Sei to shining sei

Sei whales (Balaenoptera borealis) are part of the group of toothless whales Myticeti or baleen whales. Fast swimming (up to 50 km/h (31 mph)) Sei whales live across all oceans traveling long distances alone or in small groups and sometimes foraging in large herds. R.C. Haldane called Sei whale the “most graceful of all whales”. These slender giants with dark grey back can reach 20,000 kg and up to 20 meters in size and live up to 70 years. The baleen whales became such giants recently, about 3 millions years ago, due to favorable ocean conditions. Sei whales do not like to dive deep, only to about 300 meters. They mostly are sinking below the water surface and not arching the back like many other whales. A small group of baleen whales - Balaenoptera, including Sei whale, developed a large throat pouch that is decorated by nice throat grooves that can be seen on the pale bottom side of the whale when the whale jumps out of the water.

Sei whale (Balaenoptera borealis) mother and calf as seen from the air, public domain image by Christin Khan, NOAA / NEFSC, via commons.wikimedia.org

For a long time, cetaceans have been thought to have either an extremely limited sense of smell or none at all. More recently some members of baleen whales have been shown to have the necessary "hardware" to smell. They did loose their teeth though (the teeth buds do form in utero but do not develop). Instead baleen whales acquired complex filter-feeding mechanism. Baleen plates (formed by highly flexible keratin, think our nails and hair) are hanging from the roof of the mouth and retain the plankton, small fish, squids efficiently filtering the water gulped by whales and assembling tasty ocean-food for swallowing. Sei whales enjoy skim-feeding by traveling near the water surface with the open mouth. When the luck brings the school of fish the Sei whale happily engulfs large volumes of fishy water at once and swallows fish without chewing. Interestingly the tongue in baleen whales is greatly reduced. Sei whales consume 900 kg (2,000 lb) of food every day to nourish their giant body!

Sei whales were almost hunted to the extinction with over 300,000 whales killed by humans in 20th century. At some point the population of Sei whale was estimated to be only few thousands in each hemisphere. Multiple conservation efforts and protection laws allowed to stop the decline. Currently Sei whale is an endangered species and the commercial whaling of Sei is prohibited worldwide since 1986. Mass beaching (up to 300 whales) of Sei whales occasionally happens presumably due to toxic algae growth in subtropical waters. Killer whales, damaging ship encounters, diseases and internal parasites are other causes of Sei whale deaths. Current population of Sei whales is estimated to be about 65,000 - 80,000 and not showing bottleneck effects.

The migration patterns and reproduction are topics where we have very little information about Sei whales. Sei whales “speak” low-frequency pulse language. Lucky observers may hear Sei whale singing during breeding season.

Today, we release the chromosome-length genome assembly for the Sei whale, Balaenoptera borealis! This assembly follows the short-read data model, for more information please see our Methods page. The assembly was done from primary fibroblasts established from a skin sample provided by Charlie Potter, Smithsonian Institution, Washington, DC, US, in May 1989 from a whale stranded on the Atlantic coast of the USA. The primary fibroblast cell line (BBS-1) was established by Mary Thompson at the Laboratory of Genomic Diversity led by Dr. Stephen O’Brien. We acknowledge Drs. Melody Roelke-Parker, Carlos Driscoll, Christina Barr, David Goldman and Stephen Lindell for preservation of the cell line collection. The passage 4 was used to make the sequencing libraries.

Browse the 22 assembled chromosomes of the Sei whale in the interactive Juicebox.js session below. The count is consistent with the established karyotype (2n=44, W. Nash, Atlas of Mammalian chromosomes, 2020, p. 729).

References:

1. Gatesy J, Geisler JH, Chang J, Buell C, Berta A, Meredith RW, Springer MS, McGowen MR. A phylogenetic blueprint for a modern whale. Mol Phylogenet Evol. 2013 Feb;66(2):479-506.

2. Graphodatsky AS, Perelman PL, O’Brien SJ. Atlas of mammalian chromosomes. 2nd ed. Wiley-Blackwell; 2020. pp. 727-732

3. Horwood, Joseph. Sei Whale: Balaenoptera borealis, Eds: William F. Perrin, Bernd Würsig, J.G.M. Thewissen, Encyclopedia of Marine Mammals (Second Edition), Academic Press, 2009, Pages 1001-1003, ISBN 9780123735539.

4. Kulemzina AI, Proskuryakova AA, Beklemisheva VR, Lemskaya NA, Perelman PL, Graphodatsky AS. Comparative Chromosome Map and Heterochromatin Features of the Gray Whale Karyotype (Cetacea). Cytogenet Genome Res. 2016;148(1):25-34.

