AI interpretationAI-generated
Four sequencing platforms show comparable ancient DNA performance, with minor caveats.
This study compared four next-generation sequencing platforms for ancient DNA whole-genome sequencing using six human samples from Phanagoria polis. All platforms produced acceptable quality data, and population genetic analyses showed no platform-specific bias. The MGI platform yielded longer DNA fragments, which may require caution for highly degraded samples. Overall, GeneMind, Salus, and MGI are viable alternatives to Illumina for paleogenomics.
- All four platforms produced raw sequencing data of acceptable quality with only minor differences in standard NGS metrics.
- Post-mortem damage patterns, especially C>T substitutions, were highly consistent across all platforms.
- PCA and ADMIXTURE analyses showed no platform-specific bias; all platforms clustered tightly together.
- The MGI platform showed a shift toward longer sequenced fragment lengths compared to Illumina and Illumina-like platforms.
Sample interpretation
The study analyzed six ancient human specimens from Phanagoria polis. Y-chromosome haplogroups resolved for four samples: J-BY69547, G-BY109806, G-Z44222, and C-FT155548. Mitochondrial haplogroups included U3b3, U2e2a1, U1a1a1a, and B4b1a3a. These diverse lineages reflect the genetic makeup of the ancient population at this site.
For genealogy enthusiasts
For ancestry enthusiasts, this means that data from GeneMind, Salus, and MGI platforms can be confidently combined with Illumina data for ancient DNA analyses, expanding available datasets without introducing bias. However, when studying highly degraded samples, the MGI platform's longer fragments may need special handling.
Abstract
Background: Ancient DNA (aDNA) research is one of the biological fields that has been transformed by the development of next-generation sequencing (NGS). To date, Illumina sequencing has dominated aDNA research. However, its high costs are driving the adoption of alternative sequencing platforms. Combining data generated on different platforms may introduce artifacts arising from platform-specific errors. This study systematically compared the performance of four sequencing platforms (Illumina NovaSeq 6000, GeneMind SURFSeq 5000, Salus Evo, and MGI DNBSEQ-G400) for whole-genome aDNA sequencing using the same set of six samples and libraries. Methods: Single-stranded libraries, prepared with and without enzymatic damage repair, were generated from six human aDNA specimens recovered from Phanagoria polis and sequenced on all four platforms. Data were subsampled to equal read counts per library, mapped to the human reference genome, and compared using standard NGS quality metrics. Population genetic analyses, including principal component analysis (PCA) and ADMIXTURE, were performed to assess potential platform-specific biases. Results: All platforms produced raw sequencing data of acceptable quality. Only minor differences were observed among platforms in standard NGS metrics. The MGI platform showed a shift toward longer sequenced fragment lengths compared with Illumina and the Illumina-like platforms. Post-mortem damage patterns, particularly C>T substitutions, were highly consistent across all platforms. PCA and ADMIXTURE analyses revealed no evidence of platform-specific bias: results from all platforms clustered tightly together, and platform choice had no significant effect on ancestry component estimates. Conclusions: Our findings demonstrate that the GeneMind, Salus, and MGI sequencing platforms are comparable to Illumina for paleogenomic research. Moreover, aDNA datasets generated on these platforms can be combined for downstream analyses without introducing detectable bias. However, the fragment-size shift observed on the MGI platform warrants caution and adaptation when working with highly degraded or low-endogenous-content samples.