About This Project

Humpback whales were hunted to near extinction until whaling was banned in 1963. Population recovery is slow due to long generation times and human interference. Interestingly, it seems that the near decimation of humpbacks did not lead to a bottleneck effect on their genetic variety. We intend to assemble a haplotype genome (meeting CGP standards) of Cook Islands humpbacks to understand their genetic variation and compare inter-and intra-specific differences.

Ask the Scientists

What is the context of this research?

Humpback whales are, in part, special because they are found all over the globe. The assumption has been that humpbacks are a single homogeneous species. However, recent genetic studies have revealed that global humpback whale populations are actually quite different from each other and belong to "subspecies." In addition, humpback whales are also special because they have been able to "beat cancer," which has led cancer researchers to use cetacean genomes to understand how they did so.

While scientists have a scaffold of the humpback genome, this assembly is incomplete and does not meet CGP "platinum-level" genome standards. Such a genome would advance both subspeciation research and cetacean cancer research.

What is the significance of this project?

A genome is assembled by putting together a large number of short genetic sequences (a scaffold). Scaffolds are made of random fragments which are aligned into "contigs". The resulting partial scaffold has both contigs and gaps (portions of the unknown genome). The existing humpback genome is 2558 separate fragments. In 2020, CGP set a standard for a platinum-level genome, which entails a per-chromosome assembly (for humpbacks, one sequence per chromosome).

This project will contribute to two significant advancements in the genomic studies of whales. First, we will gain a reference genome for other humpback populations worldwide. Second, we can get a better sense of the relatedness of different whale species.

What are the goals of the project?

A genome is an organism's complete set of genetic instructions. This project will be using the platinum-standard levels set by the CGP to generate the humpback genome. As a result, the goal of this project is to obtain a complete platinum-level genome of the Cook Islands humpback whale.

This will consist of one sequence per chromosome (assumed to be between 42 and 46), in haplotype format (which means we will be preserving what is inherited from both parents), and fully annotated (so we can create a library of what genes code for what). The goal is to obtain a full reference genome that can be used to understand other humpbacks and other whale species.