Wang et al. BMC Genomics 2012, 13:529 http://www.biomedcentral.com/1471-2164/13/529 file 7). In this set of data, 25 orthologous gene pairs had a Ka/Ks value > 1 suggesting that strong positive selec- tion acts on these genes. Among the sequences with Ka/ Ks values > 1, a number of genes are involved in protein metabolism, such as peptide deformylase, cathepsin, cysteine proteinase and metalloendopeptidase, suggest- ing this process is critical for the differentiation of the B. tabaci species complex. Between Asia II 3 and MED, a total of 1,221 orthologs had Ka and Ks rates and the mean values of Ka, Ks and Ka/Ks were 0.0092, 0.0729 and 0.201. The list of Asia II 3 and MED genes with Ka/ Ks and functional annotation is presented in Additional file 8. The distribution of Ka/Ks between Asia II 3 and MED is similar to that of Asia II 3 and MEAM1, in which 7.9% of the genes had a high Ka/Ks>0.5, 44.8% of the genes were highly conserved (Ka/Ks<0.1) and 25 genes had a Ka/Ks >1. Even though a number of genes under positive selection have been identified in our study, the simple Ka/Ks calculations are quite conserva- tive and may fail to detect positive selection even when it exists [40]. Further studies using more sophisticated site and branch specific models are needed for estimat- ing Ka/Ks. Sequences with very weak amino-acid similarity The 2,966 sequence pairs between Asia II 3 and MEAM1 had a mean homology of 98.27% and the hom- ology for individual gene pair ranged from 70.43% to 100% (Additional file 5). Among these sequence pairs, only 94 show 100% homology (Additional file 5). This is Page 8 of 13 much lower compared to the 604 identical sequences between MEAM1 and MED [30]. These results further suggest that the divergence between Asia II 3 and MEAM1 is much higher that that between MEAM1 and MED (Figure 4). To reveal the proteins responsible for the differences between the two species, the functions of sequence pairs with weak amino-acid similarity were analyzed. Interestingly, many of the divergent genes were related to protein kinase and metabolism, such as Pro- tein kinase C (89.39%), Serine/threonine-protein kinase (90.42%), glutathione S-transferase (92.59%) and ethano- laminephosphotransferase (92.75%) (Additional file 5). To gain further insights into the diverged sequences, we compiled sequence identify data into gene functional groups using the Kyoto Encyclopedia of Genes and Gen- omes (KEGG) classifications. To prevent false positive results, only those classes containing five or more entries were shown (Additional file 9). Interestingly, we found that several classes of genes involved in signal transduc- tion were highly conserved between the two species, such as phototransduction, taste transduction, olfactory transduction and MAPK signaling pathway (Additional file 9). On the other hand, the most divergent KEGG classes were about metabolism, such as Metabolism of xenobiotics by cytochrome P450, Glutathione metabol- ism, and Ascorbate and aldarate metabolism (Table 6). It suggests that the divergence of cytochrome P450 genes in the metabolism of xenobiotics might be important for the differentiation between MEAM1 and Asia II 3 and warrant further investigation. Table 6 Mean identity of the orthologous gene pairs by KEGG classification Description Metabolism of xenobiotics by cytochrome P450 Drug metabolism - cytochrome P450 Glutathione metabolism Ascorbate and aldarate metabolism Oxidative phosphorylation Lysosome Pentose and glucuronate interconversions Ribosome Ubiquinone and terpenoid-quinone biosynthesis Glyoxylate and dicarboxylate metabolism Other types of O-glycan biosynthesis Steroid hormone biosynthesis MAPK signaling pathway - yeast Cardiac muscle contraction Insect hormone biosynthesis Cytokine-cytokine receptor interaction Glycosaminoglycan degradation Retinol metabolism Pathway ko00980 ko00982 ko00480 ko00053 ko00190 ko04142 ko00040 ko03010 ko00130 ko00630 ko00514 ko00140 ko04011 ko04260 ko00981 ko04060 ko00531 ko00830 Number of genes 17 17 18 5 41 46 11 14 7 6 9 15 6 10 5 8 7 19 Average identity 96.99% 96.99% 97.59% 97.71% 97.84% 97.90% 98.14% 98.18% 98.19% 98.20% 98.33% 98.36% 98.37% 98.39% 98.40% 98.50% 98.51% 98.54%