Wang et al. BMC Genomics 2012, 13:529 http://www.biomedcentral.com/1471-2164/13/529 expression levels are shown in Additional file 4. To our knowledge, this is the first global analysis of gene ex- pression level in B. tabaci. Twenty annotated genes with very high expression levels (RPKM> 1,250) were found. Many of the genes with significant expression levels were involved in cell structure (e.g. actin and tubulin), ribosome (e.g. 60S ribosomal protein, 40S ribosomal protein) and energy metabolism (e.g. ATP synthase and glyceraldehyde-3-phosphate dehydrogenase) (Table 2). This finding is not surprising, as these genes are essen- tial for the survival of an organism. Next, we grouped Asia II 3 genes into three categories based on their levels of expression. Roughly, 14% of the genes were highly expressed (RPKM> 50), 25% of the transcripts were in medium level (50>RPKM>20) and 61% of the genes had a RPKM<20 (Figure 1A). Conversely, when calculating the number of reads for each gene, it was found that the small fraction of highly expressed genes constituted ap- proximately 61% of the sequenced reads, whereas only 13% of the reads were from the genes with low expres- sion levels (Figure 1B). Identification and analysis of B. tabaci protein families To compare the transcriptomes of Asia II 3, MEAM1 and MED, protein families for the three species were built. A total of 10,217 protein families were identified based on sequence similarities (Figure 2). The number of protein families for MED transcriptome was 8,405, which is much higher than that of Asia II 3 (4,938) and MEAM1 (6,174). In this comparison, both diversification and conservation of the B. tabaci transcriptomes were obvious at the protein family level. A total of 3,023 pro- tein families were conserved among the transcriptomes of Asia II 3, MEAM1 and MED which represent the core cellular and physiological proteins (hereafter “Core pro- tein families”) common to the three species. The total number of protein families found in only one species was 3,940 (2,756+582+602), which might be responsible for the differences and unique features of each species (Figure 2). However, as these transcriptomes are incom- plete, the number of species-specific protein families is likely to change when more genes are sequenced. Among these specific protein families, the majority was from MED (2,756). This is probably due to the higher sequencing amount of MED (3G) compared to Asia II 3 (1G) and MEAM1 (1G) (Additional file 1) [29,30]. To reveal the common characteristics of the whitefly tran- scriptomes, a hypergeometric test was implemented to identify enriched GO terms in the “Core protein fam- ilies”. A total of 18 protein families were significantly enriched (Table 3). Interestingly, 3 of the 18 enriched GO terms were related to nucleotide binding. This phenomenon is consistent with the previous finding in the analysis of nematode transcriptomes [33] and >50 20-50 Expression level (PRKM) Figure 1 Levels of gene expression of Asia II 3 transcriptome. A. Percentages of Asia II 3 genes that belong to high (RPKM>50), medium (50>RPKM>20) and low (RPKM<20) expression levels based on the total number of Reads Per Kilobase per Million mapped reads (RPKM). B. Numbers of reads mapped to the genes of high (RPKM>50), medium (50>RPKM>20) and low (RPKM<20) expression levels. The exact values are shown on the top of each bar. demonstrates the importance and conservation of nu- cleotide binding proteins in different species. The other major GO terms enriched in the “Core protein families” were related to amino acid transporter, protein folding, proteolysis and peptidase, suggesting the critical roles of protein transportation and metabolism among the three B. tabaci species (Table 3). >50 20-50 <20 Expression level (PRKM) 13,076 1,725 A B 35 ) sd 30 n a su 25 o h t ( 20 s e n e 15 g f ro 10 e b m 5 u N 0 4,500 )s4,000 d an3,500 s ou3,000 h t (s2,500 d ea2,000 r fo1,500 r e b1,000 m uN 500 0 7,578 4,159 Page 4 of 13 31,881 884 <20