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Abstract Exome capture is an effective tool for surveying the genome for loci under selection. However, traditional methods require annotated genomic resources. Here, we present a method for creatingcDNAprobes from expressedmRNA, which are then used to enrich and capture genomicDNAfor exon regions. This approach, called “EecSeq,” eliminates the need for costly probe design and synthesis. We tested EecSeq in the eastern oyster,Crassostrea virginica, using a controlled exposure experiment. Four adult oysters were heat shocked at 36°C for 1 hr along with four control oysters kept at 14°C. StrandedmRNAlibraries were prepared for two individuals from each treatment and pooled. Half of the combined library was used for probe synthesis, and half was sequenced to evaluate capture efficiency. GenomicDNAwas extracted from all individuals, enriched via captured probes, and sequenced directly. We found that EecSeq had an average capture sensitivity of 86.8% across all known exons and had over 99.4% sensitivity for exons with detectable levels of expression in themRNAlibrary. For all mapped reads, over 47.9% mapped to exons and 37.0% mapped to expressed targets, which is similar to previously published exon capture studies. EecSeq displayed relatively even coverage within exons (i.e., minor “edge effects”) and even coverage across exonGCcontent. We discovered 5,951SNPs with a minimum average coverage of 80×, with 3,508SNPs appearing in exonic regions. We show that EecSeq provides comparable, if not superior, specificity and capture efficiency compared to costly, traditional methods.