Whale, whale, whale

The humpback whales (Megaptera novaeangliae) are one of the larger rorquals, members of the Balaenopteridae family that includes the blue, fin, Bryde's, sei and minke whales. Humpback whales are famous for breaching and showing their tails when they dive. This dramatic sight makes them very popular with whale watchers!

Humpback whale wild head photo © Bill Hunnewell

There are different theories as to how humpback gets its name as some say its because they have a distinct hump in front of their small dorsal fins whereas others say that the name comes from the hump that forms when they arch their back when diving.

They have dark backs ranging in color from dark grey to blue-black, and paler bellies (some completely white, some more mottled). Humpbacks have distinctive knobby heads and jaws, long flippers and broad tail flukes. They can grow to around 15 meters in length and weigh up to 30 tonnes with female humpback whales usually being larger than males.

Humpbacks are known for their long-distance migrations. At the start of winter, humpback whales migrate north past New Zealand to the tropical South Pacific, where they mate and give birth. At the end of winter, they travel back towards Antarctica. The trips between feeding and breeding grounds can cover distances of 8,000 kilometers and more. Researchers have recorded individual whales swimming for as many as nine weeks non-stop!

Like other large whales, the humpback was a target for the whaling industry. The species was once hunted to the brink of extinction; its population fell by an estimated 90% before a 1966 moratorium. While numbers have partially recovered to some 80,000 animals worldwide, entanglement in fishing gear, collisions with ships and noise pollution continue to affect the species. Currently, it is listed as endangered on the red list of IUCN.

The chromosome-length assembly was generated using a skin sample provided to us by Barbie Halaska, Necropsy Manager at The Marine Mammal Center in Sausalito, California. As the world’s largest marine mammal hospital, the Center generates research findings and scientific outputs at volumes similar to top academic institutions. In addition, the Center serves as a resource and thought leader in animal care, education and scientific communities.

Humpback whale, Baker Beach San Francisco. Credit Barbie Halaska © The Marine Mammal Center

This is a $1K-strategy genome assembly with the short-insert draft generated using w2rap contigger (Clavijo et al. 2017) and Hi-C-scaffolded using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details, and check the interactive contact map of the humpback whale’s 22 chromosomes below! Special thanks to Pawsey Supercomputing Centre and DNA Zoo Australia team at the University of Western Australia for computational and analyses support of the upgrade.

This sample was collected by The Marine Mammal Center under the Marine Mammal Health and Stranding Program (MMHSPR) Permit No. 18786-04 issued by the National Marine Fisheries Service (NMFS) in accordance with the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The work at DNA Zoo was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03.

We thank Barbie Halaska and Ben Neely for their help with this genome assembly. Learn more about the impact of The Marine Mammal Center’s scientific research by visiting the Center’s website at MarineMammalCenter.org!

Blog post by Parwinder Kaur, with contributions from Daniel Lim, Giancarlo Rulli and Barbie Halaska

Oh my cod

We’re excited to announce that Australia’s largest freshwater fish, the iconic Murray cod (Maccullochella peelii), has been added to DNA Zoo’s genomic database.

The Murray cod is one of Australia’s most iconic fish; a freshwater species that can grow to ∼1.8 metres in length, weigh more than 100 kilograms and live to ≥48 years old. This species is of conservation concern as it has undergone strong population contractions in the last century. It is also popular for recreational fishing and is of growing interest to the aquaculture industry.

Photo Description - Murray cod (Maccullochella peelii). Photo credits - Guo Chai Lim [CC BY-NC-ND 2.0], via flickr.com

The story of the Murray cod is not much different to that of most Australian endangered species. Due to its previous abundance, the cod was commercially fished from the early years of European arrival. Changes to its natural habitat and competition from introduced fish species have also had a big impact on Murray cod numbers declining.

The Murray cod inhabits the Murray-Darling Basin, which spreads through New South Wales, South Australia, Queensland, the Australian Capital Territory, and Victoria. Thousands of interconnected creeks and rivers run through the basin and below it you’ll find a complex system of aquifers and groundwater.

Also known as 'pigs of the waterways,' Murray cod are highly aggressive and territorial. They'll also eat almost anything that gets in their way; fish make up the majority of the diet of mature Murray cod, but they have also been known to eat ducks, cormorants, freshwater turtles, water dragons, snakes, mice and frogs.

The chromosome-length assembly we are releasing today is based on the draft assembly by Austin et al., 2017 generated using Illumina and Nanopore sequencing approach. This draft was scaffolded to 24 chromosomes with 20,178,257 PE Hi-C reads generated by DNA Zoo labs using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). You can find more details on our Methods page, and check out the interactive Hi-C contact map or the 24 chromosomes below!

The sample for Hi-C was kindly provided by David Carter and Dylan Skinns, CEO and General Manager of Sales and marketing respectively, from Austral Fisheries Pty Ltd. The Hi-C work was supported by resources provided by DNA Zoo Australia, The University of Western Australia (UWA), La Trobe University team with funding from the Australian Research Council (DE190100636). We gratefully acknowledge the computational support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.

Murray cod, once listed as 'Critically Endangered' on the International Union for Conservation of Nature's Red List has been upgraded to 'Of Least Concern' as numbers increase. They're still however listed as 'Vulnerable' under the Environmental Protection of Biodiversity and Conservation Act. According to some estimates, cod numbers have been as low as 10% of those that existed before European settlement.

The cod has moved from being considered as a plentiful source of food to an important but threatened part of the Murray-Darling ecosystem. We hope the chromosome-length genome assembly resource for the Murray cod supports ongoing population genetics, conservation and management research; as well as assisting with better understanding the evolutionary ecology and history of the species.

Toujours l'emur

The common name for Eulemur collaris, is debatable. They're sometimes known as the red collared lemur, the collared brown lemur, or even a combination of the two, the red collared brown lemur. This name debate potentially comes from the notable sexual dimorphism between the male and female individuals. The male lemurs are brownish-gray with a dark stripe of fur down their backs whereas females have reddish to brown bodies and a gray face. Both have the same striking red-orange eyes. [1].

Collared Brown Lemur (Eulemur collaris) by jadonald, [CC-BY-NC], via iNatrualist.org

Unlike most lemur species, the collared lemur is not female dominant and shows no clear dominance hierarchy. They are a sociable species and live in groups ranging from 3-12 individuals. Larger groups can form based on food availability [2]. However, the costal forests in Madagascar they call home have become more fragmented due to slash and burn agriculture and charcoal production. The collared lemur is now considered endangered in the wild but there are successful breeding populations in captivity. Conservationists hope they can reintroduce these populations back into the wild as they play an integral role as seed dispersers in their ecosystems [3].

Today, we release the genome for the collared lemur, Eulemur collaris)! This is a $1K genome assembly with a contig N50 = 44 Kb and a scaffold N50 = 110 Mb (browse the map below). For assembly procedure details, please see our Methods page. Many thanks to the Duke Lemur Center for providing the sample used for this genome assembly! Consider symbolically adopting a lemur here, to support animal care at the Duke Lemur Center as well as conservation programs in Madagascar.

This is the 5th lemur species we've released here on the DNA Zoo! Check out the assembly pages for these fascinating primates, Blue-eyed black lemur (E. flavifrons), Mongoose lemur (E. mongoz), Gray mouse lemur (M. murinus), and finally the Coquerel's sifaka (P. coquereli). There's more lemur species to come, so make sure you're subscribed to our mailing list to ensure you don't miss our latest releases!