Dr Manu Kumar Gundappa

Post-doctoral research


I am a post-doctoral research fellow on a BBSRC funded consortium project called 'AquaLeap: Innovation in Genetics and Breeding to Advance UK Aquaculture Production'. Within this project, I am: i) leading the assembly and annotation of a new genome resource for the European flat oyster (Ostrea edulis) using multiple sequencing technologies in collaboration with Dr Tim Bean (Roslin Institute), which will be used to support future breeding programmes and genetic analyses, and ii) testing the importance of structural variants as markers of disease resistance in Atlantic salmon, in collaboration with Prof. Ross Houston and Dr Diego Robledo at the Roslin Institute. I am also in the process of writing up several papers from my PhD research on salmonid genome evolution.

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 (WGD) in the evolution of salmonid genomes and physiological systems. I used phylogenomic approaches to further our understanding of lineage-specific ohnologue resolution (Robertson et al. 2017), revealing duplicated regions in the genome that began to diverge specifically in the common ancestor of anadromous salmonids (paper in prep).


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, 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. Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication. Genome Biol. 22: 103. doi: 10.1186/s13059-021-02323-0.

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.  https://doi.org/10.1038/s41467-020-18972-x


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 Assembly for the Danube salmon: https://www.ncbi.nlm.nih.gov/assembly/1818171 


K-mer analysis of a haploid Danube salmon genome (50x coverage, Illumina 2x250bp dataset). Credit for Danube salmon image: Alexander Czernin.