1a. Objectives (from AD-416)
1) Perform large-scale sequencing using 454 and Solexa sequencing technologies to generate a draft whole genome sequence of the fire ant Solenopsis invicta, 2) To assemble and annotate draft genome, 3) To perform comparative genomic analyses, 4) To perform large-scale EST study to significantly increase the breadth and depth of transcriptome coverage of the fire ant Solenopsis invicta, 5) To develop an oligo microarray for fire ants for gene expression studies using all available sequence data and 6) To develop a custom assay for screening SNPs for linkage and population genomic studies of fire ants.
1b. Approach (from AD-416)
We will generate >5 Gb of 454 sequence using DNA from a pooled sample of Gp-9B haploid males and a pooled sample of Gp-9b males from one Gp-9Bb queen. We will assemble the sequence data using 454 software (Newbler) in conjunction with in-house assembly/software pipelines available at the Swiss Institute for Bioinformatics. We will perform annotation, SNP identification, and comparative genomics analyses using our own analysis pipelines. We also will generate DNA sequence data for the transcriptome of S. invicta by sequencing normalized cDNA libraries using 454 pyrosequencing technology. All resulting sequences will be run through an automatic pipeline to assemble and preliminarily annotate the sequences. A 4 X 44K feature microarray will be developed and utilized for several experiments focusing on innate immunity, reproductive physiology, and social organization (including studies of Gp-9, a single gene associated with social organization in this ant). A SNP panel will be developed and utilized to construct a moderately dense linkage map. Finally, a web-based platform integrating these data in an easily accessible format will be developed.
3. Progress Report
This project is related to sub-objective 2.1 of this in-house project: Identify new pathogens of fire ants using traditional exploratory and molecular-based methods. The objective of this cooperative research project is to use a metagenomics approach to identify new viruses infecting the fire ant Solenopsis invicta and subsequently use genomic tools and resources to study the biology (distribution, pathogenicity, etiology, molecular evolutionary history) of newly discovered viruses. This project was initiated only very recently. Thus, no progress on project has been made at this point. Progress on this project was monitored by means of frequent email communications, telephone communications, and visits to the collaborator’s lab by the ARS scientist.