Prairie chicken genome crosses the chromosome

Isolated and fragmented prairie chicken populations have become a model system for conservation. These include the critically endangered Attwater's prairie chicken, a subspecies of prairie chick that is among the rarest birds in the world, and is the subject of extensive and ongoing conservation efforts.

To facilitate conservation of Attwater’s and other prairie chickens, we are releasing a chromosome-length genome assembly for the greater prairie chicken Tympanuchus cupido. The draft assembly, T_cupido_pinnatus_GPC_3440_v1 (NCBI accession: GCA_001870855.1), was created by Revive & Restore.

To give a sense of how chromosomes evolved across the bird lineage, we are also incorporating the band-tailed pigeon (Patagioenas fasciata) assembly we have shared in Dudchenko et al., bioRxiv, 2018, based on a draft published in Murray et al., Science, 2017, into the DNA Zoo site, here. Whole genome alignments of both assemblies to the chicken genome assembly GRCg6a are shown below.

Whole genome alignments between the chicken chromosomes and the new assemblies for the greater prairie chicken (left) and the band-tailed pigeon (right).

Note that the data for the draft genome was generated for T. cupido pinnatus subspecies of the prairie chicken, and the sample for the Hi-C upgrade came from T. cupido attwateri.

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!