Tweaking 3 mammalian genomes

Today, we suggest a few tweaks to three publicly available chromosome-length genome assemblies: for the grey short-tailed opossum Monodelphis domestica, here; the European rabbit Oryctolagus cuniculus, here; and the grey mouse lemur Microcebus murinus, here.

A study in Scarlet

2018 was the year of the dog, so, as it comes to a close, we are releasing a chromosome-length, de novo genome assembly for the Golden Retriever dog breed! The assembly, created exclusively using short Illumina reads, was done in collaboration with the Broad Institute.

This genome assembly has contig N50 equal to 133Kb and scaffold N50 equal to 59Mb, the latter determined by the size distribution of the dog’s 39 chromosomes. Since the best current dog reference, CanFam3.1 (NCBI accession GCF_000002285.3; contig N50: 267Kb; scaffold N50: 63Mb), comes from a Boxer (Lindblad-Toh et al., 2005), the new genome should facilitate inter-breed comparisons. A dotplot comparing the assemblies is below.

Note a 10Mb inversion with respect to CanFam3.1 chromosome 9. This inversion is shared by the dingo genome assembly and hence likely represents the ancestral form.

Happy New Year everyone! Don't stop retrievin' in 2019!

Welcome to the DNA Zoo!

Over a quarter of all assessed species are threatened with extinction [1]. The DNA Zoo is a consortium focused on facilitating conservation efforts through the rapid generation and release of high-quality genomics resources. We believe that these efforts can not only aid threatened nonhuman populations, but will greatly facilitate our understanding of our own species - Homo sapiens.

To begin, we are sharing chromosome-length genome assemblies for 50 mammalian species, including 14 endangered or vulnerable species. Most of the shared assemblies were created by upgrading fragmentary genome assemblies shared by other groups at the NCBI Assembly database. We improved these drafts using Hi-C. The rest were assembled from scratch using Hi-C and DNA-Seq. In each case, the resulting genome assemblies have chromosome-length scaffolds.

Check out the Assemblies webpage to see what's available, and the Methods page to find out more about our latest approaches for genome assembly. To make sure the data can have the greatest possible impact, we are sharing the data with minimal restrictions on usage and publication.

Visitors - young and old - may enjoy learning more about our assembled species by reading the Chromognomes comic series, a collaboration between DNA Zoo and Adam Fotos.

Finally, we are extremely grateful to the many zoos and individual partners who have donated samples and otherwise supported this effort. Check out the Collaborators page to learn more.

DNA Zoo is always looking for additional samples. If you have samples from a species we have not yet released, or would like us to upgrade a published draft, feel free to get in touch. Through the generous support of our commercial partners, we are often able to make end-to-end genomes, from relatively low quality material, at no charge.

Follow the project on Twitter @thednazoo or join the mailing list to stay up-to-date.

Welcome to the DNA Zoo!