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).

Bearded seals, they grown on you

The bearded seal (Erignathus barbatus) gets its name from the long white whiskers on its face. These whiskers are very sensitive and are used to find food on the ocean bottom. Bearded seals inhabit circumpolar Arctic and sub-Arctic waters that are relatively shallow (primarily less than about 1,600 feet deep) and seasonally ice-covered. In U.S. waters, they are found off the coast of Alaska [1], which is where the specimen behind this blog post came from.

Bearded seals are closely associated with sea ice, particularly pack ice. As such, they are sensitive to changes in the environment that affect the annual timing and extent of sea ice formation and breakup. Fun fact, bearded seals can sleep vertically in open water with their heads on the water surface! Like all marine mammals, bearded seals are protected under the Marine Mammal Protection Act. [1]

Today, we share the chromosome-length genome assembly for the bearded seal. The draft assembly was generated by the DNA Zoo team from short insert-size PCR-free DNA-Seq data using w2rap-contigger (Clavijo et al. 2017), see (Dudchenko et al., 2018) for details. Work was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03 issued by the National Marine Fisheries Service (NMFS) under the authority of the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The specimen used in this study was collected by Louis Binderman and provided by the National Marine Mammal Tissue Bank, which is maintained by the National Institute of Standards and Technology (NIST) in the NIST Biorepository, and which is operated under the direction of NMFS with the collaboration of USGS, USFWS, MMS, and NIST through the Marine Mammal Health and Stranding Response Program and the Alaska Marine Mammal Tissue Archival Project. We thank Ben Neely for his help with this sample!

This is the third earless seal genome (Phocidae) in the DNA Zoo collection after the harbor seal (Phoca vitulina) and the Northern elephant seal (Mirounga angustirostris). We have already made an observation, that the earless seal genomes appear to be very similar to each other, see here. In support of this analysis, see below how the new earless seal genome assembly compares to the harbor seal genome. Once again, the genomes appear to be identical up to chromosome #2 in the harbor seal which appears as two separate chromosomes in the bearded seal (#4 & #1).

Whole genome alignment plot between the genome assemblies of the harbor seal (GSC_HSeal_1.0_HiC) and the bearded seal (Erignathus_barbatus_HiC).