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Genome Biology & Evolution
We are combining genome sequencing, comparative genomics, phylogenetics and gene expression profiling to explore the role of genome duplication in fish evolution, to reconstruct the evolution of gene families, and to infer patterns of genome evolution
Huchen (Hucho hucho) next to a circos plot depicting the rediploidization history in salmonid genomes, after Gundappa et al. 2021 (MBE). Credit for Huchen image: Madhusudhan Gundappa (Twitter: @fish_lines)
Representative papers:
Redmond AK, Casey D, Gundappa MK, Macqueen DJ, McLysaght A. Independent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor. Nat Commun. 14: 2879. doi: 10.1038/s41467-023-38714-z.
Gundappa MK, To TH, Grønvold L, Martin SAM, Lien S, Geist, J, Hazlerigg D, Sandve SR, Macqueen DJ. 2021 Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution. Mol Biol Evol. msab310. doi:10.1093/molbev/msab310
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
Redmond AK, Zou J, Secombes CJ, Macqueen DJ, Dooley H. 2019. Discovery of All Three Types in Cartilaginous Fishes Enables Phylogenetic Resolution of the Origins and Evolution of Interferons: Front. Immunol. 10:1558.
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. DOI: 10.1186/s13059-017-1241-z
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