Using Targeted Sequencing for the Discovery of Intron Sequences with Baits Derived from Transcriptome Data

Over the past decade, the advent of next-generation DNA sequencing technology has enabled genome sequences of model organisms. However, sequencing costs are still limiting the characterization of many other organism genomes. For many, transcriptome sequences are the only available data or can more easily be obtained.

We highlight the use of MYbaits Target Enrichment Kits in combination with long sequencing reads (454 Life Sciences) to discover intronic sequences in a plant and animal species where only transcriptome sequences were available. Here, biotinylated RNA probes (80 – 100 mer) are designed starting from transcript sequences to enrich genomic DNA fragments. 454 shotgun sequencing (reads length: 400 – 600 bp) of the enriched population enable the discovery of intronic sequences adjacent to exons, the mapping of exons and exon-intron junctions, and possibly the identification of non-coding transcriptional and regulatory elements. Among other applications, accessing intron sequences will allow addressing many fundamental phylogenetic and population questions.