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.

The right whale to save

Today, we release the genome of one of the most endangered whale species, the North Atlantic right whale Eubalaena glacialis.

The North Atlantic right whale is a large baleen whale historically found near the coast of the western and eastern North Atlantic [1]. They can reach roughly 52 feet (16 m) long and 70 tons (60,000 kg), and may still be seen from the Labrador Sea to the coast of South Carolina, Georgia and Florida [2]. They are readily distinguished from other cetaceans by the absence of a dorsal fin on their broad back.

Their name is derived from being the "right" whale for whalers to easily harvest. Hundreds of years of whaling along with continued human interaction has reduced the population to less than 400 whales, making the North Atlantic right whale one of the world’s most endangered large whale species. It is one of four marine mammals in NOAA's Species in the Spotlight, with more information here and here. We hope that this genome can help ongoing research efforts and highlight the plight of this species.

This is the second baleen whale (Mysticeti) genome in the DNA Zoo collection after the Bryde’s whale Balaenoptera edeni. See below the whole-genome alignment plots to see how karyotypes of the two species (2n=44 for the Bryde’s whale and 2n=42 for the NA right whale) relate to each other. Both genome were generated following the $1K strategy described in (Dudchenko et al., 2018).

Whole-genome alignment plots between the genome assemblies of the North Atlantic right whale (Eubalaena_glacialis_HiC) and the Bryde’s whale (Balaenoptera_edeni_HiC). The genomes are highly syntenic with chromosome #20 in the right whale corresponding to two separate chromosomes in the Bryde’s whale (#18 and #16).

This 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 NOAA (T. Rowles and B. Bonde) from Amelia Island, Florida, USA. The specimen was provided by the National Marine Mammal Tissue Bank, which is maintained by the National Institute of Standards and Technology (NIST) in the NIST Biorepository, 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.

Fintastic beasts and where to find them

We celebrate the World Marine Mammal Conference held in Barcelona this week by releasing three new chromosome-length marine mammal genome assemblies: for the harbor porpoise (Phocoena phocoena), here; the long-finned pilot whale (Globicephala melas), here; and the melon-headed whale (Peponocephala electra), here.

The long-finned pilot whale assembly is an upgrade based on the draft generated by the Canada’s Genomic Enterprise. The harbor porpoise and the melon-headed whale are the $1K-model DNA Zoo genomes, see (Dudchenko et al., 2018) for details. The samples used for this work were received from the National Marine Mammal Tissue Bank maintained by the National Institute of Standards and Technology (NIST) in the NIST Biorepository.

The harbor porpoise (Phocoena phocoena) is one of six species of porpoise, commonly observed inhabiting coastal areas of Asia, North America, Europe and Africa (the individual assembled by the DNA Zoo came from Homer, Alaska). The name ‘porpoise’ derives from the Latin word ‘porcus’, which means hog and ‘piscis’ meaning fish, literally meaning sea pig. (Interesting since pigs and cetaceans are both even-toed ungulates. The latin name, Phocoena phocoena, on the other hand, means ‘big seal’, which is a pinniped in the distantly related carnivora order...) The harbor porpoise is roughly the size of a human, with a dark gray back, intermediate shades of gray along their sides, white belly and a white throat with a gray chin patch. The most apparent difference between a harbor porpoise and dolphin is that the harbor porpoise has no beak, a smaller, less curved dorsal fin, and small pointed flippers.

Image by skeeze from Pixabay [Pixabay License], via pixabay.com

The long-finned pilot whale (Globicephala melas), named for its unusually long pectoral fins, is a toothed whale approximately 20 feet long that mainly eats soft squid. They are social creatures that have at times formed groups of up to a thousand animals. They prefer the deep temperate to subpolar oceanic waters of the North Atlantic and southern Pacific (the individual assembled by the DNA Zoo came from the North Atlantic).

Pilot whale spyhop, photo by Barney Moss [CC BY 2.0 (https://creativecommons.org/licenses/by/2.0)], via Wikimedia Commons

The melon-headed whale (Peponocephala electra) is also a toothed whale, but is small to medium sized at about 10 feet long. These whales prefer deep tropical/subtropical waters across the globe (the individual assembled by the DNA Zoo came from Hawaii). Similar to pilot whales, these whales can form groups of up to 1000 individuals. Studies have shown that they maintain a matrilineal structure such that females remain in groups with their mothers, whereas males move between groups (similar to some killer, sperm and pilot whales).

NOAA/Andrea Bendlin MMPA#15240

Like all marine mammals, the melon-headed whale, the long-finned pilot whale and the harbor porpoise are protected under the Marine Mammal Protection Act.

This 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 specimens used in this study was collected by: Carol A. Stephens (harbor porpoise; Homer, Alaska), the New England Aquarium (Belinda Rubenstein; long-finned pilot whale; Brewster, Breakwater Beach, Massachusetts) and the Hawaii Pacific University (Kristi West; long-finned pilot whale; Kahului, Hawaii). Specimens were provided by the National Marine Mammal Tissue Bank, which is maintained by the National Institute of Standards and Technology (NIST) in the NIST Biorepository, 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.

Along with the research highlighted this week at the World Marine Mammal Conference, we hope that the continued generation of high-quality genome assemblies will help advance the marine mammal science and conservation efforts. If you have specimens that you can share make sure to reach out, and stay tuned for more marine mammal genome assemblies coming out in the next few weeks on the DNA Zoo website!