PRJNA423022
Expressed Exome Capture Sequencing (EecSeq): a method for cost-effective exome sequencing for all organisms with or without genomic resources
Exome capture is an effective tool for surveying the genome for loci under selection. However, traditional methods require an annotated genome and/or transcriptome. Here, we present a method for creating cDNA probes from expressed mRNA, which are then used to enrich and capture genomic DNA for exon regions. This "EecSeq" approach 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 hour along with four control oysters kept at 20° C. Stranded mRNA libraries were prepared for two exposed and two control individuals and pooled. Half of the combined library was used for probe synthesis and half was sequenced to evaluate capture efficiency. Genomic DNA was 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 the mRNA library. For all mapped reads, over 47.9% mapped to exons and 37.0% mapped to expressed targets, which is similar to previously published exon captures. In contrast, EecSeq displayed relatively even coverage within exons (i.e. minor "edge effects") and across exon GC content. We discovered 5,951 SNPs with a minimum average coverage of 80X, with 3,508 SNPs appearing in exonic regions. We show that EecSeq provides comparable, if not superior, specificity and capture efficiency compared to costly, traditional methods.