A genome to blue your mind

The blue monkey, Cercopithecus mitis, is an Old World monkey species endemic to Central and East Africa. Though called blue monkeys, they are actually more gray in appearance. As frugivores, the majority of the blue monkey's diet consists of fruit but they also eat leaves and occasionally insects. Wild populations of blue monkeys display interspecies cooperation, notably with red-tailed monkeys (C. ascanius) for extra protection against predators [1].

Cercopithecus mitis by Yvonne A. de Jong, [CC BY-NC-SA], via inaturalist.org

Today, we release the genome assembly for the blue monkey, Cercopithecus mitis. The genome was generated using a sample from the T.C. Hsu Cryo-Zoo at the University of Texas MD Anderson Cancer Center stored all the way back in 1978! We thank Drs. Asha Multani, Sen Pathak, Richard Behringer, Liesl Nel-Themaat and Arisa Furuta in the Department of Genetics at the MD Anderson Cancer Center for their help with this sample.

There are several recognized subspecies of the blue monkey [2]. At different times in history, they may have been viewed as separate species entirely, but have been later recategorized as subspecies. Our analysis of the mitochondrial sequence for the individual monkey that donated sample for this assembly suggests it is a Cercopithecus mitis albogularis, more commonly known as the Sykes' monkey.

This is a $1K genome assembly, following the protocol outlined on out Methods page. This genome assembly has a contig N50 = 28 Kb and a scaffold N50 = 51 Mb. Check out the 36 chromosomes (2n=72) of the blue monkey in the interactive JuiceBox map session below!

Whether you're interested in Old or New World monkeys, we've got you covered. This is the sixth Old World monkey species we've released here on the DNA Zoo blog and the 18th primate overall! Check out our $1K de novo assemblies for the Guinea baboon (Papio papio), the Allen's swamp monkey (Allenopithecus nigroviridis), and the Patas monkey (Erythrocebus patas).

For the greater galago

The brown greater galago (Otolemur crassicaudatus) is also commonly known as bush babies. This cutesy name likely came from the high-pitch cries they can make as well as the large, round eyes.. The eyes of the brown greater galago are not only adorable, they provide excellent night vision as they are nocturnal like most other galago species. In addition, the oversized, bat-like ears of the greater brown galago can point in opposite directions and can furl and unfurl their ears to best track insects in the dark [1].

Otolemur crassicaudatus by Hans Hillewaert, [CC BY-NC-ND 2.0], via flickr.com

We would like to graciously thank the Duke Lemur Center for providing the material used in this genome assembly! For the past 35 years, the Duke Lemur Center has collaborated and organized conservation programs in Madagascar to protect the many precious lemur species endemic to the area. Please consider symbolically adopting a lemur help support conversation efforts!

Today, we release the chromosome-length genome for the greater brown galago, Otolemur crassicaudatus! This is a $1K genome, with a contig N50 = 74 Kb and a scaffold N50= 91 Kb.

For assembly procedure details, please see our Methods page. Explore the 31 chromosomes of the greater brown galago in the interactive Hi-C map below.

This is the 6th Lemuriforme species and the 17th primate we've released here on the DNA Zoo blog! Leaping for more lemurs? Check out the assembly pages for the Mongoose lemur (Eulemur mongoz) , the Collared lemur (Eulemur collaris) , and the Gray mouse lemur (Microcebus murinus). Don't forget to subscribe to our mailing list below and give us a follow on Twitter @thednazoo to stay up to date on our latest releases!

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