A Brassica exon array for whole-transcript gene expression profiling

• Published in: PloS one 2010-09, Vol.5 (9), p.e12812
• Main Authors: Love, Christopher G, Graham, Neil S, O Lochlainn, Seosamh, Bowen, Helen C, May, Sean T, White, Philip J, Broadley, Martin R, Hammond, John P, King, Graham J
• Format: Article
• Language: English
• Subjects: Acids; Allopolyploidy; Annotations; Arabidopsis; Arabidopsis thaliana; Arrays; Bioinformatics; Brass plating; Brassica; Brassica - genetics; Brassica rapa; Datasets; DNA probes; Environmental changes; Environmental effects; Exons; Gene expression; Gene Expression Profiling - methods; Gene sequencing; Genes; Genetics and Genomics/Bioinformatics; Genetics and Genomics/Gene Expression; Genetics and Genomics/Plant Genetics and Gene Expression; Genome, Plant; Genomes; Genomics; Information sources; Oligonucleotide Array Sequence Analysis - methods; Oligonucleotides; Orthology; Plant Biology/Plant Genetics and Gene Expression; Probes; Proteins; Public domain; Ribonucleic acid; RNA; Studies; Transcription; Transcription, Genetic
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0012812

Affymetrix GeneChip® arrays are used widely to study transcriptional changes in response to developmental and environmental stimuli. GeneChip® arrays comprise multiple 25-mer oligonucleotide probes per gene and retain certain advantages over direct sequencing. For plants, there are several public GeneChip® arrays whose probes are localised primarily in 3' exons. Plant whole-transcript (WT) GeneChip® arrays are not yet publicly available, although WT resolution is needed to study complex crop genomes such as Brassica, which are typified by segmental duplications containing paralogous genes and/or allopolyploidy. Available sequence data were sampled from the Brassica A and C genomes, and 142,997 gene models identified. The assembled gene models were then used to establish a comprehensive public WT exon array for transcriptomics studies. The Affymetrix GeneChip® Brassica Exon 1.0 ST Array is a 5 µM feature size array, containing 2.4 million 25-base oligonucleotide probes representing 135,201 gene models, with 15 probes per gene distributed among exons. Discrimination of the gene models was based on an E-value cut-off of 1E(-5), with ≤98% sequence identity. The 135 k Brassica Exon Array was validated by quantifying transcriptome differences between leaf and root tissue from a reference Brassica rapa line (R-o-18), and categorisation by Gene Ontologies (GO) based on gene orthology with Arabidopsis thaliana. Technical validation involved comparison of the exon array with a 60-mer array platform using the same starting RNA samples. The 135 k Brassica Exon Array is a robust platform. All data relating to the array design and probe identities are available in the public domain and are curated within the BrassEnsembl genome viewer at http://www.brassica.info/BrassEnsembl/index.html.