It takes one to snow one

From the Himalayas to the southern Siberian mountain range, the snow leopard (Panthera uncia) can be found on the prowl for its next meal. Snow leopards are no strangers to harsh terrains, travelling anywhere from 48 to 80 square miles [1]. These powerful predators can jump up to 50ft and can take down prey three times its own size [2]!

Young snow leopard by Tambako The Jaguar, [CC BY-ND 2.0], via flickr.com

To survive and blend in with snowy, mountainous environments, snow leopards have large paws that act as natural snowshoes and thick fur coats to protect them from harsh conditions. Their light-colored coats have dark rosette patterns that are unique to each individual [3]. Unfortunately, their beautiful coats are sought after by poachers. The IUCN lists the snow leopard as vulnerable, with their wild population in decline. Other threats to snow leopard populations include habitat loss and climate change.

Today, we share the chromosome-length assembly for the snow leopard, thanks to Kiara from the Oklahoma City Zoo. Before she passed in late 2017, she provided the sample for this genome assembly allowing for her genome to live on indefinitely. We thank the Oklahoma City Zoo staff and especially Candice Rennels and Jennifer D'Agostino for their help with this sample!

This is a $1K genome assembly with contig N50 = 65 Kb and scaffold N50 = 141 Mb. See Dudchenko et al., 2018 for procedure details. This is the fifth species in the DNA Zoo collection from the Pantherinae subfamily of cats, the others being the tiger, jaguar, leopard, and the clouded leopard. Stay tuned for more!

Back in Black

The black rhinoceros (Diceros bicornis) is the smaller of the two African rhinoceros species, but still stands just shy of 6ft tall at the shoulders. These mammals are not only massive, but quite fast. Weighing in at up to 1.5 tons, they can still reach a top speed of 34 mph while running on just their toes [1]!

As herbivores, the rhino intakes around 120 pounds of foliage, and does so by browsing on woody plants and shrubs [2]. They’re specially equipped with a notably pointed upper lip that’s used to pull the leaves off the branches and into their mouths.

The black rhinoceros sports two large horns on its head, in contrast to the white rhinoceros which bares only a single horn. In the wild these horns are used to ward off encroaching animals and defend territory. Large horns therefore are very desirable when searching for a mate.

"Black rhino" by Paul Albertella [CC BY 2.0], via flickr.com

Black rhino numbers once soared into the hundreds of thousands across sub-saharan Africa, but during the early 1990’s these numbers dwindled down to as low as 2,500 due to unregulated hunting and poaching [3]. This was an immense 98% drop in population. However, the numbers have been on the rise, with wild black rhinoceros population reaching more than 6,421 [4]. The IUCN lists these beautiful animals as critically endangered. Read more about these animals here.

Today, we release a chromosome-length genome assembly of the black rhinoceros. This is a $1K genome assembly with contig N50 = 87 Kb and scaffold N50 = 59 Mb. See Dudchenko et al., 2018 for details on the procedure. Thank you to SeaWorld for providing the sample for this assembly. This is the third rhinoceros in our collection, and completes the assembly of both African rhinoceros species, the other being the white rhinoceros (Ceratotherium simum). Additionally, we have previously shared the assembly of the Indian rhinoceros (Rhinoceros unicorns).

Announcing the release of updated genome annotations

Announcing the release of updated (version 2) genome annotations, plus the initial release of 39 newly annotated DNA Zoo genomes!

tl;dr, the entire set of >2.9 million protein-coding genes spanning 109 mammalian genomes, can be found here (see also Wasabi mirror).  This set is much improved over the version 1 annotations, with the fraction of missing mammalian BUSCOs down to 5% (from 10%). We’ve called on average 28141 genes per species (Min 22,417 Eidolon helvum, Max 45,707 Saimiri boliviensis). 95.3% of genes are assigned to 74,713 orthogroups. 9165 species specific genes have been assigned to 2609 orthogroups.

All protein files, transcripts and the gff3 can be found in data release folders associated with each individual assembly. Orthofinder summary files are found here, while the file that contains the orthogroups are found here

What did we do differently?

Remember that in the 1st attempt, we used genes contained in the Swiss-prot reference.  To update, in brief, we added more reference material. Non-coding RNAs, transcript evidence from other species focusing on adding coverage to carnivores, rodents, and primates. This additional transcript information has dramatically improved our ability to detect genes in genomes.

See this blog post for information on the original version 1 genome annotations. 

The updated maker control file is here:, and the reference fastas used are located here. Given these files, the runs should be fully reproducible. 

Each annotation took between 48 and 72 hours to run across 80 cores, for a total of about 450,000 core-hours!

The Phylogeny

The phylogeny of these 109 mammals (plus the Ostrich used as an outgroup) was computed using OrthoFinder 2.4.0. The image is below, and the Newick text file is here. 

What’s next?

1. We can still do better, but for this we need RNAseq data! If you have transcriptome data for any of the DNA Zoo genomes, and would like to share it, I’d be happy to update the annotation! This would really help us improve both the completeness of the genomes, but also the accuracy.

2. Is your favorite gene missing? Let us know and we can see where it went.