The first metazoan to be sequenced was a nematode (Caenorhabditis elegans), and
understanding the genome of this model organism has led to many insights about all
animals. Although eleven nematode genomes have been published so far and approximately
twenty more are under way, the vast majority of the genomes of this incredibly diverse
phylum remain unexplored. Next-generation sequencing has made it possible to generate
large amounts of genome sequence data in a few days at a fraction of the cost of traditional
Sanger-sequencing. However, assembling and annotating these data into genomic resources
remains a challenge because of the short reads, the quality issues in these kinds of data, and
the presence of contaminants and co-bionts in uncultured samples. In this thesis, I describe
the process of creating high quality draft genomes and annotation resources for four
nematode species representing three of the five major nematode clades: Caenorhabditis sp. 5,
Meloidogyne floridensis, Dirofilaria immitis, and Litomosoides sigmodontis. I describe the new
approaches I developed for visualising contamination and co-bionts, and I present the
details of the robust workflow I devised to deal with the problems of generating low-cost
genomic resources from Illumina short-read sequencing.
Results:
The draft genome assemblies created using the workflow described in this thesis are
comparable to the draft nematode genomes created using Sanger sequencing. Armed with
these genomes, I was able to answer two evolutionary genomics questions at very different
scales. The first question was whether any non-coding elements were deeply conserved at
the level of the whole phylum. Such elements had previously been hypothesised to be
responsible for the phylum body plan in vertebrates, insects, and nematodes. I used twenty
nematode genomes in several whole-genome alignments and concluded that no such
elements were conserved across the whole phylum. The second question addressed the
origins of the highly destructive plant-parasitic root-knot nematode Meloidogyne incognita.
Comparisons with the newly sequenced Meloidogyne floridensis genome revealed the
complex hybrid origins of both species, undermining previous assumptions about the rarity
of hybrid speciation in animals.
Conclusions:
This thesis demonstrates the role of next-generation sequencing in democratising genome
sequencing projects. Using the sequencing strategies, workflows, and tools described here,
one can rapidly create genomic resources at a very low cost, even for unculturable
metazoans. These genomes can be used to understand the evolutionary history of a genus or
a phylum, as shown