for the upgrade!

Quollity genomic resource

The Northern quoll (Dasyurus hallucatus) is the smallest of the four Australian quoll species with adults weighing around 0.5-1 kg (males are larger than females). Northern quoll populations have declined by more than 75% since the introduction of poisonous cane toads, which the quolls mistake for food.

Photo Description: Northern Quoll (Dasyurus hallucatus). Photo credits: S J Bennett, CC BY-NC 2.0, via Creative Commons

The Northern quoll is a medium-sized carnivorous marsupial found in northern Australia. Northern quolls are relatively short-lived for an animal of their size, especially males which in the wild normally die soon after mating at only 1 year of age before their own offspring are born. During the mating season (around June to September), males expend considerable energy fighting other males, and do not survive to breed a second year. Females den in tree hollows, hollow logs and rock crevices; they raise a litter of up to eight young. At the end of the breeding season, the Northern quoll population is comprised almost entirely of mature females and their young. Females may live for two or three years.

Once widespread across northern Australia, the northern quoll now only occurs in fragmented populations and is classified as endangered by the IUCN. They reported to be critically endangered in the Northern Territory, and populations in Western Australia are vulnerable to extinction at very fast rates. The northern quoll's demise is attributed to several factors, including predation by invasive pests and habitat destruction, but more notably its predation on the toxic introduced cane toad. Several strategies are currently being investigated to combat the threat of cane toads, including targeted gene flow, training aversion behaviour, and engineering genetic resistance to the toad's toxin.

To support the above conservation efforts further, we share the first chromosome-length genome assembly for the northern quoll. This is a collaborative effort of DNA Zoo labs with Assoc. Prof. Ben Phillips and Dr Stephen Frankenberg from University of Melbourne along with Dr Adnan Moussalli from Museums Victoria. The chromosome-length assembly is based on a draft assembly produced using 10x Genomics Chromium linked-read sequencing of a male northern quoll fibroblast cell line, established from a tissue sample kindly provided by the Territory Wildlife Park, and assembled using Supernova with additional funding from the Hermon-Slade Foundation.

A liver sample from the same animal was used for the Hi-C sequencing. The 10X draft assembly was scaffolded with 722,045,107 PE Hi-C reads generated by DNA Zoo labs and processed using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details. Check out the interactive contact map of the Northern quoll’s 7 chromosome-length scaffolds below!

We hope that this assembly will provide a valuable genomics resource for northern quoll conservation, including the analysis of population genetics data and the development of genetic strategies to enable population recovery.

We gratefully acknowledge the resources provided by The University of Melbourne, Museums Victoria, The University of Western Australia and DNA Zoo, Aiden Lab at Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre.

Keeping it batty

One of the largest bat species in the world, the Indian flying fox (Pteropus medius aka Pteropus giganteus) can have wingspans of 1.2 - 1.4 meters wide [1]! Though they can look intimidating in flight, have no fear! For the Indian flying fox primarily eats fruits and nectar. In fact, they are often viewed as pests by farmers due to the destruction they can wreck on farms and orchards. That being said, the Indian flying fox plays an integral role in pollination and seed dispersal of many keystone plants in their home range across the Indian subcontinent [2].

Indian Flying Fox by Sergey Yeliseev, [CC BY-NC-ND 2.0], via flickr.com

The Indian flying fox can live in large roosts, sometimes comprising of hundreds of individuals! These roosts can be occupied for over a decade, preferring to roost in trees such as the banyan, fig, and tamarind trees. These large roosts are ideal for the Indian flying fox, as they are polygynandrous, or where both male and female bats mate with multiple partners in a breeding season [3].

As zoonotic diseases become more of concern, virologists and epidemiologists have been particularly interested in the Indian flying fox, a known asymptomatic carrier for the Nipah virus. Humans infected with the Nipah virus can experience encephalitis, severe illness, and death. Understanding the unique features of the Indian flying fox genome may help researchers identify evolutionary features of zoonotic diseases, like the Nipah virus.

Pteropus giganteus colony, Goa, India by Vladimir Yu, Arkhipov, Arkhivov, [CC BY-SA 3.0], via wikimedia.org

Today, we share the chromosome-length assembly for the Indian flying fox, Pteropus giganteus also known as Pteropus medius (read more about the naming issue on Wikipedia). This genome is a Hi-C upgrade for the draft genome assembly generated by Fouret et al., (2020). Many thanks to the Houston Zoo for providing the sample used for this chromosome-length Hi-C upgrade. Please visit our Methods page for more details on the assembly procedure, and check out the interactive Juicebox.js map below for the Hi-C contact map of the 19 chromosomes of the Indian flying fox!

This is our 11th bat species released here on the DNA Zoo blog and the third Pteropus bat, or mega-bats genus! While you're here, don't forget to check our the assembly pages for the large flying fox (Pteropus vampyrus) and the Madagascan flying fox (Pteropus rufus). Stay tuned for more bat genomes to come, and Happy Bat Week!

Citations: Fouret, J., Brunet, F.G., Binet, M., Aurine, N., Enchéry, F., Croze, S., Guinier, M., Goumaidi, A., Preininger, D., Volff, J.-N., Bailly-Bechet, M., Lachuer, J., Horvat, B., Legras-Lachuer, C., 2020. Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding. Front. Microbiol. 11, 1807. https://doi.org/10.3389/fmicb.2020.01807