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United States Department of Agriculture

Agricultural Research Service

Research Project: FUNCTIONAL GENOMIC STUDIES OF FORMOSAN SUBTERRANEAN TERMITES (COPTOTERMES FORMOSANUS) Project Number: 6435-32000-012-06
Project Type: General Cooperative Agreement

Start Date: Sep 28, 2007
End Date: Jul 31, 2012

Objective:
Sequencing and profiling of functional transcripts constructed in expressed sequence tags (ESTs) of Coptotermes formosanus to fulfill the following objectives: a) Identifying and annotating of genes specifically associated with post-embryonic polyphenism (caste differentiation and development); b) Discovering of genes specifically responding to environmental cues and internal signals (pesticides, food sources, juvenile hormones, etc.); and c) Characterizing of genes uniquely involved in critical physiological pathways (digestion, molting, immunity, etc.). The fulfillment of these objectives would directly lead to achieving the following goals: a) providing biochemical/physiological/molecular bases for disruption of colony formation, development and survival; b) Discovering novel target site(s) that would be developed into new control strategies that could be incorporated into effective area-wide integrated management of Formosan subterranean termites. The overall objectives of this cooperative research are to determine genes that are unique to termites - specifically reproductive and development associated genes e.g. nymph or soldier formation mechanisms with specific emphasis on Coptotermes formosanus while also examining cellulosic material hydrolyzing enzymes for agriculture and industry. We will also concentrate on private and public database and website development strategies.

Approach:
A cDNA library representing expressed genes in each different developmental stage of Coptotermes formosanus has been constructed. To facilitate transcriptome analysis and rare gene discovery, repeated transcripts were proportionally removed from the cDNA library using the procedure of cDNA normalization. The cDNA library would contain approximately 400,000 independent clones, an estimate of at least 16X coverage of the entire expressed genes, provided that the protein-coding capacity of invertebrate genomes is in the range of 16,000 to 25,000 genes. The sequencing and gene data assembly of the cDNA library will be cooperatively conducted in JCVI. We will continue Sanger sequencing of EST clones and perform SoLID sequencing to determine differential gene expression. EST sequences will be compared against existing databases and annotated using the Basic Local Alignment Search Tool (BLAST). Batches of sequences will be sequentially released to GenBank for public access. Unique genes and singletons would be selected and gene expression analysis. Differentially-expressed genes or development-stage specific genes will be preferentially analyzed quantitatively (such as real-time PCR) or qualitatively (such as gene silencing by RNA interference).

Last Modified: 7/25/2014
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