Cetacean Genomes Project Updates
News and updates related to the Cetacean Genomes Project for scientists, academics, and students interested in genomics and the application of these tools for conservation and management.
This page will provide scientists with updates on projects, protocols, relevant publications, and news. Our goal is to keep our scientific partners updated on the state of cetacean genomics, facilitate genomics research, and invite participation in the project. Please send news items, publications announcements, and suggestions to help keep this blog informative and current.
Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing
July 23, 2021
The “Sample Preparation” group from the Vertebrate Genomes Project has posted the preprint of their article describing preservation methods and DNA extraction methods optimized to obtain ultra-high molecular weight DNA necessary for long-read DNA sequencing used to generate reference genomes. Obtaining adequate samples for cetacean reference genomes remains difficult, as tissues can rarely be obtained immediately after death and flash-frozen to preserve the DNA, RNA and tissue integrity. This paper provides guidance on which methods of sample preservation and DNA extraction are optimal, and which to avoid!
Dahn, H., J. Mountcastle, J. Balacco, et al. 2021. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing. https://www.biorxiv.org/content/10.1101/2021.07.13.451380v1.
Special issue of Nature on the Vertebrate Genomes Project, featuring the vaquita reference genome
May 3, 2021
A special issue of the journal Nature was published on April 29th, highlighting the Vertebrate Genomes Project, and including the VGP flagship paper and the milestone of publishing 16 reference genomes. The vaquita reference genome publication, featured on the cover of the most recent issue of Molecular Ecology Resources, is one of the VGP genomes, linked to the Nature special issue collection of papers. Several news stories reviewed the VGP accomplishments and the role of NOAA marine mammal tissue collections in advancing genomic studies.
DNAzoo releases Hi-C genome assemblies for rough-toothed dolphin, pantropical spotted dolphin, Atlantic spotted dolphin, and eastern spinner dolphin
April 5, 2021
DNAzoo, a consortium focused on facilitating conservation efforts through rapid generation and release of genomic resources, is using their $1000 genome process to sequence 35 cetacean draft genomes. DNAzoo uses high-coverage Illumina short-read sequencing combined with Hi-C contact mapping to generate chromosome-length scaffolded genomes. With this update, the DNAzoo includes 21 cetacean assemblies.
“Flipping over genomes: https://www.dnazoo.org/post/flipping-over-genomes
Genome insights give cause for optimism in the ongoing battle to save the vaquita
March 4, 2021
A "News and Views" perspective by Annabel Whibley was published in Molecular Ecology Resources to accompany publication of the vaquita genome assembly and analysis by Phil Morin and colleagues. The perspective emphasizes the "exceptionally high-quality draft genome assembly of the vaquita", and discusses the challenges in generating such genomes, and the benefits of generating reference-quality genomes across taxonomic groups to "provide genomic infrastructure to support genome research and conservation of related species".
Whibley, A. (2021) Genome insights give cause for optimism in the ongoing battle to save the vaquita. Mol Ecol Res, doi: 10.1111/1755-0998.13345
Mexico Population Genomics Conference 2020
The 2020 Mexico Population Genomics conference (MexPopGen5: https://mexpopgen.wordpress.com/) was held virtually in December, and I had the opportunity to give a virtual presentation on the vaquita reference genome. Presentations were pre-recorded with time for live question/answer sessions, and many of the presentations are available on YouTube at https://www.youtube.com/channel/UCOvGSovorjUiVjtDnul-4CA/videos. Our short (12 min.) vaquita genome presentation can be seen at: https://www.youtube.com/watch?v=P4mCOZG-BDk
Vaquita porpoise reference genome published
November 20, 2020
Our paper “Reference genome and demographic history of the most endangered marine mammal, the vaquita” has been published in the journal Molecular Ecology Resources. The publication describes the sequencing and assembly of the reference genome for the vaquita by the Vertebrate Genomes Project (VGP), and analysis of genome-wide heterozygosity and historical population size. This genome assembly is the first cetacean reference genome completed by the VGP, and the most complete and high-quality cetacean genome to date. The vaquita has the lowest genomic variation of any mammalian species, resulting from over 250,000 years persistence as a small population. This result suggests that the vaquita genome is likely to have purged much of the deleterious mutations that could lead to inbreeding depression, and gives us hope that the species is more likely to recover from the current crisis if it can be protected from gillnets.
