Wang et al. BMC Genomics 2012, 13:529 http://www.biomedcentral.com/1471-2164/13/529 transition over transversion (ts/tv) was determined for the 5’UTR, CDS and 3’UTR as well. Using the KaKs Cal- culator, we also estimated the substitution rates for non- synonymous sites (Ka) and synonymous (Ks) sites (YN method) [52,53]. Phylogeny of Asia II 3, MEAM1 and MED The orthologous genes among Asia II 3, MEAM1 and MED were selected for sequence alignment using MUSCLE [54] and the aligned fragments were extracted for phylogen- etic analysis using MEGA 5 [55]. The evolutionary history was inferred using the neighbor-joining method [56]. All positions containing gaps and missing data were eliminated and the within population polymorphisms were not included for divergence estimation. The analysis involved a total of 686,101 positions in the final dataset. The evolu- tionary distances were computed using the Maximum Composite Likelihood method [57] and are in the units of the number of base substitutions per site. SNP analysis To reveal the mechanism of divergence between Asia II 3 and MEAM1, we analyzed the potential SNP sites in CDS of the orthologous gene pairs between the invasive and indigenous whitefly species. The orthologous gene pairs of Asia II 3 & MEAM1 and Asia II 3 & MED were subjected to SNP analysis according to the previous de- scription with slight modifications [58]. In short, the Illumina sequencing reads were mapped to the ortholo- gous CDS regions of each gene using TopHat (V1.2.0) with the following parameters: -g1 -r 200 –mate-std-dev 20 -I 10000 [59]. All possible SNP sites with the mini- mum read depth of 10 reads were then identified by SAMTools (V0.1.13) based on aligned outcomes [60]. The analyses of amino acid mutation and functional an- notation were performed by a custom-written algorithm. Additional files Additional file 1: Summary of Asia II 3, MEAM1 and MED transcriptomes. Additional file 2: Top BLASTx hits from NCBI nr database. BLASTx results against the NCBI nr database for all the distinct sequences with a cut-off E value above 1.0E-5 are shown. BT: Bemisia tabaci. Additional file 3: Gene Ontology comparison of Asia II 3, MEAM1 and MED transcriptomes. The Gene Ontology (GO) terms are summarized in three main categories: biological process, cellular component and molecular function. The left y-axis indicates the percentage of genes within a specific category in that main category. The right y-axis means the number of genes in a category. A. GO comparison between Asia II 3 and MEAM1. B. GO comparison between Asia II 3 and MED. Additional file 4: Gene expression level of Asia II 3 transcriptome. The length of each distinct sequence and numbers of raw reads for each gene are listed. Swissprot and nr annotations were shown as well. RPKM: reads per kilobase per million mapped reads. Page 11 of 13 Additional file 5: List of the orthologous gene pairs between Asia II 3 and MEAM1. The length of coding sequence, homology and Swissprot, nr annotations are shown. Additional file 6: Sequence divergence between Asia II 3 and MED transcriptomes. Additional file 7: Ka and Ks of each orthologous gene pairs between Asia II 3 and MEAM1. Ka: nonsynonymous substitution rate; Ks: synonymous substitution rate. Additional file 8: Ka and Ks of each orthologous gene pairs between Asia II 3 and MED. Ka: nonsynonymous substitution rate; Ks: synonymous substitution rate. Additional file 9: Mean sequence identity by KEGG classification. The KEGG pathway description and ID are shown. Number of sequences: total number of sequences in a specific KEGG pathway. Additional file 10: SNP sites in the coding sequence of orthologous gene pairs between Asia II 3 and MEAM1. Additional file 11: SNP sites in the coding sequence of orthologous gene pairs between Asia II 3 and MED. Competing interests The authors declare that they have no competing interests. Authors’ contributions XWW, QYZ, JBL and SSL conceived and designed the experimental plan. XWW, QYZ, JBL and GHY performed experiments. XWW, QYZ and YJW analyzed and interpreted the sequence data. XWW and SSL drafted the manuscript. All authors read and approved the final manuscript. Acknowledgements Financial support for this study was provided by the National Basic Research Program of China (Project 2009CB119203), and the National Natural Science Foundation of China (Project 31021003, 31071686). We thank Laura Boykin for editing the manuscript. Author details 1Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China. 2The University of Queensland, Queensland Brain Institute, Brisbane, Qld 4072, Australia. Received: 19 April 2012 Accepted: 28 September 2012 Published: 4 October 2012 References 1. Dinsdale A, Cook L, Riginos C, Buckley Y, De Barro PJ: Refined global analysis of Bemisia tabaci (Gennadius) (Hemiptera: Sternorrhyncha: Aleyrodoidea) mitochondrial CO1 to identify species level genetic boundaries. Ann Entomol Soc Am 2010, 103:196–208. 2. De Barro PJ, Liu SS, Boykin LM, Dinsdale AB: Bemisia tabaci: a statement of species status. Annu Rev Entomol 2011, 56:1–19. 3. Hu J, De Barro PJ, Zhao H, Wang J, Nardi F, Liu SS: An extensive field survey combined with a phylogenetic analysis reveals rapid and widespread invasion of two alien whiteflies in china. PLoS One 2011, 6:e16061. 4. 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