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Title: The Danube salmon genome : testing the importance of whole genome duplication in salmonid life history evolution
Author: Gundappa, Manu Kumar
ISNI:       0000 0004 7972 5193
Awarding Body: University of Aberdeen
Current Institution: University of Aberdeen
Date of Award: 2019
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Salmonids fish offer an excellent vertebrate model to investigate evolution following whole genome duplication (WGD). The salmonid ancestor underwent WGD by autotetraploidization 88-103 Mya ('Ss4R') and the process of reverting to a diploid state (rediploidization) is still in process, with around half of the created gene duplicates ('ohnologues') conserved in extant species. There has been a recent 'explosion' of new salmonid genomic resources, with reference genome sequences created for all the commercially-valuable genera and species, including Atlantic salmon. The overall aim of my PhD research was to generate and annotate a highquality draft genome sequence for the Danube salmon (Hucho hucho), and use the resource to better understand rediploidization and genome evolution in the context of life-history evolution. In evolutionary terms, it sits within a lineage that is closely related to many well-studied salmonids (e.g. Atlantic and Pacific salmon) that share an ancestral capacity for anadromy. I generated a haploid Danube salmon individual (embryo) and the genomic DNA was sequenced using short-read sequencing with paired-end and mate pair libraries at high coverage. The final assembly was 2.55 Gb in size with a scaffold N50 of 269.65 Kb. Genome annotation predicted a total of 41,404 gene models in the final version. The finished Danube salmon genome was used alongside other available salmonid genomes to perform a comparative genomic analysis. The aim was to better understand a recently defined process called lineagespecific ohnologue resolution (LORe). I created a 'phylogenomic map' of ohnologue divergence across five salmonid genera, providing unprecedented information on LORe in different salmonid lineages. The analysis revealed multiple rediploidization events nested within salmonid phylogeny that correlate with species diversification. Overall, my thesis reports the assembly and efficient exploitation of the Danube salmon genome to address key questions related to Ss4R and the potential role of WGD in salmonid evolution.
Supervisor: Secombes, Christopher Sponsor: University of Aberdeen ; Goverment of Karnataka ; India
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: Salmonidae