A sharp looking genome

North American porcupine is a large rodent in the New World porcupine family. There are only three genera in this family: Erethizon, Chaetomys and Coendou. Recently we assembled the Brazilian porcupine Coendou prehensilis, one of 16 species from the tree porcupines (Coendou) genus.

Today, we share the chromosome-length assembly for the North American porcupine Erethizon dorsatum, the only member of the Erethizon genus. This genome assembly is based on the draft generated by Canada’s genomic enterprise, shared here. We thank Houston Zoo’s North American porcupine Ernie for the sample used for Hi-C library preparation!

Check out below how the 21 chromosomes of the new North American porcupine genome assembly relate to those of the Brazilian porcupine. Despite the animals being relatively close relatives, with only 10 million years since the species diverged [1], the karyotypes are rather different, with a lot of chromosome breaks in the Brazilian porcupine as compared to the North American one (North American porcupine chr 2 corresponds to chr 3 and 14 in the Brazilian porcupine; chr 3 to chro 33 and 37 etc.). Compare this to the last 10 million years of cat nap!

Left: whole genome alignment plot between the new assembly for the North American porcupine (GSC_porc_1.0_HiC) and the chromosome-length assembly for the Brazilian porcupine (Coendou_prehensilis_HiC). Right: same plot for the clouded leopard (Neofelis_nebulosa_HiC) and domestic cat (Felis_catus_8.0) genome assemblies. Despite the fact that the pairs of species on the left and the right plot are separated by the same evolutionary distance (~10MY), multiple large-scale chromosomal events have left their trace in the New World porcupine lineage while the feline karyotype remained essentially unchanged.

Hoot of the presses

In the 1990s the spotted owl Strix occidentalis was catapulted into the spotlight over logging debates in the US Pacific Northwest. Despite federal protection beginning in 1990, the owl is still declining in the Northwest owing to habitat loss, fragmentation, and competition with barred owls [1].

In collaboration with a team led by Zach Hanna (UCSF), Jack Dumbacher (California Academy of Sciences), Michal Levy-Sakin (Dovetail Genomics), Rauri Bowie (UC Berkeley), Pui Kwok (UCSF) and Jeff Wall (UCSF), we are today happy to share a chromosome-length genome assembly for the spotted owl.

Below is our standard comparison between the newly assembled genome for the spotted own and the domestic chicken genome assembly (by the International Chicken Genome Sequencing Consortium). Though not quite as dramatic as those seen in the golden eagle, we do see a number of karyotypic rearrangements, including the breakage of chicken chr #1 (forming owl #6 and #2) and the fusion of chicken #4 and #5 (creating #3 in spotted owl).

Whole genome alignment between the chromosome-length genome assembly of the spotted owl (Strix_occidentalis_HiC) and the chicken genome assembly (GRCg6a).

Cloudy with a chance of leopards

It is estimated that fewer than 10,000 clouded leopards (Neofelis nebulosa) remain in the wild [1].

Almost everything we know about clouded leopards comes from research on captive populations, much of it done by the Smithsonian's National Zoo, Khao Kheow Open Zoo in Thailand, The Zoological Parks Organization of Thailand and Nashville Zoo. Read more (and see how you can help) on the Smithsonian’s National Zoo & Conservation Biology Institute website, here!

To help with the ongoing conservation efforts, in collaboration with our colleagues from the Smithsonian Conservation Biology Institute and the Brigham Young University, we share the chromosome-length genome assembly for the clouded leopard. We thank the Houston Zoo for providing the sample used for Hi-C library preparation!

The draft genome assembly for the clouded leopard was generated by Paul Frandsen and Madeline Bursell at Brigham Young University in collaboration with Warren Johnson and Klaus-Peter Koepfli at the Smithsonian Conservation Biology Institute, and Rebecca Dikow from the Smithsonian Institution Data Science Lab. The draft assembly was generated using MaSuRCA.

See below how the 19 chromosomes of the clouded leopard assembly relate to those of domestic cat (from Pontius et al., Genome Res., 2007). A nice illustration of the highly stable felid karyotype across the ~10.8 million years of cat evolution [2]!

It is interesting to note that our scaffolding revealed a huge, 78Mb inversion on one (not both!) of copies of chromosome 2 in the animal whose genomic material was used for scaffolding. (This chromosome corresponds to cat chromosome 8). The zoo keepers believe the animal to be healthy. By contrast, we found no evidence of the inversion in the leopard used for contigging.

While these types of polymorphic rearrangements have been observed in some mammalian species, this is the first time one has been reported in the cat lineage. We hope to look into this rearrangement and its prevalence in the clouded leopard population further, so stay tuned!

Whole-genome alignment between the new clouded leopard genome assembly (Neofelis_nebulosa_HiC) and the genome assembly of the domestic cat (Felis_catus_8.0) (left); rearrangement on one of the copies of chr2 (cat homolog chr8) (right). A leopard may not be able to change its spots, but it sure can change its dot plots!