Wheat Zapper

Wheat Zapper performs colinearity analysis across grass genomes (wheat, Oryza sativa, Sorghum bicolor, and Brachypodium distachyon) to predict gene order in non-sequenced grasses for comparative genomics.

Key Features:

• Colinearity analysis: Performs synteny-based comparisons among wheat, rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium (Brachypodium distachyon) to infer gene order.
• Automated primer design: Generates primers for experimental validation based on inferred genomic regions.
• Intron/exon boundary prediction: Predicts intron and exon boundaries for annotated or inferred genes.
• Visual representation: Produces graphical visualizations of genomic relationships using Circos 0.53.
• Sequence export: Provides downloadable FASTA sequences for downstream analyses.

Scientific Applications:

• Comparative genomics: Enables comparative analysis of genome structure among cereals and related grasses.
• Gene order prediction: Predicts the arrangement of genes in non-sequenced grass species using conserved colinearity.
• Orthology identification: Supports identification of putative orthologous genes across model and crop grasses.
• Evolutionary inference: Assists studies of evolutionary dynamics of genome architecture in grasses.

Methodology:

Relies on conservation of gene order among grass genomes by comparing known sequences from model species to predict gene arrangements in non-sequenced species; validation against the maize genome showed correlation r > 0.83 between predicted and actual gene positions and an accuracy of 0.65 when compared to the Genome Zipper application.