Tetraploid peanut genome assembly published in Nature Genetics

Recently, the DNA Zoo collaborated with the International Peanut Genome Initiative to create a chromosome-length reference for the cultivated peanut. This is the first tetraploid genome assembly in our collection!

This paper was published in Nature Genetics. We are grateful to our many collaborators from the University of Georgia, Hudson Alpha Institute of Biotechnology, Instituto de Botánica del Nordeste (CONICET-UNNE), Iowa State, National Center for Genome Resources, LGDP, LG Chem, Université de Montpellier, Embrapa Genetic Resources and Biotechnology, Kazusa DNA Research Institute, National Institute of Plant Genome Research, Agricultural Research Service, Industrial Crops Research Institute, Laboratory of Oil Crops in Huanghuaihai Plains, UC Davis Genome Center, Department of Energy Joint Genome Institute, USDA, and especially to our colleagues at ICRISAT for providing the sample and collaboration on the Hi-C analysis and scaffolding.

Today, we release the latest version of the chromosome-length tetraploid peanut genome assembly. Visit this page on PeanutBase for updated genome data and gene model annotations!

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).