UTILITY OF NEXT-GENERATION SEQUENCING FOR ANALYSIS OF HORTICULTURAL CROP TRANSCRIPTOMES

Abstract

New high-throughput sequencing (HTS) technologies enable application of global molecular approaches to horticultural crops. Such technologies will impact many of the current uses of molecular tools in plant evolution, phylogenetics, fingerprinting, linkage mapping and marker-assisted selection, among others. HTS applications for transcriptome studies include gene discovery and empirical annotation of genome sequences, expression profiling and study of transcript processing events including alternative splicing. The objective of this study was to assess the utility of Illumina (Solexa) HTS-based RNA-sequencing (RNA-seq) for transcriptome studies in horticultural crops. Bioinformatics tools were used to analyze RNA-seq datasets from Arabidopsis thaliana, Brachypodium distachyon and Zea mays. The short read RNA-seq data were aligned to the respective annotated reference transcript models and used to assess transcript detection and coverage for varying amounts of data. This analysis provides insights into the value of the RNA-seq approach for broad and deep sampling of the transcriptomes of horticultural crops for purposes of expression profiling, genome annotation efforts and providing a foundation for hypothesis-generating approaches.