An overview of arthropod genomics, mitogenomics, and the evolutionary origins of the arthropod proteome

Arthropods represent the largest majority of animal biodiversity and include organisms of economic interest and key model species. It is thus unsurprising that the genome of an arthropod, the fruit fly Drosophila melanogaster, was among the very first to be sequenced (Adams et al. 2000) and that to date, about 21 Drosophila genomes as well as a variety of other arthropod genomes have been sequenced. Despite this promising start, current sampling is biased towards economically relevant species, and a suitable close outgroup to the arthropods, which is necessary to polarise genomic studies, is still missing. Among the suitable outgroups to the Arthropoda, the Nematoda represent one of the largest components of the extant animal biomass, and their economic importance is comparable to that of the more biodiverse arthropods. As with the Arthropoda, the importance of the nematodes is reflected in the fact that the very first animal genome to be sequenced was that of the nematode Caenorhabditis elegans (The C. elegans genome consortium 1998). Despite the nematodes being phylogenetically close to the arthropods (Aguinaldo et al. 1997; Copley et al. 2004; Dopazo and Dopazo 2005; Philippe et al. 2005; Irimia et al. 2007; Roy and Irimia 2008; Dunn et al. 2008; Belinky et al. 2010; Hejnol et al. 2009; Holton and Pisani 2010), this group is composed of highly derived species, both genetically and morphologically. Accordingly, their genomes are unlikely to be of great utility in understanding arthropod genome evolution. Some genomic data (mostly in the form of transcriptomes) are now available for other smaller ecdysozoan phyla, and some genomes (Priapulida and Tardigrada) are on the horizon. Nonetheless, enough genomic information is now available for the Arthropoda (Table 3.1) to justify an investigation into the evolution of their genome. Such an analysis, however, is intimately dependent on the availability of a robust phylogenetic background, and to a lesser extent, robust divergence times for the nodes in the background phylogen