Syed, Zainulabeuddin

Objectives

The aim of our work is to identify and characterize chemosensory receptors underlying critical life history traits in disease vectors (mosquitoes and sand flies) and agricultural pests (spotted wing drosophila and screwworm fly). To accomplish this goal, we incorporate a number of strategies such as de novo genome and transcriptome assembly, gene expression analysis, SNP calling and phylogenetic analysis. Future projects may involve QTL analysis.

Spotted wing drosophila: annotation and phylogenetic analysis of chemosensory receptor superfamily, antennal transcriptome analysis in two physiological states, sex biased gene expression, population variation in chemosensory receptor superfamily. 

Sand flies: annotation and phylogenetic analysis of chemosensory receptor superfamily, species and population variation in chemosensory receptor superfamily. 

Mosquitoes: annotation and phylogenetic analysis of chemosensory receptor superfamily, antennal transcriptome analysis in two physiological states, population variation in chemosensory receptor superfamily. 

Screwworm fly: annotation and phylogenetic analysis of chemosensory receptor superfamily, antennal transcriptome analysis to identify sex biased gene expression.

Research Personnel

Zain Syed (PI)

Paul Hickner (Post-Doctoral Researcher)

Nicolas Pearson (Laboratory Technician)

Software

Trinity: transcriptome assembly

RAxML: phylogenetic analysis

Soap de novo or Abyss: de novo genome assembly

Samtools: Sam/Bam file 

VCFtools: analysis of SNP data

Bcftools: SNP calling

Bowtie2: read alignment

BWA-mem: read alignment

Cufflinks: gene expression analysis

Publications

Hickner PV, Mori A, Rund SSC, Sheppard AD, Cunningham JM, Chadee DD, Duffield GE,

Severson DW. 2017. Identification of QTL determining diel flight activity in male Culex pipiens mosquitoes from autogenous and anautogenous strains. J Heredity (in review).

Hickner PV, Rivaldi CL, Johnson CM, Siddappaji M, Raster GJ, Syed Z. 2016. The making of a

pest: Insights from the evolution of chemosensory receptor families in a pestiferous and invasive fly, Drosophila suzukii. BMC Genomics17:648.

Hickner PV, Mori A, Zeng E, Tan JC, Severson DW. 2015. Whole transcriptome responses

among females of the filariasis and arbovirus vector mosquito Culex pipiens implicate TGF-β signaling and chromatin modification as key drivers of diapause induction. Funct Integr Genomics DOI 10.1007/s10142-015-0432-5.