Wang et al. BMC Genomics 2012, 13:529 http://www.biomedcentral.com/1471-2164/13/529 Background The whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a species complex composed of at least 31 morphologically indistinguishable cryptic species (hereafter referred to as "species") [1-6]. These species differ genetically as well as in host range, fecundity, in- secticide resistance, mating behavior and ability to trans- mit begomoviruses [7-12]. While many species within the B. tabaci complex cause no obvious harms to agri- cultural production; some members of this species com- plex are highly invasive and cause extensive damage to agricultural, horticultural, and ornamental crops through direct feeding or the transmission of plant viruses [13,14]. Two species of the B. tabaci complex, Middle East - Asia Minor 1 (previously known as biotype B; hereafter MEAM1) and Mediterranean (previously known as biotype Q; hereafter MED) have risen to inter- national prominence due to their global invasion during the last 20 years [8,15]. MEAM1 and MED originated from the Middle East Asia Minor and Mediterranean Basin regions respectively, and have invaded many coun- tries around the world [3,16]. Extensive evidence has indicated that the invasion of MEAM1 and MED are associated with the displacement of their closely related indigenous whitefly species [8,14]. The invasion of an alien whitefly species and competi- tion between invasive and indigenous species are mediated by many abiotic and biotic factors. Efforts have been made to understand the factors that contribute to the incursion of the two species into new regions and the displacement of indigenous species. For example, the invasion of MEAM1 is assumed to be associated with its high adapt- ability under various environmental stresses and host plants [9,10,17,18]. Liu et al. [8] also revealed that the dis- placement of indigenous whitefly species by MEAM1 is associated with the behavior of mating interference. On the other hand, the spread of MED is closely related to its ability to maintain high levels of resistance to major classes of insecticides [19-22]. Despite these advances, the molecular mechanisms underlying the extraordinary cap- acity of MEAM1 and MED to spread and ultimately dis- place the native species remains largely unknown. Furthermore, previous studies have mainly focused on sin- gle gene or individual aspect of the B. tabaci biology, a global picture of the genetic factors associated with the in- vasion of these two whitefly species is still lacking. The genomic divergence between invasive and indigen- ous species is valuable for determining how phenotypes specific to invasive species have been formed [23]. By exam- ining the divergence of large numbers of genes, a overall picture of genetic differences and invasion mechanisms may be attained [24]. Here, we propose that a global ana- lysis of genomic divergence among the B. tabaci species complex will reveal the molecular mechanisms underlying Page 2 of 13 the biological invasions of MEAM1 and MED. First, the B. tabaci species are reproductively isolated, but retain suffi- cient genetic similarity for comparative analyses [4,25,26]. Second, the whitefly species went through an allopatric di- vergence process and showed significant differences in sur- vival and reproductive performance [16,27,28]. This warrants exploring the interspecies evolutionary processes through the comparison of orthologous genes. Third, at least 31 species have been delineated for the B. tabaci com- plex including 2 invasive species and 29 indigenous species. The rich diversity of invasive and indigenous species allows extensive cross comparisons of orthologous genes among difference members of the complex, which will facilitate the elucidation of invasive mechanisms. The transcriptomes of two invasive whitefly species MED and MEAM1 have been sequenced using Illumina sequencing technology [29,30]. In this study, we sequenced the transcriptome of an indigenous B. tabaci species - Asia II 3 (previously known as biotype ZHJ1) and generated 52,535 distinct sequences. These tran- scriptome sequences provide a rich molecular resource for functional analysis of the native B. tabaci species. In order to gain further insights on how genes have diverged between the indigenous and invasive whiteflies, we compared the global sequence divergence between the transcriptomes of Asia II 3 and the invasive species MEAM1 and MED. The identification and analysis of di- vergent sequences between the indigenous and invasive whitefly species opens the door for future investigations on the molecular mechanisms of B. tabaci invasion. The approach described in this manuscript will significantly accelerate the identification of genetic variation under- lying adaptation in B. tabaci and other invasive species. Results and discussion Illumina sequencing and assembly of Asia II 3 transcriptome Using Illumina technology, the transcriptome of the in- digenous Asia II 3 whitefly species was sequenced. A total of 16,871,140 reads of 74 base pairs long were obtained in a single run and were assembled into 144,103 contigs (average length: 201 bp) with SOAPde- novo software [31]. The contigs were assembled into 77,263 scaffolds (mean size: 359 bp) and further clus- tered into 52,535 distinct sequences (mean size: 466 bp) (Table 1). Overall, these results are comparable to the transcriptome of the invasive MEAM1 which contains 104,722 scaffolds (mean size: 326 bp) and 57,741 distinct sequences with an average length of 479 bp (Additional file 1) [30]. However, compared to the transcriptome of MED, which contains 168,900 distinct sequences, the number of genes in the Asia II 3 transcriptome is much less. This is probably due to the lower number of se- quencing reads in the transcriptomes of Asia II 3 (16.8