Tian et al. BMC Genomics 2010, 11:187 http://www.biomedcentral.com/1471-2164/11/187 Page 10 of 19 Figure 7 Tachystatin-type and linear AMPs. A. Multiple sequence alignment of tachystatin-type AMPs. A red arrow represents a phase 0 intron; B. Model structure of naickin-1 and its superimposition with tachystatin-B1; C. Nahelixin. Signal peptide and mature peptides are shaded in gray and yellow, respectively. In the alignment of nahelixin with known AMPs from frog, identical residues are bolded and shadowed in yellow while conservative substitutions are in gray. Structure modeled ab initio is displayed in ribbon with hydrophobic residues in pink and hydrophilic residues in blue. The helical wheel projection shows the amphiphilic characteristics of nahelixin. Putative proprotein cleavage sites are boxed in black. Tt: Tachypleus tridentatus, Pc: Psalmopoeus cambridgei, Al: Acrocinus longimanus, Bh: Bradysia hygida, Mc: Mesembryanthemum crystallinum, Mj: Mirabilis jalapa, Pa: Phytolacca americana, Ppa: Pseudis paradoxa. genomics approaches is becoming quite valuable. Some examples include hormones from nematode and mos- quito, odorant binding-like proteins from honey bee, opossum immune genome, and reptile venom genes [78-82]. However, most strategies used are primarily based on sequence similarity that is useful in finding orthologues of known genes. An additional computa- tional search strategy depends on the presence of con- served structural motifs within a peptide superfamily. Such examples include the identification of fungal DLPs and mammalian b-defensins [32,83]. Here, we identified the N. vitripennis AMPs in a genomic scale by using an integrated strategy which combines similarity search, pattern recognition and AMP characteristics (see addi- tional file 1). Our previous and current studies indicate that at least 44 AMPs are present in N. vitripennis. In comparison with A. mellifera AMPs [18,25,26], we found an obvious complexity increase of immune peptides in the parasitic wasp, both in number and protein precursor size (Figure 9). For example, N. vitripennis has three abaecins, six defensins and fourteen nasonins whereas A. mellifera has only 1 abaecin, 2 defensins and lacks nasonins. Besides changes in number, N. vitripennis also undergoes wide sequence extension. For instance, mem- bers in the nabaecin family from N. vitripennis have an extended carboxyl-terminus of about 65 residues relative to A. mellifera while nahymenoptaecins underwent dupli- cation in their amino- or carboxyl-terminus (Figures 5 and 6, also see [26]) which largely enlarges their molecu- lar size. In addition, the same type AMPs (e.g. defensins) also considerably change in several aspects: 1) The length variation in the n-loop (i.e. nasonins); 2) The develop- ment of a wrapper disulfide bridge [84] (i.e. navitricins); 3) Carboxyl-terminal extension (i.e. navidefensin1s) (Figure 10); and 4) For nasonin-2 and -6, the nasonin-like domain (NLD) repeats 4-5 times and thus represents another type of complexity increase (Figure 11). In comparison with several non-Hymenopteran insects whose genome sequences have been released (e.g. D. melanogaster and A. gambiae from Diptera, B. mori from Lepidoptera, and T. castaneum from Coleoptera)