Ing the CDS, we first aligned unigenes to nr, then Swiss-Prot

Ing the CDS, we first aligned unigenes to nr, then Swiss-Prot, then KEGG, and finally COG. Unigenes aligned to a higher priority database will not be aligned to lower priority database. The alignments end when all alignments were finished. Proteins with highest ranks in BLAST results were taken to decideDe novo Assembly of Sequencing Reads and Sequence ClusteringThe cDNA library was sequenced on the Illumina sequencing platform. Image deconvolution and quality value calculations were performed using the Illumina GA pipeline 1.3. The raw reads were cleaned by removing adaptor sequences, empty reads and low quality sequences (reads with unknown sequences `N’). De novo transcriptome assembly was carried out with short reads assembling program ?Trinity [21]. Trinity firstly combined reads with certain length of overlap to form longer fragments, which are Table 3. Putative genes involved in castes differentiation.Gene Annotation hexamerin 1 hexamerin 2* b-glycosidase* bicaudal D CYP4U3v1 GGPP synthase cytochrome oxidase III*Gene ID Unigene30435 Unigene34583 Unigene34266 Unigene55044 CL6118.Contig1 Unigene57705 UnigeneLength (bp) 374 2575 1238 1072 1998 25331948 526Subject ID BAG48838.1 AAU20852.2 AAL40863.1 EFA07458.1 ABB86762.2 BAJ79290.1 YP_002650710.Species AZP-531 site Reticulitermes speratus Reticulitermes flavipes Rhyparobia maderae Tribolium castaneum Reticulitermes flavipes Reticulitermes speratus Dermatophagoides pteronyssinusE value 2E-50 0 4E-76 1E-132 0 4E-40 6E-*denotes a gene selected for qPCR. doi:10.1371/journal.pone.0050383.tTranscriptome and Gene Expression in TermiteFigure 8. The qPCR analysis of putative genes involved in caste get AZP-531 differentiation and aggression. The x-axis indicates three different castes. The y-axis indicates the relative expression value of uingene. (A) mRNA relative expression values for hexamerin 2. (B) mRNA relative expression values for b-glycosidase. (C) mRNA relative expression values for bicaudal D. (D) mRNA relative expression values for Cyp6a20. Letters above each bar denote significantly different groups. Significant differences were identified by a one-way ANOVA with means separated using Tukey’s HSD (P,0.05). doi:10.1371/journal.pone.0050383.gthe coding region sequences of unigenes, and then the coding region sequences were translated into amino sequences with the standard codon table. So both the nucleotide sequences (59?9) and amino sequences of the unigene coding region were acquired. Unigenes that cannot be aligned to any database are scanned by ESTScan, producing nucleotide sequence (59?9) direction and amino sequence of the predicted coding region [28].Mononucleotide repeats were ignored because it was difficult to distinguish genuine mononucleotide repeats from polyadenylation products and single nucleotide stretch errors generated by sequencing.Gene Mining and Quantitative Real Time PCRTotal RNA was extracted from heads of workers, soldiers and larvae using TRIzol following the manufacturer’s protocol. Approximately 1 mg of DNase I-treated total RNA was converted into single-stranded cDNA using a PrimeScript RT regent reagent Kit (perfect real time) (TaKaRa, Dalian, China). The cDNA products were then diluted 80-fold with deionized water before use as a template in real-time PCR. The quantitative reaction wasEST-SSR DetectionPutative SSR markers were predicted among the 116,885 unigenes using Serafer [49]. The parameters were adjusted for identification of perfect di-, tri-, tetra-, penta-, and hexanucleotid.Ing the CDS, we first aligned unigenes to nr, then Swiss-Prot, then KEGG, and finally COG. Unigenes aligned to a higher priority database will not be aligned to lower priority database. The alignments end when all alignments were finished. Proteins with highest ranks in BLAST results were taken to decideDe novo Assembly of Sequencing Reads and Sequence ClusteringThe cDNA library was sequenced on the Illumina sequencing platform. Image deconvolution and quality value calculations were performed using the Illumina GA pipeline 1.3. The raw reads were cleaned by removing adaptor sequences, empty reads and low quality sequences (reads with unknown sequences `N’). De novo transcriptome assembly was carried out with short reads assembling program ?Trinity [21]. Trinity firstly combined reads with certain length of overlap to form longer fragments, which are Table 3. Putative genes involved in castes differentiation.Gene Annotation hexamerin 1 hexamerin 2* b-glycosidase* bicaudal D CYP4U3v1 GGPP synthase cytochrome oxidase III*Gene ID Unigene30435 Unigene34583 Unigene34266 Unigene55044 CL6118.Contig1 Unigene57705 UnigeneLength (bp) 374 2575 1238 1072 1998 25331948 526Subject ID BAG48838.1 AAU20852.2 AAL40863.1 EFA07458.1 ABB86762.2 BAJ79290.1 YP_002650710.Species Reticulitermes speratus Reticulitermes flavipes Rhyparobia maderae Tribolium castaneum Reticulitermes flavipes Reticulitermes speratus Dermatophagoides pteronyssinusE value 2E-50 0 4E-76 1E-132 0 4E-40 6E-*denotes a gene selected for qPCR. doi:10.1371/journal.pone.0050383.tTranscriptome and Gene Expression in TermiteFigure 8. The qPCR analysis of putative genes involved in caste differentiation and aggression. The x-axis indicates three different castes. The y-axis indicates the relative expression value of uingene. (A) mRNA relative expression values for hexamerin 2. (B) mRNA relative expression values for b-glycosidase. (C) mRNA relative expression values for bicaudal D. (D) mRNA relative expression values for Cyp6a20. Letters above each bar denote significantly different groups. Significant differences were identified by a one-way ANOVA with means separated using Tukey’s HSD (P,0.05). doi:10.1371/journal.pone.0050383.gthe coding region sequences of unigenes, and then the coding region sequences were translated into amino sequences with the standard codon table. So both the nucleotide sequences (59?9) and amino sequences of the unigene coding region were acquired. Unigenes that cannot be aligned to any database are scanned by ESTScan, producing nucleotide sequence (59?9) direction and amino sequence of the predicted coding region [28].Mononucleotide repeats were ignored because it was difficult to distinguish genuine mononucleotide repeats from polyadenylation products and single nucleotide stretch errors generated by sequencing.Gene Mining and Quantitative Real Time PCRTotal RNA was extracted from heads of workers, soldiers and larvae using TRIzol following the manufacturer’s protocol. Approximately 1 mg of DNase I-treated total RNA was converted into single-stranded cDNA using a PrimeScript RT regent reagent Kit (perfect real time) (TaKaRa, Dalian, China). The cDNA products were then diluted 80-fold with deionized water before use as a template in real-time PCR. The quantitative reaction wasEST-SSR DetectionPutative SSR markers were predicted among the 116,885 unigenes using Serafer [49]. The parameters were adjusted for identification of perfect di-, tri-, tetra-, penta-, and hexanucleotid.