Further ruminations

Gerenuk (Litocranius walleri) is an exceptionally long-necked antelope from East Africa. They feed at higher reaches than most other gazelles and antelopes: standing on their hind legs they can reach as high as eight feet off the ground [1]!

Due to habitat loss and fragmentation today the gerenuks are classified as near threatened [2]. Populations have declined by 25 percent over the last 14 years, and it is now estimated that gerenuk is close to meeting the threshold for being uplisted to vulnerable [1].

Today, we share the chromosome-length assembly for the gerenuk. This is another upgrade from a recent Science paper by Chen, Qiu, Juiang, Wang, Lin, Li et al. We are grateful to Houston Zoo for donating a sample that was used for in situ Hi-C library preparation needed for the upgrade!

This is the third member of the Bovidae family in our collection. The Bovidae are the most diverse group of living ungulates that includes many agriculturally important animals such as cattle, goat and sheep. See below how the genome assemblies of the three genomes (the bison Bison bison, the sable antelope Hippotragus niger and the gerenuk Litocranius walleri, all corresponding to 2n=60 karyotype) align to the genome of the cow, from (Zimin et al., Genome Biol. 2009). Just as noted in our last post on ruminant genomes, complex rearrangements are observed on the sex chromosome (aligning to chr#30 in the cow). Stay tuned for more ruminant genome assemblies!

Whole-genome alignments between the three DNA Zoo genome assemblies from the Bovidae family, bison (Bison_UMD1.0_HiC), sable antelope (Sable_antelope_masurca.scf_HiC) and gerenuk (GRK_HiC), to the cattle genome assembly (Bos_taurus_UMD_3.1.1). Note that the bison genome assembly used for this analysis is updated as compared to the one originally released.

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!