title: WheatExp: an RNA-seq expression database for polyploid wheat.
abstract: BACKGROUND
  For functional genomics studies, it is important to understand the dynamic expression profiles of transcribed genes in different tissues, stages of development and in response to environmental stimuli. The proliferation in the use of next-generation sequencing technologies by the plant research community has led to the accumulation of large volumes of expression data. However, analysis of these datasets is complicated by the frequent occurrence of polyploidy among economically-important crop species. In addition, processing and analyzing such large volumes of sequence data is a technical and time-consuming task, limiting their application in functional genomics studies, particularly for smaller laboratories which lack access to high-powered computing infrastructure. Wheat is a good example of a young polyploid species with three similar genomes (97 % identical among homoeologous genes), rapidly accumulating RNA-seq datasets and a large research community.
  
  
  METHODS
  We present WheatExp, an expression database and visualization tool to analyze and compare homoeologue-specific transcript profiles across a broad range of tissues from different developmental stages in polyploid wheat. Beginning with publicly-available RNA-seq datasets, we developed a pipeline to distinguish between homoeologous transcripts from annotated genes in tetraploid and hexaploid wheat. Data from multiple studies is processed and compiled into a database which can be queried either by BLAST or by searching for a known gene of interest by name or functional domain. Expression data of multiple genes can be displayed side-by-side across all expression datasets providing immediate access to a comprehensive panel of expression data for specific subsets of wheat genes.
  
  
  CONCLUSIONS
  The development of a publicly accessible expression database hosted on the GrainGenes website - http://wheat.pw.usda.gov/WheatExp/ - coupled with a simple and readily-comparable visualization tool will empower the wheat research community to use RNA-seq data and to perform functional analyses of target genes. The presented expression data is homoeologue-specific allowing for the analysis of relative contributions from each genome to the overall expression of a gene, a critical consideration for breeding applications. Our approach can be expanded to other polyploid species by adjusting sequence mapping parameters according to the specific divergence of their genomes.
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA. sppearce@ucdavis.edu.
authors.forename: Stephen
authors.initials: S
authors.lastname: Pearce
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA. havazquezgross@ucdavis.edu.
authors.forename: Hans
authors.initials: H
authors.lastname: Vazquez-Gross
authors.affiliation: USDA-Agriculture Research Service, Western Regional Research Center, Albany, CA, 94710, USA. herin@ucdavis.edu.
authors.forename: Sayer Y
authors.initials: SY
authors.lastname: Herin
authors.affiliation: USDA-Agriculture Research Service, Western Regional Research Center, Albany, CA, 94710, USA. davidhane@gmail.com.
authors.forename: David
authors.initials: D
authors.lastname: Hane
authors.affiliation: USDA-Agriculture Research Service, Western Regional Research Center, Albany, CA, 94710, USA. yi.wang@ars.usda.gov.
authors.forename: Yi
authors.initials: Y
authors.lastname: Wang
authors.affiliation: USDA-Agriculture Research Service, Western Regional Research Center, Albany, CA, 94710, USA. yong.gu@ars.usda.gov.
authors.forename: Yong Q
authors.initials: YQ
authors.lastname: Gu
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, 95616, USA. jdubcovsky@ucdavis.edu.|Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. jdubcovsky@ucdavis.edu.
authors.forename: Jorge
authors.initials: J
authors.lastname: Dubcovsky
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics; D030561:Databases, Nucleic Acid; D018506:Gene Expression Regulation, Plant; D011123:Polyploidy; D018749:RNA, Plant / Q000235:genetics; D014908:Triticum / Q000235:genetics*
chemical_list: D018749:RNA, Plant