You don’t know Jac

Reeves’s muntjac also known as Chinese muntjac (Muntiacus reevesi) is a deer species found widely in southeastern China and Taiwan. It has been introduced in Belgium, the Netherlands, the UK, Ireland and Japan, and proved invasive outside its native range [1].

Today, we are sharing a chromosome-length genome assembly for the Reeves’s muntjac. This is an upgrade from a recent paper in Science by Chen, Qiu, Juiang, Wang, Lin, Li et al. We thank SeaWorld for helping us with the sample used to generate Hi-C data for the upgrade!

See below our usual analysis of the karyotype of the new chromosome-length genome assembly for the Reeves’s muntjac (2n=46) against that of a cow (2n=60), from (Zimin et al., Genome Biol. 2009). Rearrangements outside of centric and tandem fusions seem rare. A notable exception is the sex chromosome (#5 in the Reeves’s muntjac, #30 in cattle) where the rearrangement picture is more complex.

Whole-genome alignment between the new chromosome-length genome assembly for the Reeves’s muntjac (CIJ_HiC) and that of cattle (Bos_taurus_UMD_3.1.1).

Excitingly, this is one of the rare occurrences where chromosome painting data is available from previous research. The data allows for independent validation of the karyotype predicted by the assembly. See Fig. 4 (copied below) from (Frohlich et al., PLoS ONE, 2017) that shows hybridization patterns of appropriate cattle painting probes for 6 Reeves’s muntjac’s chromosomes: MRE1=chr#1, MRE2=chr#2, MRE3=chr#3, MRE4=chr#4, MRE5=chr#6, MRE11=chr#10. While the chromosome painting data was not used during the generation of the assembly, they are in perfect agreement!

Frohlich et al., PLoS ONE, 2017; Fig. 4: Rearrangements on Chinese muntjac chromosomes MRE1–5 and 11 are demonstrated by hybridization patterns of appropriate cattle painting probes (on the right). MRE1 corresponds to chr#1 in the new assembly, MRE2 to chr#2, MRE3 to chr#3, MRE4 to chr#4, MRE5 to chr#6 and MRE11 to chr#10.

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.