Feline good about 2022

The leopard cat, Prionailurus bengalensis, is slender cat-size felid with luxurious tawny rosette-spotted fur with white underbelly inhabiting Asia (from India, Himalayas to Korean peninsula and all the way south to Java and Philippines). Northern subspecies are markedly heavier, robust and vicious, while Southern cats are smaller and friendlier. Fur color and length variations across the range led to distinction of many subspecies (some recently promoted to species) at present narrowed to mainland (P.b. bengalensis and P.b. euptilura), Sunda (P. javanensis javanensis, P.j. sumatranus), and pending revision smaller islands subspecies (P.b. iriomotensis, alleni) (Luo et al., 2014, Patel et al., 2017, Kitchener et al., 2017).

Prionailurus bengalensis by zoologistiques, [CC BY 2.0], via flickr.com

This nocturnal solitary hunter mostly feeds on rodents, but also smaller mammals, birds, reptiles and insects, rarely ravaging nearby farms for fowl. Agile leopard cats rest on trees, live in the forest undergrowth and can swim. Northern cats breed in mid-winter, while Southern breed all year around with gestation up to 70 days with 2-3 kitten litters. With the population over 50 000 Prionailurus bengalensis is not endangered (CITES Appendix II and protected in Hong Kong) but still can be threatened by the habitat loss.

The leopard cat was domesticated in China about 5,000 years ago! This means that wildcats were, in fact, domesticated once in the Middle East/North Africa region, about 10,800 years ago, and again, from a different species in China approximately 5,000 years later (see this PLOS ONE article). The common domestic cat (Felis catus) however appears to have replaced the leopard cats in China sometime after 3000 BCE. In continuation of the intertwined history between the species, recently crossing of leopard cat and domestic cat created the Bengal cat breed with rare among domestic cats spotty coat pattern!

Today, we share a chromosome-length assembly of the leopard cat based on the PriBen1.0 genome assembly generated and shared via NCBI by A. Komissarov, L. Dalen, A. Wilting and T. Gilbert. The chromosome-length upgrade was done with Hi-C generated using cultured cells from primary fibroblast cell line (passage 4) provided by Polina Perelman (Institute of Molecular and Cellular Biology). Captive male Tuo (PBE-54, NIHAC LC94004) was brought from Tallin Zoo Park (Dr. Vladimir Feinstein) and brought to NIH Asian cats colony. The animal belongs to most Northern euptilura subspecies (Luo et al., 2014, Patel et al., 2017). The cell line was established from skin biopsy by Mary Thompson, in the Laboratory of Genomic Diversity at NCI-Frederick lead by Dr. Stephen O’Brien, and later preserved by Drs. Melody Roelke, Carlos Driscoll, Christina Barr, Stephen Lindell, and David Goldman at the Section of Comparative Behavioral Genomics, NIAAA. The scaffolding was done using 3D-DNA and Juicebox Assembly Tools. We thank the DNA Zoo Novosibirsk team and DNA Zoo Australia team at the University of Western Australia as well as Pawsey Supercomputing Centre for their help with this assembly!

Leopard cat has standard felid karyotype with 2n=38. The centromere repositioning chromosome banding pattern and morphology from F1 to E4 (Bredemeyer et al., 2021). Check out the interactive map of the leopard cat chromosomes below!

In the "The animal kingdom, or zoological system, of the celebrated Sir Charles Linnæus" (Class I. Mammalia: Containing a complete systematic description, arrangement, and nomenclature, of all the known species and varieties of the mammalia, or animals which give suck to their young) the leopard cat is referred to as the Bengal tiger-cat, making this a perfect release to start 2022, the year of the Tiger! Happy 2022 everyone!!!

Blog post by Pasha Dobrynin, Polina Perelman, Ashling Charles and Parwinder Kaur

Going, going, dugong

Commonly referred to as ‘sea cows’, dugongs are gentle giants which feed on seagrasses which grow along shallow coastlines of the Indo-pacific. Although the name of ‘sea cow’ is typically attributed to dugong, other herbivorous sea mammals belonging to the same order Sirenia, such as the North American manatee (check out the assembly page here), have also been referred to by the title.

Dugong by Jason Tong, [CC BY 2.0], via flickr.com

Dugongs are large aquatic mammals which can grow up to 4 meters in length and a ton in weight. Given their size, it is perhaps unsurprising that their closest living land relative is the elephant. Adults do not have any natural predators, although calves may be targeted by killer whales and saltwater crocodiles. Dugongs are exclusively marine creatures, and do not enter freshwater regions.

Like their nickname implies, dugongs mainly feed on seagrass. They are picky eaters, however, preferring easily digestible low-fiber seagrass with high nitrogen content. They also dislike eating from ‘meadows’ where seagrass is abundant, instead opting for sparse areas. Contrary to the vegetarian implications of their nickname, some dugongs are omnivorous. E.g. dugongs living along the Australian coast have been known to feed on jellyfish and shellfish.

Dugongs live in coastal regions from the western Pacific Ocean to the eastern coast of Africa, but most of the world’s dugongs are currently found in Australian waters. They have been found in the ocean territories of 37 countries but have disappeared from parts of east and south-east Asia. Dugongs are currently listed as ‘vulnerable’ by the IUCN. Their numbers have decreased significantly in recent times, mainly due to habitat degradation and fishing-related fatalities. Dugongs have historically been hunted for their meat, bones and oil, and although hunting has ceased in most areas, poaching persists.

Today, we release the chromosome-length genome assembly for the dugong (Dugong dugon)! We thank Natasha Tay and Erina Young from Murdoch University for their help with the sample! Sample processing, library preparation and data collection was supported by resources provided by DNA Zoo Australia, The University of Western Australia (UWA). We gratefully acknowledge the computational support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.

This is a $1K genome assembly with a contig N50 = 64 Kb, and a scaffold N50 = 119 Kb. Please check out our Methods page for assembly procedure details, and check out the interactive map of the 25 dugong chromosomes below! 2021 was going, going and is now dugong so follow us on twitter @thednazoo and subscribe to our mailing list below to keep up with all the 2022 releases.

A-maize-ing snake

Meet the corn snake Pantherophis guttatus! This snake unfortunately resembles the venomous copperhead and is often killed as a result of this mistaken identity. The truth is that corn snakes lack functional venom and are harmless to humans (although they will strike if disturbed).

Photo Description: A corn snake couple (Pantherophis guttatus). Photo credits: Tanya Orsini [Public domain], via flickr.com

The corn snake is found throughout the southeastern and central United States and is named for the species' regular presence near grain stores, where it preys on mice and rats that eat harvested corn. The Oxford English Dictionary cites this usage as far back as 1675, whilst other sources maintain that the corn snake is so-named because the distinctive, nearly-checkered pattern of the snake's belly scales resembles the kernels of variegated corn.

American corn snakes are popular pets everywhere except Australia. It is a prohibited invasive animal in Australia under the Biosecurity Act of 2014. If released into the wild in Australia, corn snakes could prey on and out-compete native species.

Today we share a chromosome-length assembly for Pantherophis guttatus based on the draft generated by Ullate-Agote et al 2014 & Ullate-Agote et al 2020. We are grateful to Shedd Aquarium for their help with the Hi-C sample used for the upgrade! We are also grateful to the DNA Zoo Australia team at the University of Western Australia and Pawsey Supercomputing Centre for the computational support for this genome assembly. We hope that the new chromosome-length genome assembly will help promote corn snakes as a model species.

Check out the interactive Juicebox.js instance below for the interactive Hi-C contact map of the 18 corn snake chromosomes, and visit the assembly page for more detail!