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Background  The subterranean termite  Odontotermes formosanus  (Shiraki) is a serious insect pest of trees and dams in China. To date, very little is known about genomic or transcriptomic data for caste differentiation and aggression in  O. formosanus . Hence, studies on transcriptome and gene expression profiling are helpful to better understand molecular basis underlying caste differentiation and aggressive behavior in  O. formosanus .    Methodology and Principal Findings  Using the Illumina sequencing, we obtained more than 57 million sequencing reads derived from the heads of  O. formosanus . These reads were assembled into 116,885 unique sequences (mean size  =  536 bp). Of the unigenes, 30,646 (26.22%) had significant similarity with proteins in the NCBI nonredundant protein database and Swiss-Prot database (E-value<10 −5 ). Of these annotated unigenes, 10,409 and 9,009 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. In total, 19,611 (25.52%) unigenes were mapped onto 242 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). A total of 11,661 simple sequence repeats (SSRs) were predicted from the current transcriptome database. Moreover, we detected seven putative genes involved in caste differentiation and six putative genes involved in aggression. The qPCR analysis showed that there were significant differences in the expression levels of the three putative genes  hexamerin 2 ,  β-glycosidase  and  bicaudal D  involved in caste differentiation and one putative gene  Cyp6a20  involved in aggression among workers, soldiers and larvae of  O. formosanus .    Conclusions  To our knowledge, this is the first study to characterize the complete head transcriptome of a higher fungus-cultivating termite using high-throughput sequencing. Our study has provided the comprehensive sequence resources available for elucidating molecular basis underlying caste differentiation and aggressive behavior in  O. formosanus .

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Characterization of Head Transcriptome and Analysis of Gene Expression Involved in Caste Differentiation and Aggression in Odontotermes formosanus (Shiraki)