5. Slater GJ, Goldbogen JA, Pyenson ND. Independent evolution of baleen whale gigantism linked to Plio-Pleistocene ocean dynamics. Proc Biol Sci. 2017; 284(1855):20170546.

Getting off on the black foot

Black-footed ferrets (Mustela nigripes) once occupied much of the grasslands of the North American Great Plains. Starting in the 19th century, however, this habitat diminished due to its conversion to croplands and pastures for agriculture, which in turn decimated the prey base that the ferrets relied upon, particularly their preferred prey, prairie dogs. In addition, diseases such as sylvatic plague also caused populations of black-footed ferrets to decline. Due to these declines, black-footed ferrets were listed as endangered in the USA in 1967 but then eventually presumed extinct in 1979.

Capone, the black-footed ferret. Photo credits: Paul Marinari (NZCBI). Image provided by Klaus-Peter Koepfli.

Fortunately, in 1981 a single, small population of ferrets was discovered near Meeteetse, Wyoming. The last surviving individuals of this group were used to start an ex-situ captive breeding program through the coordination of the U.S. Fish & Wildlife Service and multiple Association of Zoos & Aquariums (AZA) zoos. As a result of these joint efforts, a species recovery plan was developed and implemented for what continues to be one of the most ambitious conservation breeding and reintroduction program in North America, with more than 10,000 black-footed ferret kits having been born since 1986. Today, about 650 ferrets are living either in captivity or in the wild.

Despite these successes, black-footed ferrets still remain at risk of extinction due to disease susceptibility and multiple genetic challenges that may be related to the small number of founders (only 7) that were used to initiate the conservation breeding program. Previous studies using traditional genetic markers have shown that modern black-footed ferrets have low genetic variation. Further analyses using genomic data will provide a more in-depth view of genetic erosion, inbreeding levels, and mutational load, all of which can affect fitness. Black-footed ferrets are also the focus of ongoing efforts to support the species’ recovery through biotechnology tools such as interspecies somatic cell nuclear transfer, which led to the first female cloned black-footed ferret, ‘Elizabeth Ann’ (Wisely et al., 2015). Such studies are greatly facilitated by generating and using an annotated reference genome assembly (Formenti et al. 2022).

Today, we release the chromosome-length assembly of a male black-footed ferret named ‘Capone’ that came from the ferret conservation breeding colony at the Smithsonian’s National Zoo and Conservation Biology Institute in Front Royal, Virginia. Capone was selected because this animal is partly descended from the last wild-caught male in Meeteetse, WY. The draft assembly was generated using a combination of 10X Genomics linked-reads, done at HudsonAlpha Discovery in Huntsville, Alabama, and optical mapping data generated by Bionano Genomics in San Diego, California. The draft was then upgraded to chromosome-length using Hi-C data generated by the DNA Zoo team. We are already using this assembly for in-depth studies on the conservation genomics of this iconic species.

The assembly contains 19 chromosome-length scaffolds, consistent with the 2n=38 karyotype. This differs from the 2n=40 of a closely related domestic ferret M. putorius furo. The difference is due to the largest chromosome in the black-footed karyotype (HiC_scaffold_1 in the musNig1_HiC assembly) corresponding to two separate chromosomes in the domestic ferret. Browse this chromosomes and and the remaining 18 of them in the interactive Juicebox.js session below, and don't forget to check out the corresponding assembly page.

Blog post by Sergei Kliver, Paul Marinari, and Klaus-Peter Koepfli.

Hoppy new year!

Happy Year of the Rabbit everyone! To celebrate, we share the chromosome-length assembly of the New England cottontail, Sylvilagus transitionalis, the only rabbit native to parts of New England and eastern New York.

The New England cottontail, Sylvilagus transitionalis, was once a widespread rodent across the North East. However, as their preferred habitat of forest thickets declined due to urban development, so did the wild population of the New England Cottontail. Today, biologists believe there are only around 13,000 New England cottontails left. Read more about efforts to restore the New England cottontail on https://newenglandcottontail.org/.

New England cottontail rabbit by Steve McDonald, [CC BY 2.0], via flickr.com

New England cottontails are medium-sized rabbits that look a lot like eastern cottontails except for the fact that they have black hair on the front side of the ears and between their ears (appropriate for the Year of the Black Rabbit!). Females are larger than males. And it was a female sample that we received via the T.C. Hsu CryoZoo from the M.D. Anderson Cancer Center, originally frozen back in 1979! Using the sample, we generated a short-read genome assembly (contig N50 = 24Kb, scaffold N50 = 79Mb).

Browse the 23 chromosomes of the New England cottontail, Sylvilagus transitionalis in the interactive Juicebox session below, and find more information and links on the corresponding assembly page!