3 An Overview of Arthropod Genomics, Mitogenomics, and the Evolutionary Origins of the Arthropod Proteome Davide Pisani, Robert Carton, Lahcen I. Campbell, Wasiu A. Akanni, Eoin Mulville and Omar Rota-Stabelli Contents 3.1 Introduction................................................ 41 3.2 Arthropod Mitogenomes: Useful, but Hazardous Small Genomes ............... 42 3.2.1 Mitogenomic Studies................................... 42 3.2.2 The Structure of the Arthropod Mitochondrial Genome ............................... 44 3.2.3 Arthropod Mitogenomes: A Composition Nightmare .................................................... 44 3.2.4 The Hazards of Using Arthropod Mitochondrial Genomes for Phylogenetics ......................................... 46 3.3 Arthropod Comparative Genomics ......... 46 3.3.1 Uneven Taxonomic Sampling..................... 48 3.3.2 Heterogeneity of Genome Sizes and Shortage of microRNA ........................ 49 3.4 A Genomic Phylostratigraphic Analysis of the Arthropod Proteomes .................... 50 3.4.1 A Robust Phylogenetic Framework for Genomic Studies ................................... 50 3.4.2 Expanding Our Understanding of the Arthropod Comparative Genomics ..................................................... 51 3.4.3 The Evolution of Orphan Gene Families in Arthropoda .............................................. 52 3.4.4 Conserved Rate of Gene Gain with Some Surprises ...................................................... 55 3.5 Conclusions ................................................. 56 Appendix: Methods for the Analyses Presented in this Chapter ........................................................ 56 A. Generation of the Onychophoran Transcriptome ...................................................... 56 B. Mitogenomic Compositional Analyses ............... 57 C. Phylogenetic Analyses......................................... 57 References ................................................................ 58 3.1 Introduction 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 arthro- pod, the fruit fly Drosophila melanogaster, was among the very first to be sequenced (Adams et al. 2000) and that to date, about 21 Drosophila D. Pisani (&) School of Biological Sciences and School of Earth Sciences, University of Bristol, Woodland Road, Bristol, BS8 1UG, UK e-mail: Davide.Pisani@bristol.ac.uk R. Carton Á L. I. Campbell Á W. A. Akanni Á E. Mulville Department of Biology, The National University of Ireland, Callan Building, Maynooth, County Kildare, Ireland e-mail: robcarton@gmail.com L. I. Campbell e-mail: lahcencampbell@yahoo.ie W. A. Akanni e-mail: waakanni13@gmail.com E. Mulville e-mail: eoin.d.mulvihill@nuim.ie O. Rota-Stabelli IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige (TN), Italy e-mail: omar.rota@fmach.it A. Minelli et al. (eds.), Arthropod Biology and Evolution, DOI: 10.1007/978-3-642-36160-9_3, Ó Springer-Verlag Berlin Heidelberg 2013 41