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Dr Manu Kumar Gundappa

Post-doctoral research


I am currently a BBSRC research fellow funded by the Roslin Institutional Strategic Programme. A primary interest of my research lies around salmonid fish with focus on comparative and functional genomics of multiple species, while also performing applied research looking into population level variation (structural variation and SNPs) to exploit traits relevant to production and disease resistance in aquaculture. I also have a great interest in understanding the role of whole genome duplication in genome evolution and collaborate with multiple groups on this task. In addition, I am also involved in projects working on the genomics of European flat oyster (Ostrea edulis) making extensive use of the high-quality reference genome assembly we have generated for this species.

Postgraduate research

My PhD was funded by an Elphinstone Scholarship from the University of Aberdeen, with additional support from the Government of Karnataka, India. I sequenced, assembled and annotated a high-quality draft genome of the Danube salmon (Hucho hucho), a purely freshwater salmonid species, which is a sister lineage to a major clade of anadromous salmonids. The goal was to better understand the role played by whole genome duplication in the evolution of salmonid genomes and physiological systems. I used phylogenomic approaches to further our understanding of lineage-specific ohnologue resolution, revealing duplicated regions in the genome that began to diverge specifically in the common ancestor of anadromous salmonids (Gundappa et al. 2022, MBE).

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Biography and previous work

I was previously awarded a 1st class MFSc degree in Fish Genetics and Breeding by the Central Institute of Fisheries Education, Mumbai, India. My master’s research focused on using in silico approaches to identify putative essential genes and therapeutic candidates in the bacterium Aeromonas hydrophila. Before this, I was awarded a 1st class BFSc degree by the College of Fisheries, Mangalore, India wherein I was exposed to various fields of Fisheries Science. I have broad interests spanning of evolutionary genetics, fish genetics, aquaculture and fish breeding.  




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.


Peñaloza C, Preston J, Green M, Helmer L,  Kean-Hammerson J, Nascimento-Schulze JC, Minardi D, Gundappa MKMacqueen DJ, Hamilton J, Houston RD, Bean TP. 2022. Genome-Wide Association and Genomic Prediction of Growth Traits in the European Flat Oyster (Ostrea edulis). Front. Genet. 13: 926638. doi: 10.3389/fgene.2022.926638


Sambade IM, Casanova A ,Blanco A, Gundappa MK, Bean TP, Macqueen DJ, Houston RD,  Villalba A, Vera M, Kamermans P, Martínez P. 2022. A single genomic region involving a putative chromosome rearrangement in flat oyster (Ostrea edulis) is associated with differential host resilience to the parasite Bonamia ostreae. Evol Appl.

Bakke FK, Gundappa MK, Matz H, Stead DA, Macqueen DJ, Dooley H. 2022. Exploration of the Nurse Shark (Ginglymostoma cirratum) Plasma Immunoproteome Using High-Resolution LC-MS/MS. Front Immunol. 13:873390. doi: 10.3389/fimmu.2022.873390.


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.


Gundappa MK, To TH, Grønvold L, Martin SAM, Lien S, Geist, J, Hazlerigg D, Sandve SR, Macqueen DJ. Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution. Mol Biol Evol. 2021;msab310. doi:10.1093/molbev/msab310

Gillard GB, Grønvold L, Røsæg LL, Holen MM, Monsen Ø, Koop BF, Rondeau EB, Gundappa MK, Mendoza J, Macqueen DJ, Rohlfs RV, Sandve SR, Hvidsten TR. 2021. Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication. Genome Biol. 22: 103. doi: 10.1186/s13059-021-02323-0.

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

Bertolotti AC, Layer RM, Gundappa MK, Gallagher MD, Pehlivanoglu E, Nome T, Robledo D, Kent MP, Røsæg LL, Holen MH, Mulugeta TD, Ashton TJ, Hindar K, Sægrov H, Florø-Larsen B, Erkinaro J, Primmer CR, Bernatchez L, Martin SAM, Johnston IA, Sandve SR, Lien S, Macqueen DJ. 2020. The structural variation landscape in 492 Atlantic salmon genomes. Nature Commun. 11: 5176.


Robertson FM, Gundappa MK, Grammes F, Hvidsten TR, Redmond AK, Lien, S. Martin SAM, Holland PW, Sandve SR, Macqueen DJ. 2017. Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification. Genome Biol. 18:111. 

Genome Assemblies:


European flat oyster:

Danube salmon: 


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