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.

Whole genome alignment between the chromosomes of the new Golden Retriever genome assembly and the 39 chromosomes of CanFam3.1 (Lindblad-Toh et al., 2005).

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.

Comparison of chromosome 9 in CanFam3.1, canFamDis_HiC, the new Golden Retriever dog genome assembly, and ASM325472v1_HiC, the chromosome-length dingo assembly from an earlier DNA Zoo release.

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

Plant one on me

Today, we share the chromosome-length genome assemblies for two petunia species, the white Petunia axillaris and the red Petunia exserta. These were done in collaboration with Michel Moser and Cris Kuhlemeier at the University of Bern. The P. axillaris assembly is based on a previously published draft from (Bombarely, Moser et al. 2016), and the P. exserta is generated using hitherto unpublished data.

Petunia is genus of 20 species of flowering plants of South American origin. P. axillaris is one of the two species that were used to create the world's most popular bedding plant, the petunia hybrid Petunia x hybrida [1]. P. exserta was only discovered in the Serras de Sudeste of Brazil in 1987 and is already considered to be near extinction in the wild [2].

Learn more about petunias and petunia genetics from (Bombarely, Moser et al. 2016)!