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 hovering around 5,500 [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.

A tail with a hoppy ending

The brush rabbit, Sylvilagus bachmani, is one of several species of cottontail rabbits. They have a short, fluffy tails that may be white or gray in color. Inhabiting the western costal region of North America, brush rabbits may be found foraging through shrub-lands, woodlands, and coniferous forests. Though they rarely leave the brush for long, they may be seen basking in the sun in nice weather. If they’re feeling particularly excited or playful, brush rabbits can binky, jumping up in the air while twisting their bodies and kicking their feet [1]!

Brush rabbit by Allan Hack, [CC BY-ND 2.0], via flickr.com

The brush rabbit are prolific breeders, producing around 3 litters with an average of four offspring a year [2]. The population is kept in check by their many predators, including snakes, foxes, coyotes, and bobcats. When startled, brush rabbits may thump their back feet on the ground in surprise! Brush rabbits avoid predators by running at speeds of 40 km/hr in zig zag patterns [3].  

Originally sampled in 1976, this assembly was created from primary fibroblasts obtained from T.C. Hsu CryoZoo at the University of Texas MD Anderson Cancer Center. 44 years later, we share the chromosome length assembly of the brush rabbit. This is a $1K genome assembly with contig N50 = 58 Kb and scaffold N50 = 116 Mb. See Dudchenko et al., 2018 for details on the procedure.

This is only a second chromosome-length genome assembly for a rabbit in our collection: previously we shared a few tweaks to the European rabbit genome assembly from the Broad institute (Lindblad-Toh et al., 2011), here. The second genome gives us the first opportunity to compare karyotypes within the rabbit family. Included below is the whole-genome alignment plot between the two rabbit genomes: the genome appear to be highly collinear, with two fusion events (circled in blue) apparent responsible for the difference in karyotypes: 2n=44 in the European rabbit vs 2n=48 in the brush rabbit!

Whole-genome alignment plot between the only other rabbit with a chromosome-length genome assembly before the brush rabbit, the European rabbit (assembly OryCu2.0_HiC, from the Broad institute with DNA Zoo tweaks) and the new brush rabbit genome assembly (Sylvilagus_bachmani_HiC).