Vaquita genome study in the news
November 9, 2020
An article in Smithsonian Magazine online this week discussed the publication of the vaquita reference genome sequence. The article, entitled “Vaquita Genome Offers Hope for Species’ Survival” highlighted the broader story of obtaining the tissue samples, driving them from San Felipe, Mexico to San Diego, California, USA, to culture cells in the San Diego Zoo’s “Frozen Zoo”, and the potential impact of the research on vaquita conservation.
Revive & Restore announces Summer 2020 Wild Genomes project awards
November 6, 2020
The non-profit conservation technology organization Revive & Restore announced the ten recipients of their first “Wild Genomes” awards. The competition invited researchers to address conservation issues for species using genomic data. They received 58 applications from 19 countries, and awarded 10 projects, including the “Five Whales” project from the Cetacean Genomes Project. Funding was received in May, 2020, and combined with matching funds from the Marine Mammal and Turtle Division (SWFSC) and the NOAA National Oceanographic Partnership Program (NOPP).
Blue whale reference genome assembly released by National Center for Biotechnology Information
October 6, 2020
The National Center for Biotechnology Information has just released the completed blue whale reference genome assembly, from a North Pacific blue whale! Similar to the vaquita genome, this assembly included all of the Vertebrate Genome Project's sequencing and scaffolding technologies, and resulted in a highly contiguous assembly in only 106 scaffolds, with 99.82 percent of the sequence assigned to the 21 autosomes plus sex chromosome scaffolds.
DNAzoo releases more cetacean chromosome-length Hi-C genome assemblies
September 28, 2020
DNAzoo, a consortium focused on facilitating conservation efforts through rapid generation and release of genomic resources, is using their $1000 genome process to sequence 35 cetacean draft genomes. DNAzoo uses high-coverage Illumina short-read sequencing combined with Hi-C contact mapping to generate chromosome-length scaffolded genomes. To date, DNAzoo has released 16 cetacean genomes, with plans to complete 19 more cetacean species genomes in the coming months. See the Cetacean Genome Project genome status table for listings of the species completed and in progress by DNAzoo.
Vertebrate Genomes Project/ NOAA 5-cetacean genomes project
September 25, 2020
The Cetacean Genomes Project has started a project to sequence 5 more platinum-quality reference genomes from cetaceans that help span the diversity in the cetacean phylogeny. The project has been jointly funded by the Marine Mammal and Turtle Division, Southwest Fisheries Science Center, the NOAA National Oceanographic Partnership Program (NOPP), and Revive & Restore. The targeted species are:
- Gray whale (Eschrichtius robustus)
- Blainville's beaked whale (Mesoplodon densirostris)
- North Atlantic right whale (Eubalaena glacialis)
- False killer whale (Pseudorca crassidens)
- Amazon River dolphin (Inia geoffrensis)
Stay tuned for updates on the progress of these genome sequencing and assembly projects!
Vaquita and Blue Whale Genomes Added to the Ensembl Genome Browser
August 20, 2020
The vaquita and blue whale genomes have been added to the Ensembl Genome Browser as part of the Ensembl 101 release on August 20, 2020. These were two of the six new genomes contributed by the Vertebrate Genomes Project.
Ensembl allows for the following:
- Provides genome annotation
- Integrates annotation with other available biological information
- Makes the data and analysis tools available via the web
The Browser also includes comparative genomics, variation, and regulatory data.
Letter to the Journal: Marine Mammal Science
August 17, 2020
A letter to the journal Marine Mammal Science entitled “Building genomic infrastructure: Sequencing platinum-standard reference-quality genomes of all cetacean species” was published online on August 17, 2020. The letter was authored by a group of 16 marine mammal and genomics researchers.
The primary goals of the Letter are:
- Educate marine mammal biologists on the levels of genome completeness and quality and how they are relevant to cetacean research
- Provide examples of the utility of reference-quality genomes for cetacean species research and conservation
- Outline the primary goals of the Cetacean Genomes Project
Meet the Blogger: Phillip Morin
Phillip Morin is a population and evolutionary geneticist in the Marine Mammal and Turtle Division at the Southwest Fisheries Science Center in La Jolla, California. Phil’s interests include applying genetic and genomic methods to understand cetacean taxonomy, demography, and population structure, and their application to conservation and management.