Anotter day, anotter genome

The North American river otters (Lontra canadensis) are extremely adaptable to their environments, which explains their wide range of habitats across the North American continent. Hot or cold, low or high elevations, these semi-aquatic mammals can be found in most waterways. Even more, they don’t let the “river” in their name limit them, these otters are happy to also take up residence in lakes, ponds, and marshes [1].

Otter-able, by Valerie [CC BY-NC-ND 2.0], via flickr.com

In the early 19th and 20th century, river otters were trapped and traded for their valuable fur. As the fur trade declined, North American river otters’ populations have increased and stabilized with the help of reintroduction programs [2]. Today, their habitats in some areas are still under threat of destruction and water pollution.

These otter-ly adorable animals are well-known for their playful antics. Though amusing to watch, chasing and wrestling are thought to be an integral part of teaching survival skills to their young. North American river otters are often seen sliding down, rolling around, and rubbing themselves onto surfaces. While it may look silly, this behavior is a way to mark their territory, as their scent glands are located near the base of their tails.

Interestingly, whether the North American river otter is loyal to one significant otter or if they see otter-people, is still up for debate. Some research indicates that otters may mate for life with one partner, while other studies have identified polygamy among river otter populations [3].

Today, we are releasing a chromosome-length genome assembly for the species. This is an upgrade for the genome generated by the Canada’s Genomic Enterprise (available here). The sample for the Hi-C upgrade was donated by Belle, a female North American river otter living at the Houston zoo.

This is the fifth member of the weasel (Mustelidae) family in our collection. See below how the new genome compares to the Eurasian otter Lutra lutra. We generated the Eurasian otter genome assembly together with the Wellcome Sanger Institute and shared it a blog post from October, here. A formal paper describing this assembly is now out, read it here!

Whole genome alignment plot between GSC_riverotter_1.0_HiC, the new chromosome-length genome assembly for the North American river otter, and mLutLut1.1, the chromosome-length Eurasian otter genome assembly.

Fangtastic assembly

Meet the Northern Long-eared bat, Myotis septentrionalis (pronounced "my-oh-tis sep-ten-tree-oh-nal-is"). You may be forgiven for not recognizing the particular name, as it's also been known as the Northern bat ('septentrionalis' means "of the north"), and was previously assigned a different taxonomy (formerly a Mytois keenii subspecies). Rest assured, regardless of the nomenclature confusion, there is no mistaking this amazing bat with those distinctive long ears!

Northern Long-eared Bat, by Brookhaven National Laboratory [CC BY-NC-ND 2.0], via flickr.com

The Northern Long-eared bat shares many features with other species of other North American Myotis: these are fairly small bats with a body mass between 5-8 g, a body length of about 50 mm. The Northern's wingspan of about 200 mm is among the largest for a bat its size, and it has been suggested that the larger wing area coupled with a relatively longer tail are adaptations enabling foraging for insects occupying interior forest areas (whereas other North American Myotis bats generally forage in more open areas). And don't forget about the ears - it's likely that the extra surface area comes in handy when feeding in dense forests while stationed on a tree (known as "gleaning"). This foraging strategy is a distinctive behavior of these bats, though it can also can capture it's prey in flight (known as "aerial foraging") like other Myotis species. It's a stealthy eater too: the Northern Long-eared is able to emit an ultrasonic call to identify moth prey items that are nearly undetectable by the moth itself.

Despite a broad historic range spanning the boreal forests across Canada through eastern and north central United States, the Northern Long-eared bat is currently listed as a federally Threatened species under the Endangered Species Act [1]. Massive population declines are due primarily to a fungal pathogen causing White-nose Syndrome, a disease that has impacted many North American bats. In a grim twist of fate, these bats were previously so ubiquitous that there was little investment in understanding their natural history, thus detailed historical records regarding their ecology and behavior is limited. They have always been a tricky species to locate because they are much more solitary bats than other North American species.

