Krill genomics
Antarctic krill (Euphausia superba) (Image credit: Simon Payne, Australian Antarctic Division)
Antarctic krill (Euphausia superba) are incredibly abundant in the Southern Ocean (biomass estimated to be 500 million tonnes) and form a critical ecological link between photosynthetic phytoplankton and species at higher levels in the food chain such as fish, seabirds and whales. The Australian Antarctic Division (AAD) has a strong krill research program that examines the species' ecology and provides information to help manage the krill fishery.
Krill Genome
A huge amount of effort has gone into sequencing the Antarctic Krill genome and a paper summarising this project was published in 2023. The work was led by Changwei Shao and a team of researchers from China with contributions from scientists based in Australia, Germany, Italy and Denmark. This genome sequencing project was technically challenging since the genome is 48 billion base pairs (it's the largest animal genome ever to be sequenced) and the gene coding regions are buried in vast regions of repetitive sequences (short repeats and transposable element). See paper here. A general summary of the paper is also available (BGI website article).
Past Projects
Most of the krill genetics work being done at the AAD when I was leading the ecological genetics group (2016-2020) was done by two former post-docs Laurence Clarke and Léonie Suter. Laurence studied the Antarctic krill microbiome and investigated using these bacterial communities to tell us about connectivity of krill populations (read paper here). Léonie worked on sex-determination mechanisms in krill to help explain the highly skewed sex-ratios often observed when sampling krill in the Southern Ocean (see paper here).
As part of my Bob Hawke Antarctic Science Fellowship (2011-2014) I worked on a couple projects focused on ecological genomics of Antarctic krill. The original aim of the fellowship was to initiate a krill genome project to facilitating deeper understanding of this important species. However, estimates krill genome size which came out just as the project started indicated the species has a very large genome (~50 Gb), making a genome project unfeasible (new DNA sequencing technology and a lot more resources changed this, see above!). Instead we used high-throughput sequencing to characterise components of the genome and at the same time address ecologically important questions.
(1) Studying krill population structure using RAD sequencing
We developed a large number of genetic markers from the krill genome using restriction associated DNA (RAD) sequencing. This is essentially a method which allows you to characterise part of the genome (reduced representation sequencing). We obtained over a billion sequences from >140 krill collected at sites throughout the Southern Ocean and thousands of variable markers were identified using standard RAD-seq methodology. Once we started looking at the data in detail we found that most markers were from genomic sequences present in multiple copies. The krill's very large genomes contain an increased proportion of repetitive DNA sequences. These consist of a diverse array of repetitive elements present at a broad range of frequencies (i.e. from duplicates to thousands of copies!)
To characterize the multicopy markers, we recorded sequence counts from variable nucleotide sites rather than the derived genotypes; we also examined mitochondrial DNA which is much easier to characterise. Although these analyses effectively fingerprinted individual krill, no population structuring was observed. Overall, our results are consistent with panmixia of krill throughout their distribution. This result may indicate ongoing gene flow. However, krill’s enormous population size means genetic differentiation may not occur on an ecologically relevant time- scale even if demographically separate populations exist.
So, krill turned out to a very tricky organism to work with, but we managed to produce the most detailed population genetic dataset available for Antarctic krill, provided some insight into the krill genome and clarified the genetic view of krill stock structure for fisheries management (see link to publication below for more information).
(2) Krill transcriptomics
Previous work carried out in the AAD krill aquarium has shown that elevated carbon dioxide levels can severely impact the development of krill embryos (and another paper here) As part of ongoing work to examine this finding further we characterised gene expression of developing krill at various levels of carbon dioxide. This project produced a large amount of sequence data and the first step was to create a detailed transcriptome (i.e. catalog of genes) for the species. Then by comparing data from krill larvae at different CO2 levels, the genes genes underlying the response to CO2 levels were cataloged. These data are reported in a publicly accessible database: KrillDB
Publications
Shao C, Sun S, Liu K, Wang J, Li S, Liu Q, Deagle B, [+ 41 other contributors], Meyer B,Fan G (2023) The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights. Cell 186: 1279-1294 (PDF)
Clarke LJ, Suter L, Rob King R, Bissett A, Bestley S, Deagle BE (2021) Bacterial epibiont communities of panmictic Antarctic krill are spatially structured Molecular Ecology (PDF)
Suter L, Polanowski AM, King R, Romualdi C, Sales G, Kawaguchi S, Jarman SN, Deagle BE (2019) Sex identification from distinctive gene expression patterns in Antarctic krill (Euphausia superba). Polar Biology (Open Access)
Clarke LJ, Suter L, King R, Bissett A, Deagle BE (2019) Antarctic krill are reservoirs for distinct Southern Ocean microbial communities. Frontiers in Microbiology 9:3226 (PDF)
Sales G, Deagle BE, Calura E, Martini P, Biscontin A, De Pittà C, Kawaguchi S, Romualdi C, Meyer B, Costa R, Jarman SN (2017) KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba). PLOS ONE 12: e0171908 (PDF)
Jarman SN, Deagle BE (2016) Genetics of Antarctic krill. Book Chapter In: Biology and Ecology of Antarctic Krill (ed.Siegel). Springer (Hamburg). Pages 247-277 (Abstract)
Deagle BE, Faux C, Kawaguchi S, Meyer B, Jarman SN (2015) Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy the water. Molecular Ecology 24: 4943-4959 (PDF)
Collaborators
So Kawaguchi, Léonie Suter, Laurence Clarke and Rob King (Australian Antarctic Division)
Changwei Shao (Chinese Academy of Fishery Sciences)
Gabriele Sales, Chiara Romualdi and others (University of Padova, Italy)
Bettina Meyer (Alfred Wegener Institute, Germany)
Steve Nichol (University of Tasmania, Australia)
Simon Jarman (University of Western Australia)