Aye-aye captain

Perhaps one of the most peculiar species of primates, the aye-aye (Daubentonia madagascariensis) is a nocturnal, arboreal insectivore is found only in Madagascar. It is believed that the common name for this species came from the "exclaim of surprise and astonishment" by the French naturalist Pierre Sonnerat at the sight of the animal. However, it was later pointed out that the name is quite similar to the Malagasy name for the animal "hai hai" [1].

Aye-aye by nomis-simon, [CC BY 2.0], via wikimedia.org

Aye-ayes spend the majority of their lives in solitude in the canopies of the forests. The most notable characteristic of the aye-aye is their long, skeletal middle finger which is used to tap into trees to unearth larvae using a method called "tap foraging". The aye-aye is the only primate to use echo-location, and it's middle digit serves as it's primary sensory organ. Their odd appearance may have contributed to the superstition by some natives of Madagascar that they are an incredibly unlucky omen. Unfortunately this has led to many being killed onsite [3]. Coupled with deforestasion this has led to the aye-aye becoming endangered (see IUCN).

Today we share the genome assembly for the aye-aye, Daubentonia madagascariensis. This is a $1K genome assembly, with a contig N50 = 215 Kb and a scaffold N50 = 211 Mb. For assembly procedure details, please see our Methods page. We graciously thank the Duke Lemur Center for providing the sample used to generate this chromosome-length assembly. Please check out the interactive Juicbox.js session below to explore the 15 chromosomes of the aye-aye:

Upon its initial classification, the aye-aye was believed to be a kind of rodent. This was a understandable presumption, as the aye-aye has ever growing incisors that are characteristic of the order Rodentia. Their cat-like face also led to some debate whether the aye-aye should be a a felid. Eventually, it was established that aye-ayes are lemurs! For some preliminary analysis, we aligned the new chromosome-length aye-aye reference, Daubentonia_madagascariensis_HiC (2n=30) against the collared lemur assembly Eulemur_collaris_HiC (2n=50), see the dot plot below. There are a large number of rearrangements between the two genomes underlying the different chromosome count.

Whole genome alignment plot between the aye-aye, (Daubentonia_madagascariensis_HiC) (2n=30) against the collared lemur, (Eulemur_collaris_HiC).

We're not monkeying around here, this is the 6th Lemuroidea species we've released so far and the 20th primate overall! Check out these other $1K assemblies for the Guinea baboon (P. papio), the golden lion tamarin (L. rosalia), and the Patas monkey (E. patas). Remember to follow us on Twitter @thednazoo and subscribe to our mailing list below to keep up to date on our latest releases!

Banding together

Unlike most other mongoose species, the banded mongoose, Mungos mungo, are social and prefer to band together. They live in groups of 10-20 individuals but may live in communities as large as 40 mongooses. As they are also smaller in size than other mongoose species, these groups may provide more protection. When a group of banded mongooses are approached by a predator, they group together to try and create the appearance of a larger, singular animal to intimidate the threat [1].

Banded mongoose by Cloudtail, [CC BY-NC-ND 2.0], via flickr.com

Today, we release the chromosome-length assembly for the banded mongoose, Mungos mungo! This is another $1K genome assembly, with contig n50 = 61 Kb and scaffold n50 = 129 Mb. We'd like to thank Fupi, a female banded mongoose from the Houston Zoo for donating the sample used to generate is assembly! Check out the interactive JuiceBox.js session below:

If you're interested in more assemblies from the Herpestidae family, check out our chromosome-length upgrade for the meerkat, Suricata suricatta. As always, we recommend subscribing to our mailing list below to keep up to date on our latest releases! Check back weekly for more chromosome-length genomes.

No tapiring off on assemblies

The Baird's tapir (Tapirella bairdii) is a species of tapir native to Mexico, Central America and northwestern South America. It is the largest native land mammal in both Central and South America!

Baird's Tapir by Eric Kibly, [CC BY-SA 2.0], via flickr.com

These nocturnal vegetarians are wide-ranging and responsible for eating a lot of vegetation and dispersing seeds, making them “the gardeners of the forest.” Although their long, flexible snouts (which they can move in all directions) imply familial ties with the elephant, their closest relatives are actually the horse and rhinoceros families.

The Baird's tapir has a distinctive cream-colored marking on its face, throat, and tips of its ears, with a dark spot on each cheek, behind and below the eye. The rest of its hair is dark brown or grayish brown. Females are larger than males and body mass in adults can range from 150 to 400 kilograms.

According to the IUCN, the Baird's tapir is endangered. There are two main contributing factors in the decline of the species; poaching and habitat loss. Though in many areas the animal is only hunted by a few humans, any loss of life is a serious blow to the tapir population because their reproductive rate is so slow. In Mexico, Belize, Guatemala, Costa Rica, and Panama, hunting of the Baird's tapirs is illegal, but the laws protecting them are often unenforced. Furthermore, restrictions against hunting do not address the problem of deforestation. Therefore, many conservationists focus on environmental education and sustainable forestry to try to save the Baird's tapir and other rainforest species from extinction.

Prior to the beginning of the Lowland Tapir Conservation Initiative (LTCI), little was known about the health of their populations or the places where they lived. The Houston Zoo has provided funding and support for their wild tapir satellite-collar and camera-trapping studies across the region. From these studies, they have learned that the Pantanal is the most important stronghold for the species so the Houston Zoo is supporting LTCI’s work with Brazilian landowners, schools, and the media to increase public interest and understanding of tapirs and involving them in conservation efforts.

Today, we share the chromosome-length genome assembly for the Baird's tapir, Tapirus bairdii! The genome assembly scaffolded to (2n=80) chromosomes was generated using samples provided by Noah the tapir living at the Houston Zoo. Read more about Noah and his partner Moli in this blog post by the Houston Zoo. Recently they have welcomed their first baby. Cogratulations!

This is a $1K genome assembly, generated from a draft assembly with short-insert size Illumina reads [266,035,705 PE reads] and scaffolded to chromosome length genome with Hi-C [186,199,173 PE reads]. See our Methods page for more details on the procedure. Check the interactive map of the 40 chromosomes,(2n= 80), of the Baird's tapir below!

This is the third tapir species we've released here on the DNA Zoo. Check out the assembly pages for the South American tapir, T. terrestris (2n=80), and the Malayan tapir, T. indicus (2n=52).

We gratefully acknowledge Pawsey Supercomputing Centre and DNA Zoo Australia team at the University of Western Australia for computational and analyses support for this genome assembly.

Blog post by Parwinder Kaur