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.

Tapirfect moment

The Malayan tapir (Tapirus indicus) is the largest of the tapirs and the only remaining species of tapir in the Old World [1]. The Malayan tapir was first listed as endangered in 1986, due to an ongoing decline from loss of available habitat, fragmentation of remaining habitat and increasing hunting pressure. Population declines are estimated to be greater than 50% in the past 30 years! This situation is sadly expected to continue at a slightly diminishing rate in the future as non-protected areas, which are available as logging concessions, become less available [1, 2].

To help with the ongoing conservation efforts and genetics research, today, we share a chromosome-length genome assembly for the Malayan tapir Kruze from the San Antonio Zoo. That’s him on the cover photo! See this video featuring Kruze and learn more about Malayan tapirs. The genome assembly follows the $1K model described in (Dudchenko et al., 2018).

Tapirs are odd-toed ungulates (Perissodactyla) and close relatives to rhinos and horses. See below how the genome of the Malayan tapir relates to those of its relatives. The plots confirm extremely rapid karyotypic diversification in perissodactyls suspected from multidirectional cross-species painting (see, e.g. Trifonov et al., Chromosome Res. 2008), with multiple instances of chromosome fragmentation in the rhino as compared to the tapir, and many chromosomal exchanges in the equid lineage.

Whole-genome alignment plots between the new genome assembly for the Malayan tapir Tapirus_indicus_HiC and the genome assemblies of the Southern white rhino (CerSimSim1.0_HiC, DNA Zoo upgrade of the publicly available Broad draft), the domestic horse (EquCab2.0, from Wade et al., Science 2009), and donkey (ASM303372v1_HiC, DNA Zoo upgrade of Renaud et al., 2018 draft genome assembly).

Cover photo credit: San Antonio Zoo.