Wang et al. BMC Genomics 2012, 13:529 http://www.biomedcentral.com/1471-2164/13/529 Table 1 Summary for the Asia II 3 B. tabaci transcriptome Total number of reads Total base pairs (bp) Average read length (bp) Total number of contigs Mean length of contigs ( bp) Total number of scaffolds Mean length of scaffolds (bp) Distinct sequences Sequences with E-value < 10-5 16,871,140 1,248,464,360 74 144,103 201 77,263 359 52,535 15,357 million) and MEAM1 (17 million) compared to the MED transcriptome (43.7 million) (Additional file 1) [29,30]. Even though a large number of genes (52,535) were identified, a large fraction of lowly expressed tran- scripts were probably missed due to a low number of se- quence reads (16.8 million). Functional annotation of Asia II 3 transcriptome For functional annotation, distinct sequences were searched against the non-redundant (nr) NCBI nucleotide database and a total of 16,596 genes returned an above cut-off BLAST result representing about 31.6% of all Table 2 Highly expressed genes in the transcriptome of Asia II 3 Number of readsa Gene ID BT_ZHJ1_ZJU_Unigene4448 13476 BT_ZHJ1_ZJU_Unigene5935 8392 BT_ZHJ1_ZJU_Unigene44594 6567 BT_ZHJ1_ZJU_Unigene40759 4952 BT_ZHJ1_ZJU_Unigene33425 3191 BT_ZHJ1_ZJU_Unigene36010 3122 BT_ZHJ1_ZJU_Unigene40277 3388 BT_ZHJ1_ZJU_Unigene33344 2299 BT_ZHJ1_ZJU_Unigene42468 3239 BT_ZHJ1_ZJU_Unigene38168 2689 BT_ZHJ1_ZJU_Unigene44051 3336 BT_ZHJ1_ZJU_Unigene43506 3232 BT_ZHJ1_ZJU_Unigene49876 5853 BT_ZHJ1_ZJU_Unigene43457 3079 BT_ZHJ1_ZJU_Unigene46015 3456 BT_ZHJ1_ZJU_Unigene37661 2284 BT_ZHJ1_ZJU_Unigene38243 2286 BT_ZHJ1_ZJU_Unigene45492 3074 BT_ZHJ1_ZJU_Unigene44482 2871 BT_ZHJ1_ZJU_Unigene34665 1906 RPKMb 3433.5 3212.7 2854.2 2613.5 2213.8 1946.6 1820.6 1595.0 1584.9 1552.2 1498.4 1497.2 1473.5 1430.8 1358.3 1344.7 1319.6 1258.3 1255.2 1251.8 Page 3 of 13 distinct sequences (Additional file 2). This proportion is similar to the 20% to 40% of annotated sequences from a traditional Sanger sequenced EST library [32]. To deter- mine the possible functions of assembled Asia II 3 genes, Gene Ontology (GO) assignments were used to classify the distinct sequences. Based on sequence homology, 4,819 sequences could be categorized into functional groups under the “Molecular function”, “Biological process” and “Cellular component” divisions (Additional file 3). The functions of genes cover various biological pro- cesses and genes participate in “Cellular process” and “Metabolic process” are the most highly represented. Next, we compared the GO classification of the Asia II 3 tran- scriptome with that of MEAM1 and MED transcriptomes, respectively [29,30] and found that the distributions of gene functions from these three species are similar (Add- itional file 3). These results suggest: i) the functions of genes from Asia II 3, MEAM1 and MED are highly con- served; ii) there is no bias in the construction of the librar- ies from these B. tabaci species. Analysis of Asia II 3 gene expression The level of Asia II 3 gene expression was analyzed based on the number of Reads Per Kilobase per Million mapped reads (RPKM); and a list of all the genes and Swissprot annotation Actin-5, muscle-specific Tubulin alpha-1 chain 60S ribosomal protein L18a ADP,ATP carrier protein 2 Elongation factor 1-alpha 2 Glyceraldehyde-3-phosphate dehydrogenase ATP synthase subunit beta, mitochondrial Troponin T, skeletal muscle Elongation factor 1-alpha 40S ribosomal protein S12 Vitellogenin-A1 40S ribosomal protein S11 60S ribosomal protein L15 40S ribosomal protein S20 60S ribosomal protein L6 Ferritin, middle subunit Paramyosin, short form ATP synthase subunit alpha, mitochondrial Vitellogenin 40S ribosomal protein S2 aThe total number of reads mapped to each gene. bGene expression level was determined by calculating the number of reads for each gene and then normalizing to RPKM (reads per kilobase per million mapped reads).