title: Trends in genome dynamics among major orders of insects revealed through variations in protein families.
abstract: BACKGROUND
  Insects belong to a class that accounts for the majority of animals on earth. With over one million identified species, insects display a huge diversity and occupy extreme environments. At present, there are dozens of fully sequenced insect genomes that cover a range of habitats, social behavior and morphologies. In view of such diverse collection of genomes, revealing evolutionary trends and charting functional relationships of proteins remain challenging.
  
  
  RESULTS
  We analyzed the relatedness of 17 complete proteomes representative of proteomes from insects including louse, bee, beetle, ants, flies and mosquitoes, as well as an out-group from the crustaceans. The analyzed proteomes mostly represented the orders of Hymenoptera and Diptera. The 287,405 protein sequences from the 18 proteomes were automatically clustered into 20,933 families, including 799 singletons. A comprehensive analysis based on statistical considerations identified the families that were significantly expanded or reduced in any of the studied organisms. Among all the tested species, ants are characterized by an exceptionally high rate of family gain and loss. By assigning annotations to hundreds of species-specific families, the functional diversity among species and between the major clades (Diptera and Hymenoptera) is revealed. We found that many species-specific families are associated with receptor signaling, stress-related functions and proteases. The highest variability among insects associates with the function of transposition and nucleic acids processes (collectively coined TNAP). Specifically, the wasp and ants have an order of magnitude more TNAP families and proteins relative to species that belong to Diptera (mosquitoes and flies).
  
  
  CONCLUSIONS
  An unsupervised clustering methodology combined with a comparative functional analysis unveiled proteomic signatures in the major clades of winged insects. We propose that the expansion of TNAP families in Hymenoptera potentially contributes to the accelerated genome dynamics that characterize the wasp and ants.
authors.affiliation: School of Computer Science and Engineering, The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel. nadavrap@cs.huji.ac.il.
authors.forename: Nadav
authors.initials: N
authors.lastname: Rappoport
authors.affiliation: Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel. michall@cc.huji.ac.il.
authors.forename: Michal
authors.initials: M
authors.lastname: Linial
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D049750:Genome, Insect / Q000235:genetics*; D007313:Insecta / Q000235:genetics*; D010802:Phylogeny; D020543:Proteome / Q000235:genetics*; D040901:Proteomics / Q000379:methods; D013045:Species Specificity; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D020543:Proteome