Environmental genomics in marine zooplankton

NAISS 2023/5-449


NAISS 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



Here we perform genome assembly, population and comparative genomics in krill and Calanus copepods. These crustacean zooplankton are marine keystone species but poorly understood at the genetic level. We apply for a continuation of computational and storage resources. Our project has multiple aims: i. The genomic basis of adaptation in the Northern krill Studying patterns of genome-scale variation among 74 specimens from M. norvegica, with a focus on uncovering the genetic mechanisms that underlie adaptation to climate. The first phase of this project is completed; our ongoing work is targeting candidate and structural variants to better understand adaptation (see part i). ii. Comparative genomics across 20 krill species adapted to cold or warm waters. Our focus has been on comparing protein coding sequences to detect candidate genes evolving under positive selection in different environments. This project is completed and has been published in Molecular Biology and Evolution (see part ii). iii. genome assembly and annotation of the Arctic copepod Calanus hyperboreus. Our focus is on performing de novo assembly and characterization of genome size evolution and structural variation in this species. This work is ongoing (see part iii). Krill (86 spp) and Calanus (16 spp) are among the most abundant animals on Earth. As major consumers of sea algae and food for ecologically and commercially important mammals and fish, they are pivotal links between primary production and higher trophic levels. However, climate change is disrupting population growth and distribution, which threatens to disrupt ecosystems that we depend on for food. We know only a little about how these species are genetically adapted to the environment, and dot yet understand how they will cope with continued climate change. The mechanisms that contribute to genetic adaptation in zooplankton are not well understood, much due to a lack of genomic resources, such as reference genomes and genome-scale variation data. Krill and Calanus have notoriously large and repetitive genomes (krill: 11–48 Gbp; Calanus: ca 5–12 Gbp; 4–15x the human genome), that until recently have been untenable to assemble and analyze. No genome assembly has yet been published for any krill or Calanus. Here we are performing cutting-edge genomics in these species to learn how they are adapted to their environments and may respond to rapid ocean warming. We have assembled the 19Gbp genome of the Northern krill, an unusually widespread species, and mapped gene variants across its range. We are now performing followup analyses of processes that shape genetic variation in this species, including recombination, as well as studying molecular evolution and structural variation to better understand genetic adaptation in this species (i). We are actively performing genome assembly of the copepod Calanus hyperboreus (iii). Genome size is polymorphic in this species and possibly an adaptive trait. High arctic specimens have substantially larger genomes than Scandinavian specimens (12 vs 9 Gbp). By comparing populations, we aim to reveal the genetic elements and evolutionary processes that underlie genome size polymorphism. Access to HPC environments is essential for our project.