Genome assembly on the fly

Today we share two genome assemblies for the moth fly Clogmia albipunctata.

The first assembly was done in collaboration with Johannes (“Yogi”) Jaeger, Eva Jimenez Guri, Luca Cozzuto, Toni Hermoso Pulido, Julia Ponomarenko and Karl Wotton at the at EMBL/CRG Research Unit in Systems Biology, Barcelona (Spain) who generated and assembled the DNA-Seq data, as well as Urs Schmidt-Ott from the University of Chicago who provided the material for Hi-C. We used Hi-C to anchor, order and orient sequences into 6 chromosome-length scaffolds, as well as to remove contaminants. Funding for the Hi-C analysis was provided by the University of Chicago to Urs Schmidt-Ott.

We also share another assembly for this species, based on a draft genome assembly from Vicoso, Bachtrog, PLoS Biol. 2015, for comparison. The assemblies are largely independent, except that some of the same Hi-C data was used for both.

In Dudchenko, Science 2017, we observed that the contents of chromosome arm 2L of Drosophila melanogaster tend to be located on the same chromosome arm throughout Dipterans. As you can see below, this effect is seen in the moth fly as well!

Hi-C map of the new genome assembly for the moth fly. The 1D tracks show the the distribution of alignments of sequences from 2L chromosome arm of Drosophila melanogaster genome assembly (release 6 by The FlyBase Consortium/Berkeley Drosophila Genome Project/Celera Genomics), in dark blue, and the coverage track, in light blue. The majority of 2L alignments fall onto a single chromosome.

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.