Environmental genomics in krill

SNIC 2019/3-395


SNIC Medium Compute

Principal Investigator:

Andreas Wallberg


Uppsala universitet

Start Date:


End Date:


Primary Classification:

10615: Evolutionary Biology

Secondary Classification:

10609: Genetics (medical to be 30107 and agricultural to be 40402)

Tertiary Classification:

10608: Zoology



Krill (85 species) are keystone zooplankton for the oceans. 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 (18Gbp genome), an uniquely widespread Atlantic species. It occurs from the Mediterranean Sea to the Arctic 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. Access to HPC environments is essential for this project and with this continuation, we are entering into a more compute intense part of the project. Part 1) We have now finished long-read sequencing (Oxford Nanopore PromethION to ~30x depth of coverage) of the krill and are currently performing test assemblies using wtdbg2 on UPPMAX and PDC (Stockholm). 10X Chromium data is now being generated at SNP&Seq and will be used to perform hybrid assembly. In addition to wtdbg2, 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 has been produced will be mapped against the contigs to determine the distribution and sizes of gene families along the genome. We will use the high-performance mapper Dart and recent hybrid mappers StringTie2 and LoReAn to simultaneously map both short and long cDNAs against the assembly. Transposable elements will be annotated using RepeatMasker/RepeatModeler. Part 2) We have ordered 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. This material will be sequenced early fall 2019. 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.