Performance of Two Custom Probe Kits for In-Solution Enrichment of Ancient Avian DNA

Area of Science:

• Genomics
• Paleogenetics
• Molecular Biology

Background:

• Ancient DNA (aDNA) analysis is challenging due to low endogenous DNA content in degraded samples.
• Hybridization-based in-solution enrichment is crucial for targeting specific genomic regions and increasing endogenous DNA yield.
• Understanding the performance of different probe kits is vital, especially for non-model organisms.

Purpose of the Study:

• To evaluate and compare the performance of two commercial custom probe systems, myBaits (RNA-based) and Twist (DNA-based), for enriching ancient DNA.
• To assess their efficiency in capturing target single nucleotide polymorphisms (SNPs) from Holocene crow bone samples.
• To provide insights for optimizing ancient DNA enrichment strategies.

Main Methods:

• Enrichment of ancient crow DNA using myBaits and Twist custom probe kits targeting 104K genome-wide SNPs.
• Comparison of capture efficiency, target site detection, and DNA yield against shotgun sequencing.
• Analysis of performance across varying endogenous DNA content (0.9%-90.1%) and Holocene time periods.

Main Results:

• Both myBaits and Twist significantly improved fold enrichment and target site detection compared to shotgun sequencing.
• myBaits demonstrated higher overall capture efficiency.
• Twist captured a larger proportion of endogenous DNA but with lower target efficiency, yet showed superior performance in GC-rich regions.

Conclusions:

• myBaits and Twist kits offer distinct advantages for ancient DNA enrichment, with myBaits excelling in general capture efficiency and Twist in targeting GC-rich areas.
• The findings guide the selection of appropriate enrichment kits based on specific research goals and sample characteristics.
• This study contributes valuable data for designing effective ancient DNA enrichment protocols for non-model organisms.