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on a previously published draft from (Bombarely, Moser et al. 2016), and the P. exserta is generated using hitherto unpublished data.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)!

First chromosome-length genome assembly of a snake

Today, we're sharing a chromosome-length genome assembly for the Burmese python, the first chromosome-length assembly (as far as we know) for a snake. The assembly is based on the draft Python_molurus_bivittatus-5.0.2 (GCA_000186305.2) from (Castoe et al., 2013).

Burmese pythons are found throughout Southern and Southeast Asia where their population is decreasing, and the species is classified as vulnerable. Yet in Florida these non-native snakes are flourishing and causing the population of many native species, from birds to mammals, to plummet.

Check out the whole genome alignment to the green anole lizard genome assembly AnoCar2.0, showing nearly perfect conservation of synteny between a lizard and a snake (the species are thought to have diverged roughly 150M years ago). Comparing to the chicken, GRCg6a, allows us to examine conservation of synteny across the Sauria. This is a 250M year old group spanning the birds, non-avian dinosaurs, and non-dinosaur reptiles. The chromosome-scale synteny blocks are a real sight for Sauri(s)!

For more about this, you might want to read "The genome of the green anole lizard and a comparative analysis with birds and mammals," from (Alföldi, Di Palma et al., 2011).

Whole genome alignment between the 18 chromosomes of the Burmese python and 13 chromosomes of the green anole assembly from (Alföldi, Di Palma et al., 2011).

Whole genome alignments between the Burmese python, the green anole and chicken genome assemblies.