Wang et al. BMC Genomics 2012, 13:529 http://www.biomedcentral.com/1471-2164/13/529 Page 5 of 13 M1 families A in E e M ot r 4p 6,17 602 1,921 3,023 582 628 705 8 , 4 0 5 p ro M tei ED n f m a 2,756 ilies Asia II 3 4,938 protein families Figure 2 Protein families from the transcriptomes of Asia II 3, MEAM1 and MED. Protein families were identified for all the translated genes of the three transcriptomes using Blastp and a Markov Cluster algorithm (MCL). The total numbers of protein families belonging to each category are listed in the figure. The 3,023 protein families, which belong to all the three transcriptomes, were referred to as “Core protein families”. Identification of the orthologous genes between Asia II 3 and MEAM1, Asia II 3 and MED Possible orthologous genes between the transcriptomes of Asia II 3 and MEAM1were identified according to the diagram in Figure 3 (left). Between Asia II 3 and MEAM1, a total of 20,929 pairs of possible orthologs were identified. Among these sequence pairs, 3,308 pairs of sequences could be unambiguously mapped to the same protein in Swissprot database, suggesting strongly that they are orthologous genes (Figure 3). Based on the coding information of Swissprot hits, the untranslated region (UTR) of each gene pair was predicted (210 pairs of 5'UTR and 337 pairs of 3'UTR) and 2,966 pairs of orthologous coding sequences (CDS) were obtained (Figure 3 and Additional file 5). The features of the 2,966 orthologous genes are listed in Table 4. Similarly, 22,415 pairs of potential orthologs were identified be- tween Asia II 3 and MED (Figure 3, right). After the Swissprot annotation, 102 pairs of 5’UTRs, 102 pairs of 3’ UTRs and 2,529 pairs of CDS were identified between the transcriptomes of Asia II 3 and MED (Table 4). The average divergence for the 2,966 orthologous genes be- tween Asia II 3 and MEAM1 is 1.73%. This difference is comparable to the average divergence between Asia II 3 and MED (1.84%) and much higher than the divergence Table 3 Statistically enriched Gene Ontology terms in the “Core protein families” GO term GO:0005524 GO:0005525 GO:0003924 GO:0005811 GO:0005198 GO:0006865 GO:0006457 GO:0008152 GO:0015171 GO:0051301 GO:0005215 GO:0004252 GO:0030126 GO:0006508 GO:0000166 GO:0005506 GO:0045211 GO:0008234 MEAM1 264 70 45 72 18 11 23 77 8 15 17 24 9 49 81 47 19 13 Number of Core protein family genes mapped to each GO MED Asia II 3 222 243 55 48 29 31 51 64 19 15 18 13 14 27 85 50 17 9 14 15 18 24 20 15 7 10 52 38 55 60 24 20 18 19 15 7 Total 729 173 105 187 52 42 64 212 34 44 59 59 26 139 196 91 56 35 All transcriptome genes mapped to each GO 920 202 119 230 56 44 71 267 35 47 66 66 26 171 249 108 63 37 p-value 1.60E-16 2.55E-09 1.34E-07 1.82E-06 6.42E-06 7.50E-06 7.68E-06 9.75E-06 1.91E-05 1.99E-05 3.30E-05 3.30E-05 3.69E-05 3.90E-05 5.65E-05 6.35E-05 7.76E-05 8.46E-05 GO annotation ATP binding GTP binding GTPase activity lipid particle structural molecule activity amino acid transport protein folding metabolic process amino acid transmembrane transporter activity cell division transporter activity serine-type endopeptidase COPI vesicle coat proteolysis nucleotide binding iron ion binding postsynaptic membrane cysteine-type peptidase activity