A nosey mouse

Welcome to the Year of the Rat! In Chinese culture, rats are a sign of wealth and abundance and similarly, rodents are the most abundant and species rich order of mammals, representing 40% of all extant mammals. Shockingly, there are comparatively few rodent genomes available relative to larger, more charismatic mega-fauna like cats and dogs.

We are excited to launch 2020 and the Year of the Rat with the release of the Northern rock mouse Peromyscus nasutus (Allen 1981) genome assembly, adding to a much-needed repertoire of rodent genomes that can now be used in human biomedical research and comparative genomics. The Criceidae family of rodents, to which P. nasutus belongs, includes almost 600 species of true hamsters, voles, lemmings, and New World rats and mice – the second-largest family of mammals.

Peromyscus nasutus has a long and slender nose relative to other Peromyscus species, but it would be otherwise hard to distinguish if not for its 'nosey' appearance (nasus means 'nose' in Latin). As the common name suggests, the northern rock mouse loves rocks and doesn't live too far from rocky areas in the Southern United States (mostly Colorado and New Mexico) and Mexico. The information contained in its scientific and common names, pointing to a long-nosed rock-loving mouse, is pretty much all we know about this species, starting from 'is this a species'?

In fact, the taxonomy of the Northern rock mouse has been subject of debate for decades. Previously recognized as a subspecies of Peromyscus difficilis, genetic inquiry has recently elevated it to the full-species level and this new assembly expands opportunities for further systematic inquiry. Will P. nasatus continue to be recognized as a species, or will it be demoted to just a population of Peromyscus difficilis, a closely related species?

The tissue sample was loaned to the MacManes lab by the Museum of Southwestern Biology, as part of a larger study on how desert mammals survive intense heat and drought. It was collected in 2017 in El Malpais National Conservation Area, Cibola County, New Mexico, USA by Kayce Bell and colleagues. The full collection record can be found at http://arctos.database.museum/guid/MSB:Mamm:299083.

Farewell to the year of the pyg

We hope everyone had a great 2019! We certainly did, with 114 chromosome-length genome assemblies shared with the scientific and conservation communities. Bringing this one more up just before the year ends, we share today the genome assembly for the pygmy marmoset Cebuella pygmaea, the smallest monkey and one of the smallest primates in the world [1]. As always, we are excited to share our assemblies and data without any restrictions!

Pygmy marmoset is listed as Vulnerable by the IUCN. The biggest threats to the species are habitat loss and the pet trade [2].

This genome assembly was generated using blood samples donated by two siblings, Bjorn and Teek, from the Houston Zoo. This is a $1K model genome assembly (see Dudchenko et al., 2018 for details). See below the whole genome alignment plot comparing the new genome to the common marmoset (Callithrix jacchus) genome assembly, generated by the WashU team here.

Whole-genome alignment plot between the new genome assembly for the pygmy marmoset (Cebuella_pygmaea_HiC) and the Callithrix_jacchus-3.2 (calJac3) genome assembly for the common marmoset.

We look forward to welcoming the iron rat year with some rodent assemblies, so stay tuned. And happy assembling in 2020!

May the fossa be with you!

The fossa (Cryptoprocta ferox) is the largest carnivorous mammal on the island of Madagascar. Lemurs make up a good deal of their diets, but they also eat small mammals, fish, lizards, birds, frogs and insects [1]. The fossa is listed as a vulnerable species by the International Union for Conservation of Nature [2].

Fossas are members of the cat family (Feliformia) related to mongooses and hyenas. And like some of their cat relatives, fossas have many unique features. (In case you’ve missed it, read a bunch of mind-blowing facts about spotted hyenas in our blog post from a few weeks ago!) For example, the female fossa undergoes a strange developmental stage during adolescence known as transient masculinization, unique to fossas. It’s unclear what purpose this transient masculinization serves, but scientists hypothesize that it protects juvenile females from harassment by adult males or aggression from territorial females. Fossas also have an unusual mating system, in which a female monopolizes a mating site and chooses her mates. [1]

Today, we share the genome assembly for the fossa, generated using a sample donated by a male fossa from the Houston Zoo named Hansel. Learn more about Hansel from this Houston Zoo podcast video! The genome was generated using the DNA Zoo $1K strategy [3].

See below a whole-genome alignment plot that highlights how the chromosomes (2n=42) of the fossa genome relate to those of the domestic cat (2n=38, felCat9 based on Pontius et al., 2007). As with many members of the cat family, extensive conservation of synteny is seen among the karyotypes, with one major break/fusion event involving cat chromosomes #1 and #2. It is worth noting that some of the rearrangements like chr1 breakage is shared with hyenas and meerkats, see here.

Whole-genome alignment plot between the new genome assembly for the fossa (Cryptoprocta_ferox_HiC) and domestic cat (from Pontius et al., 2007). The karyotypes are highly syntenic except for some major rearranging involving cat chromosomes #1 and #2.