WhETS

WhETS reconstructs hexaploid wheat transcript sequences by mapping Triticeae expressed sequence tags (ESTs) and high-quality cDNA (hq-cDNA) onto rice genomic loci to estimate transcript structure, support PCR primer design, and discriminate homoeologues.

Key Features:

• EST and cDNA collection: Leverages over 1.3 million public-domain Triticeae ESTs, including approximately 850,000 wheat ESTs, plus high-quality cDNA sequences.
• Rice genomic template: Uses the complete rice genomic sequence as a template for mapping Triticeae sequences and inferring transcript structure.
• Mapping to rice loci: Maps Triticeae ESTs and hq-cDNA onto corresponding rice loci stored in an organized database.
• Arabidopsis cross-reference: Allows selection of target loci directly via a rice locus or indirectly using Arabidopsis as a reference.
• Assembly with CAP3: Assembles selected sequences into contigs and singlets using the CAP3 program.
• SNP-analysis refinement: Applies a SNP-analysis algorithm specifically developed to distinguish homoeologues in hexaploid wheat.
• Alignment to rice template: Aligns assembled contigs and singlets against the rice template sequence to visualize potential transcript structures.
• Tissue distribution annotation: Provides tissue distribution information for constituent ESTs and cDNAs.
• Intron position inference: Infers intron positions based on alignment to the rice genome.
• Export formats: Offers downloadable results in FASTA and ACE formats for downstream analysis and primer design.

Scientific Applications:

• Transcript estimation: Estimating probable transcript sequences present in hexaploid wheat cDNA samples using comparative mapping to rice.
• Homoeologue discrimination: Distinguishing homoeologous copies in hexaploid wheat through SNP-analysis-informed assemblies.
• Primer design support: Providing assembled sequences, inferred intron positions, and alignments to aid PCR primer design for wheat loci.
• Tissue-specific expression analysis: Assessing tissue distribution patterns of transcripts using constituent EST and cDNA annotations.

Methodology:

Map Triticeae ESTs and hq-cDNA onto rice loci stored in a database; select target loci via rice or Arabidopsis reference; assemble sequences with CAP3; refine assemblies using a SNP-analysis algorithm to distinguish homoeologues; align contigs and singlets to the rice template; infer intron positions from the rice genome and export results in FASTA and ACE formats.