In warm months these bats prefer snags tree hollows rather than more visible human structures like bridges and attics that other species like the Little Brown bat (Myotis lucifugus) or Big Brown bat (Eptesicus fuscus) are often detected. They spend the winter hibernating in caves like other North American bats, but prefer to hide in smaller crevices of instead of gathering in larger congregations. They might prefer the longest of winter naps, spending some of the longest hibernation periods of any Myotis, but they are frequently on the move in the summer with mothers moving their pup throughout the forest every 2-14 days.

Today, we share the chromosome-length genome assembly for the species. Contigging for this assembly was performed by Devon O'Rourke, Matt MacManes and Jeff Foster. Oxford Nanopore R9 flowcells were used to generate the initial raw data (5818511 total reads; 29116606101 total bases ; 8882 read length N50) from a single female adult specimen collected from West Tisbury, MA. These data were then basecalled with Albacore, reads trimmed with Porechop, and assembled into contigs with Flye (17,268 contigs, 1,998,235,525 bp, N50 217932). Illumina 150 bp PE reads were used to polish the scaffolds using three rounds of Racon and one round of Pilon. A second bat, a juvenile male, from Oak Bluffs, MA, was used for Hi-C data generation. This is the sixth chromosome-length bat genome assembly at the DNA Zoo, and the most contiguous genome assembly for common bats currently available!

Both bat specimen used for generating this assembly were collected thanks to Luanne Johnson, Director/Wildlife Biologist at BiodiversityWorks, who coordinated with the residents of the Martha's Vineyard island to make this project possible.

Despite over 1200 bat species throughout the world, only a few dozen genomes are currently available. We hope this contribution will enhance conservation management efforts that had previously relied on an alternative species (Myotis lucifugus) for population genetic investigations.

P.S.: We hear you fellow chiropterologists - bats don't have fangs, but the title was too fun!

And now for something otterly different!

The giant otter (Pteronura brasiliensis) is the largest of all otter species. (The largest recorded size is 2.4 meters!) These amphibious mammals are very social and live in groups of up to 20 members. They are also the noisiest of all otter species, with 22 distinct types of vocalizations. [1]

Giant otters can be found in the rivers of the Amazon basin hunting mainly for fish, but sometimes taking on larger animals like the anaconda and caiman. Even though these mammals may prey on some very formidable foes, that doesn’t mean they don’t have a soft side. Due to their good looks, otters enjoy quite the fan base online. Hundreds of photos and videos have been shared of these quirky animals on dedicated reddit pages.

The giant otter has been listed as endangered by the IUCN Red List due to habitat contamination, overfishing of prey, and infrastructure interference. The current population of giant otters is therefore fragmented and relatively small. The International Otter Survival Fund (IOSF) has been set up to help protect the 13 species of otters worldwide, including the giant otter, and help this unique family of mammals. Today, we are releasing a de novo genome assembly for the giant otter generated using our $1K model (see Dudchenko et al., 2018 for details). The samples used in this assembly come from the pair of giant otters Ella and Dru living at Moody Gardens, Galveston, TX. That’s them in the photos below!

Ella was captive born at the Philadelphia Zoo in 2008, she is the older sister to Dru who was captive born at the Philadelphia Zoo in 2009. All captive giant otters are owned by the Brazilian government and Moody Gardens work together with other AZA zoos in a cooperative management program to ensure long-term sustainability of the giant otter population.

Giant otter Dru. Photo credit: Moody Gardens. All otters have a distinct throat patch markings, notice Dru’s!

Giant otter Ella. Photo credit: Moody Gardens. Ella’s throat patch markings are almost non-existent, with mostly brown on her throat.

We thank Paula Kovig and Karen Holcroft for their help with the samples used for this genome assembly!

This is the forth genome assembly in the Mustelidae (weasel) family in our collection, after the sea otter Enhydra lutris, here, the Eurasian otter Lutra lutra, here, and the domestic ferret Mustela putorius furo, here. See how the Mustelidae assemblies relate to each other on the whole genome alignment plot below.

Whole genome alignment plots for Mustelidae assemblies at the DNA Zoo: the giant otter (Pteronura_brasiliensis_HiC), the sea otter (ASM228890v2_HiC), the Eurasian otter (mLutLut1.1), and the domestic ferret (MusPutFur1.0_HiC).