Comparative performance of the BGISEQ-500 versus Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

Sarah Siu Tze Mak Mak, Shyam Sunder Gopalakrishnan, Christian Carøe, Chunyu Geng, Shanlin Liu, Mikkel Holger Strander Sinding, Lukas F.K. Kuderna, Wenwei Zhang, Shujin Fu, Filipe Jorge Garrett Vieira, Mietje Germonpré, Hervé Bocherens, Sergey Fedorov, Bent Petersen, Thomas Sicheritz-Pontén, Tomas Marques-Bonet, Guojie Zhang, Hui Jiang, M. Thomas P. Gilbert

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    Abstract

    Background: Ancient DNA research has been revolutionised following development of “Next Generation” Sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform, on DNA extracted from eight historic and ancient dog and wolf samples.
    Results: The data generated was largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (p = 0.371) and average sequence length (p = 0718) of endogenous nuclear DNA, sequence GC content (p = 0.311), double stranded DNA damage rate (p = 0.309), and sequence clonality (p = 0.093). Small significant differences were found in single strand DNA damage rate (δS, slight lower for the BGISEQ-500, p = 0.011) and the background rate of difference from the reference genome (θ, slightly higher for BGISEQ-500, p = 0.012). This may result from the differences in amplification cycles used to PCR amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (p = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from three of the samples with overall very low levels of endogenous DNA.
    Conclusions: Although we acknowledge our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent valid and potentially valuable alternative platform for palaeogenomic data generation, that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA.
    Original languageEnglish
    Article numbergix049
    JournalGigaScience
    Volume6
    Issue number8
    Number of pages14
    ISSN2047-217X
    DOIs
    Publication statusPublished - 2017

    Bibliographical note

    This is an Open Access article distributed under the terms of the Creative Commons
    Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium,
    provided the original work is properly cited.

    Keywords

    • Ancient DNA
    • BGISEQ-500
    • Illumina HiSeq 2500
    • Comparative performance

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