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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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WheatExp: an RNA-seq expression database for polyploid wheat.

Stephen Pearce1, Hans Vazquez-Gross2, Sayer Y Herin3

  • 1Department of Plant Sciences, University of California, Davis, CA, 95616, USA. sppearce@ucdavis.edu.

BMC Plant Biology
|December 26, 2015
PubMed
Summary

WheatExp is a new database for analyzing gene expression in polyploid wheat. It helps researchers understand gene function and improve crop breeding by providing homoeologue-specific transcript data.

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Area of Science:

  • Plant genomics
  • Functional genomics
  • Bioinformatics

Background:

  • Understanding dynamic gene expression is crucial for functional genomics.
  • Polyploidy in crops like wheat complicates RNA sequencing (RNA-seq) data analysis.
  • Limited computational resources hinder analysis for smaller labs.

Purpose of the Study:

  • To develop an expression database and visualization tool for polyploid wheat.
  • To enable analysis and comparison of homoeologue-specific transcript profiles.
  • To facilitate functional genomics studies in wheat.

Main Methods:

  • Developed a pipeline to distinguish homoeologous transcripts in tetraploid and hexaploid wheat.
  • Integrated publicly available RNA-seq datasets into a comprehensive database.
  • Enabled querying by BLAST or gene name/functional domain.

Main Results:

  • WheatExp provides homoeologue-specific expression data across various tissues and developmental stages.
  • The tool allows side-by-side comparison of expression data for multiple genes.
  • Facilitates analysis of individual homoeologue contributions to gene expression.

Conclusions:

  • WheatExp empowers the wheat research community with accessible RNA-seq data for functional analysis.
  • Homoeologue-specific data is critical for understanding gene expression in polyploid wheat and for breeding applications.
  • The approach is adaptable to other polyploid species.