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Genomics Applied to Aquaculture

We develop genomic resources (e.g. genome assemblies) and apply omics methods for applications in aquaculture, including to characterize and diagnose disease agents and better understand their evolution and transmission, to study fish immune responses, and to establish associations between genomic variation and commercially-important trait variation.

Representative papers:

Bean TP, Tanguy A, Peñaloza C, Gundappa MK, Boutet I, Houston RD, Macqueen DJ, Boudry P. 2022. Two parallel chromosome‐level reference genomes to support restoration and aquaculture of European flat oyster Ostrea edulis. Evol Appl. doi: 10.1111/eva.13465


Gundappa MK, Peñaloza C, Regan T, Boutet I, Tanguy A, Houston RD, Bean TP, Macqueen DJ. 2022. Chromosome level reference genome for European flat oyster (Ostrea edulis L.). Evol Appl.

Macqueen DJ, Eve O, Gundappa MK, Daniels RR, Gallagher MD, Alexandersen S, Karlsen M. Genomic Epidemiology of Salmonid Alphavirus in Norwegian Aquaculture Reveals Recent Subtype-2 Transmission Dynamics and Novel Subtype-3 Lineages. Viruses. 13: 2549. doi: 10.3390/v13122549.


Gallagher MD, Karlsen M, Petterson E, Haugland O, Matejusova I, Macqueen DJ. 2020. Whole Genome Sequencing of SAV reveals repeated seeding events of viral strains in Norwegian aquaculture. Front. Microbiol. 11: 740.

Houston RD, Bean TP, Macqueen DJ, Gundappa MK, Yehwa J, Jenkins TL, Counter Selly S-L, Martin SAM, Stevens J, Santos E, Davie A, Robledo R. Harnessing genomics to fast-track genetic improvement in aquaculture. Nat. Rev. Genet. 21: 389–409

Gallagher MD, Ruane NM, Matejusova I, Macqueen DJ. 2020. Genome-wide target enriched viral sequencing reveals extensive ‘hidden’ salmonid alphavirus diversity in farmed and wild fish populations. Aquaculture. 522: 735117

Gallagher MD, Matejusova I, Nguyen L, Ruane NM, Falk N, Macqueen DJ. 2018. Nanopore sequencing for rapid diagnostics of salmonid RNA viruses. Sci. Rep. 8: 16307. DOI: 10.1038/s41598-018-34464-x

Bayesian phylogeny of salmonid alphavirus genomes built from an 11,681 bp alignment and analyzed in BEAST2 using the best fit nucleotide substitution model (TIM2 + G4), a relaxed molecular clock model, tip-dating, and a coalescent Bayesian Skyline population model. A discrete phylogeographical analysis was performed using ancestral reconstruction with branch colors indicating the estimated geographic location of each node. Statistical support for key nodes is indicated by posterior probability values in bold, and the ancestral location probability in brackets. From Gallagher et al. 2020. Front. Microbiol.

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