Expressed exome capture sequencing: A method for cost-effective exome sequencing for all organisms

Area of Science:

• Genomics
• Molecular Biology
• Evolutionary Biology

Background:

• Exome capture is vital for identifying genomic regions under selection.
• Traditional exome capture methods rely on pre-existing annotated genomic resources, which are often unavailable or expensive to create.

Purpose of the Study:

• To introduce and validate EecSeq, a novel method for exome capture using expressed mRNA-derived cDNA probes.
• To demonstrate that EecSeq eliminates the need for costly, custom probe design and synthesis.
• To assess the efficiency and specificity of EecSeq in a non-model organism, the eastern oyster (Crassostrea virginica).

Main Methods:

• EecSeq was developed by creating cDNA probes from expressed mRNA.
• Genomic DNA from eastern oysters (Crassostrea virginica) was enriched using these EecSeq probes.
• Capture efficiency and specificity were evaluated by sequencing enriched genomic DNA and comparing it to known exon annotations and expressed targets.

Main Results:

• EecSeq achieved an average capture sensitivity of 86.8% for all known exons, and over 99.4% for expressed exons.
• Approximately 47.9% of mapped reads targeted exonic regions, with 37.0% mapping to expressed targets.
• The method identified 5,951 single nucleotide polymorphisms (SNPs), with 3,508 located in exonic regions, demonstrating high specificity and coverage.

Conclusions:

• EecSeq offers a cost-effective and efficient alternative to traditional exome capture methods.
• The approach is particularly valuable for species lacking extensive genomic annotation.
• EecSeq provides comparable or superior specificity and capture efficiency, facilitating genomic studies in diverse organisms.