Environmental genomics in marine zooplankton

SNIC 2022/6-263


SNIC Medium Storage

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 for the projects SNIC 2021/5-453 and SNIC 2021/6-277, respectively. Our project has multiple aims: i. genome assembly and annotation of the Northern krill Meganyctiphanes norvegica. 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 (see part i; this project is nearing completion). ii. Comparative genomics across 20 krill species adapted to cold or warm waters. Our focus is on comparing protein coding sequences to detect candidate genes evolving under positive selection in different environments and estimate the rates of adaptive protein evolution using extensive transcriptome datasets (see part ii; nearing completion). 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 (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 do not know how these species are genetically adapted to the environment, or 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. To this end, we have assembled the 19Gbp genome of the Northern krill, an unusually widespread species, and mapped gene variants associated with adaptation across Arctic, Scandinavian, American and Mediterranean populations (i). This project is nearly completed and will be submitted shortly. In addition, we are comparing rates of evolution across 20 World Ocean krill species, to detect key genes associated with adaptation to different environments (ii). Lastly, we perform genome assembly of the copepod Calanus hyperboreus (iii). Genome size is polymorphic in this species and possibly an adaptive trait. High arctic specimens having substantially large genomes than Scandinavian specimens (12 vs 9 Gbp). By comparing populations, we aim to reveal the genetic elements and evolutionary processes that underlie its genome size polymorphism. Access to HPC environments is essential for our project.