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Title: On the evolution of effector gene families in potato cyst nematodes
Author: Laetsch, Dominik Robert
ISNI:       0000 0004 7429 4195
Awarding Body: University of Edinburgh
Current Institution: University of Edinburgh
Date of Award: 2018
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Potato cyst nematodes (PCN) are economically relevant plant parasites that infect potato crops. The genomes of three PCN species are available and genome data have been generated for several populations of PCN, to address questions related to the molecular basis of plant parasitism. In this thesis, I employ approaches of comparative genomics to highlight differences and similarities between PCNs and other nematode species. I present two new software solutions to address challenges associated with the field of comparative genomics: BlobTools, a taxonomic interrogation toolkit for quality control of genome assemblies, and KinFin, a solution for the analysis of protein orthology data. I apply both software solutions to genomic datasets of nematodes, platyhelminths, and tardigrades. Based on KinFin analysis of plant parasitic nematodes, I identify protein families in PCNs likely to be involved in host-parasitic interaction, termed effectors, and discuss their functions. I highlight examples of horizontal gene transfer from bacteria to plant parasitic nematodes. Through genomic data of European and South American populations of PCNs, I address variation in populations, infer phylogenetic relationships, and try to estimate the effect of selection on effector genes identified through KinFin. Furthermore, I estimate the rate of variation across the reference genomes of two PCNs.
Supervisor: Blaxter, Mark ; Stone, Graham ; Blok, Vivian Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: evolutionary biology ; bioinformatics ; genomics ; nematode ; potato cyst nematodes ; comparative genomics ; BlobTools