Bases for everyone

Today, we are happy to announce the public release of raw sequencing data to catch up with the 100 shared genome assemblies on NCBI Sequence Read Archive.

As previously, the data is shared under BioProject accession PRJNA512907. The new submission covers raw Hi-C data for 33 species and raw WGS data for 7 species. In total, the DNA Zoo BioProject data now spans 190 experiments and 11,118,071,473,442 bases!

We thank Illumina, Macrogen, Novogen, the Broad Institute and Baylor College of Medicine GARP core for their help with the data production!

As always, we share the data without restrictions: see our data usage policy here.

Subscribe below or follow us on twitter for more upcoming updates!

Celebrating 100 assemblies

Today, we are excited to hit the 100 assemblies mark on the DNA Zoo website with the release of 4 new mammalian genome assemblies: for the German Shepherd Dog (Canis lupus familiaris, German Shepherd Dog breed), here, the Eurasian otter (Lutra lutra), here, the coppery ringtail possum (Pseudochirops cupreus), here, and the golden ringtail possum aka plush-coated ringtail possum (Pseudochirops corinnae), here.

The German Shepherd Dog (GSD) is one of the most common breeds on earth. German Shepherds are known for their intelligence and strength, but are afflicted with a range of genetic diseases. To aid with the future disease and evolutionary studies, we have created a GSD genome assembly as part of a collaborative effort led by J. William O. Ballard at the School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia. The full list of people who contributed to building the resource includes: Matt A. Field, Benjamin D. Rosen, Olga Dudchenko, Eva K.F. Chan, Andre E. Minoche, Kirston Barton, Ruth J. Lyons, Daniel Enosi Tuipulotu, Richard J. Edwards, Vanessa M. Hayes, Arina D. Omer, Zane Colaric, Jens Keilwagen, Ksenia Skvortsova, Ozren Bogdanovic, Martin Smith, Erez Lieberman Aiden, Timothy P.L. Smith, Robert A. Zammit and J. William O. Ballard. The genome assembly is now available on NCBI at https://www.ncbi.nlm.nih.gov/nuccore/VSDE00000000.1/.

The Eurasian otter is a ‘Near Threatened’ species from the IUCN Red List. It is a keystone species in the UK, which is why the Wellcome Sanger Institute made assembling the genome for this species a priority as part of its 25 Genomes Project. In collaboration with Sanger, today we release the chromosome-length assembly for the Eurasian otter, here. The fasta sequence is also available through the Vertebrate Genomes Portal, here.

Finally, in collaboration with the Mallarino Lab at Princeton University we share chromosome-length genome assemblies for two more marsupials: the coppery ringtail and the golden ringtail. We are grateful to the Australian Biological Tissue Collection at the South Australian Museum that donated material used for generating the sequencing libraries for these genome assemblies. Included in the share are the homology-based annotations for the species, courtesy MacManes Lab.

We are grateful to Terry Reis (https://www.reisecology.com) for giving us permission to use his photo for the coppery ringtail possum. We were not as lucky with the golden ringtail possum, so if you guys have any photos that you would like to donate, don’t hesitate to reach out!

Et tu, Bryde’s

Bryde's (pronounced BROO-dus) whales are members of the baleen whale family. They are considered one of the "great whales," a group that also includes blue whales and humpback whales. They are named for Johan Bryde, a Norwegian who built the first whaling stations in South Africa in the early 20th century. [1]

The classification of Bryde’s whales remains unclear: the Bryde’s complex is currently thought to consist of several genetically distinct populations, so chances are with more research they might get promoted to species level! [2]

Bryde’s whales are vulnerable to many stressors and threats, including vessel strikes, ocean noise, and whaling. This is particularly true of the Gulf of Mexico Bryde’s whale subspecies (Balaenoptera edeni (GOMx subspecies)), also threatened by oil and gas activities, as well as oil spills and cleanup. Scientists believe that there are fewer than 100 GoM Bryde’s whales, making it one of the most endangered whales in the world!  [3, 4]

To help with ongoing research and conservation efforts, today we share a chromosome-length genome assembly generated from a Bryde’s whale sample collected in the Gulf of Mexico. This work was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03 issued by the National Marine Fisheries Service (NMFS) under the authority of the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The specimen used in this study was collected by NMFS Panama City Lab/Lydia Staggs and provided by the National Marine Mammal Tissue Bank, which is maintained by the National Institute of Standards and Technology (NIST) in the NIST Biorepository, and which is operated under the direction of NMFS with the collaboration of USGS, USFWS, MMS, and NIST through the Marine Mammal Health and Stranding Response Program.

Gulf of Mexico Bryde's whales are special to the Gulf of Mexico; they are not found anywhere else in the world. We don’t know a lot about them, but we do know they are the only year-round baleen whales that make their home in the Gulf. We hope that the new assembly will help with the ongoing efforts to explore genetic variation within the Bryde’s whale complex, improve our understanding of this enigmatic creature, while also providing the foundation for future bioanalytical techniques such as eDNA research!

This genome assembly was done de novo following the $1K workflow from (Dudchenko et al., 2018). Check out below the growing body of whole-genome alignments to see how the chromosomes from the new assembly relate to those of other cetaceans in the DNA Zoo collection: the beluga whale, the Pacific white-sided dolphin, the orca, the Indo-pacific dolphin and the bottlenose dolphin!

Whole-genome alignment plots between the new Bryde’s whale (Balaenoptera_edeni_HiC) genome assembly and other cetacean chromosome-length genome assemblies at the DNA Zoo: Indo-Pacific bottlenose dolphin (ASM322739v1_HiC), orca (Oorc_1.1_HiC), Atlantic bottlenose dolphin (NIST_Tur_tru_v1_HiC), Pacific white-sided dolphin (ASM367639v1_HiC) and the beluga whale (ASM228892v2_HiC).

UPD: In 2021, the Gulf of Mexico Bryde's whales have been identified as distinct species, Balaenoptera ricei. The assembly page has been correspondingly renamed and is now available at https://www.dnazoo.org/assemblies/Balaenoptera_ricei. Read more about rice's whales on NOAA Fisheries website.