Krill (85 species) are keystone zooplankton for the oceans. The Antarctic krill and the Northern krill are among the most abundant animals on the planet, and the yearly production is estimated to exceed 400s trillion individuals and 500 million tonnes in both species. As major consumers of sea algae and food for ecologically and commercially important mammals and fish, krill are a critically important link between primary production and higher trophic levels. However, climate change is already affecting the distribution of krill, which can disrupt ecosystems and important marine resources. We do not know how krill is genetically adapted to the environment, or what selection pressures that future climate change may put on krill stocks.
Insights into the evolution, adaptation and physiology of these animals have been slowed by their large genomes (12–48 Gbp; 4–16 times larger than the human genome), and no krill genome has yet been assembled. Karyological studies show that most species have 17–20 large metacentric chromosomes that appear to evolve rapidly in size over short evolutionary time-scales, suggesting that transposable elements and segmental duplications are important for genome evolution, and potentially for adaptation in krill.
In this project, we aim to perform de novo genome assembly and population genomics analyses of the Northern krill, Meganyctiphanes norvegica, an uniquely widespread Atlantic species. It occurs from the Mediterranean Sea to the Arctic ocean, including Scandinavian waters, as well as the Western North Atlantic ocean. Local stocks have developed genetic adaptations for optimal respiration and metabolism in different ambient temperatures, but the genetic mechanisms and loci are unknown. This species offers a unique opportunity to study environmental adaptation in krill. It has a ~19 Gbp genome; about 6 times the size of the human genome, which has only recently become possible to assemble.
Access to HPC environments is essential for this project.
Part 1) We will use long-read sequencing (Oxford Nanopore PromethION to ~30x depth of coverage) and hybrid assembly (Nanopore + 10X Chromium libraries) to assemble the M norvegica genome. We plan to use the highly parallel and efficient MARVEL assembler to assemble the genome, followed by scaffolding using ARCS+LINKS to further improve assembly contiguity. Transcriptome data will be mapped against the contigs to determine the distribution and sizes of gene families along the genome. Transposable elements will be annotated using RepeatMasker/RepeatModeler.
Part 2) We will then perform whole-genome sequencing using Illumina NovaSeq to map genetic variation between stocks using standard mappers (e.g. BWA, bowtie2) in order to detect genes and variants (using GATK, FreeBayes, MANTA) that show signals of divergence between cold and warm environments and may be involved in local adaptation. Lastly, genetic variation in contemporary populations will be contrasted against historical museum samples to study genetic changes that may have occurred over the last century.
The project is funded by FORMAS (2017-00413) and will help us understand how krill is genetically adapted to different environments and responds to climate change.