Cetacean Genomes Project Samples

May 14, 2020

Here you can find information on what species and types of samples are needed, and how to preserve samples for genomic sequencing and annotation.

The major requirement for long-read sequencing and scaffolding is availability of fresh tissues that yield relatively large amounts of ultra-high quality (UHQ) DNA and intact chromatin, which preserves the 3D structure in the nuclei for Hi-C. These technologies currently require fresh blood, muscle or organ tissue, or cultured cells that are preserved to maintain megabase-length DNA and RNA. Preservation of genetic material  typically involves rapid freezing and storage at less than or equal to –80°C, or culture of live cells, both of which have limited feasibility for protected species (due to sampling methods) and in many field conditions. Short-term preservation in 90-percent ethanol can also be effective, at least for DNA preservation (see protocols below). 

The data table below lists samples that we have identified as likely to meet the UHQ specifications needed for PacBio long-read sequencing, BioNano optical mapping, and Hi-C chromatin-linked sequencing. 

We are seeking samples for the remaining cetacean species. If you know of appropriately preserved samples, please let us know! If you are sampling cetaceans as part of your research or a stranding network, please use the collection and storage methods described below to collect appropriate samples. Although it is not certain that resources will be available for sequencing all species, obtaining appropriate samples is the first and most critical step. Even if you plan to complete genome sequencing of the samples, please let us know so we can avoid duplication of effort.

 

 

Last updated by Southwest Fisheries Science Center on 10/23/2020