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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

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

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!

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