|The Laboratory of Functional Genomics focuses on making use of massive amounts of data produced from genome and transcriptome sequencing projects to describe gene and protein functions and interactions.
A key feature of functional genomics studies is their genome-wide approach to questions about the function of DNA at the level of genes, RNA transcripts, and protein products. The work involves high-throughput next generation sequencing (NGS) techniques in addition to more traditional approaches. Here, we use high-throughput next generation sequencing (NGS) platforms to obtain genomic and transcriptomic sequences of organisms of interest (e.g. insects and symbionts).
In this study, insecticide resistance involving a non-model insect pest, Plutella xylostella, Illumina and Roche NGS platforms were used to generate and annotate unigene sets in a species without prior genome information.
The Roche 454 pyrosequencing produced 61,058 unigenes. Of these, 5,470 unigenes were annotated with gene ontology terms, gene names, and conserved protein families and domains. A RNA-seq dataset from P. xylostella was also generated by Illumina Hi-Seq platform.
A total of 938,116,086 reads were obtained and assembled into 294,858 contigs. Of these assembled contigs, 57,977 unigenes were annotated. Targeted searches predicted several genes that are putatively involved in the evolution of resistance (e.g., cytochrome P450s). Functional studies by RNA interference will demonstrate the exact roles of these P450 genes.
Future projects will focus on the use of insects as sources of key enzymes for biofuels and as sources of antimicrobial peptides.