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

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Mak, Sarah Siu Tze, Gopalakrishnan, Shyam, Carøe, Christian, Geng, Chunyu, Liu, Shanlin, Sinding, Mikkel-Holger S, Kuderna, Lukas F K, Zhang, Wenwei, Fu, Shujin, Vieira, Filipe G, Germonpré, Mietje, Bocherens, Hervé, Fedorov, Sergey, Petersen, Bent, Sicheritz-Pontén, Thomas, Marques-Bonet, Tomas, Zhang, Guojie, Jiang, Hui, Gilbert, M Thomas P·2017·GigaScience
DOI 10.1093/gigascience/gix049PMC PMC5570000
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Abstract

Ancient DNA research has been revolutionized 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 8 historic and ancient dog and wolf samples. The data generated were 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 (v. 0.309), and sequence clonality (P = 0.093). Small significant differences were found in single-strand DNA damage rate (ΔS; slightly 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 polymerase chain reaction–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 3 of the samples with overall very low levels of endogenous DNA. Although we acknowledge that our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent a 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.

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  • The vast majority of ancient DNA sequence data have been produced using Illumina instruments, due to their ubiquity, high data output, cost-effectiveness and relatively low error rates.

    “Although other technologies have been sporadically used (for example, SOLiD 168 , Helicos 2 , BGI-SEQ500 169 , Ion Torrent 170 ), the vast majority of aDNA sequence data have been produced using Illumina instruments, due to their ubiquity, high data output, cost-effectiveness and relatively low error rates.”

    From Ancient DNA analysis (2021) · cites this paper as [169]

  • Factors to consider in ancient genomic analyses include platform-specific sequence error profiles, magnitude of post-mortem DNA damage and contamination, base quality rescaling, read alignment parameters, database selection and taxonomic classifier parameters, and applicability conditions of statistical methods.

    “The list of factors to consider extends far beyond the minimal data requirement for specific analyses 330 and includes: platform-specific sequence error profiles 169 ; the magnitude of post-mortem DNA damage and contamination and their impact on downstream inference 55 ; base quality rescaling 57 ; read alignment parameters 180,182 ; database selection and taxonomic classifier parameters 27,238 ;”

    From Ancient DNA analysis (2021) · cites this paper as [169]

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Authors
Mak, S. S. T., Gopalakrishnan, S., Carøe, C., Geng, C., Liu, S., Sinding, M.-H. S., Kuderna, L. F. K., Zhang, W., Fu, S., Vieira, F. G., Germonpré, M., Bocherens, H., Fedorov, S., Petersen, B., Sicheritz-Pontén, T., Marques-Bonet, T., Zhang, G., Jiang, H., & Gilbert, M. T. P.
Affiliations
  • University of Copenhagen (DK)
  • BGI Group (China) (CN)
  • Barcelona Biomedical Research Park (ES)
  • Institute of Natural Sciences (BE)
  • Senckenberg Centre for Human Evolution and Palaeoenvironment (DE)
  • North-Eastern Federal University (RU)
  • Technical University of Denmark (DK)
  • DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
  • Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
Corresponding author
  • Geng, Chunyu
  • Jiang, Hui
  • Gilbert, M Thomas P
ORCID
Venue
GigaScience
Publisher
Oxford University Press (OUP)
Published
2017-06-26
Volume
6
Issue
8
Pages
1-13
ISSN
2047-217X (ISSN-L)
DOI
10.1093/gigascience/gix049
PMC
PMC5570000
OpenAlex
W2636150609
Cited by
317
References
16
Citations by year
2026: 12 · 2025: 19 · 2024: 13 · 2023: 15 · 2022: 14 · 2021: 73 · 2020: 71 · 2019: 52 · 2018: 38 · 2017: 10
FWCI
16.66
Type
journal article
Language
en
Open access
Licence
Locations
  • GigaScience (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
  • RECERCAT (Consorci de Serveis Universitaris de Catalunya) (publishedVersion, other-oa)
  • Informationszentrum Lebenswissenschaften (ZB MED) (submittedVersion, cc-by)
  • BIBSYS Brage (BIBSYS (Norway)) (submittedVersion, cc-by)
  • NORA - Norwegian Open Research Archives (submittedVersion, other-oa)
  • Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, cc-by)
  • Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion, cc-by)
  • NORA - Norwegian Open Research Archives (submittedVersion, cc-by)
Funders
  • Velux Fonden
  • Generalitat de Catalunya (681396)
  • Danmarks Frie Forskningsfond (4005-00107, 681396)
  • Aage og Johanne Louis-Hansens Fond
  • Horizon 2020 Framework Programme (H2020-MSCA, 643063, 681396)
  • National Institute of Mental Health (U01MH106874)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Keywords
BGISEQ-500, sequencing platform comparison, paleogenomics, ancient DNA, degraded DNA, library preparation, dogs, wolf, mitochondrial DNA
MeSH terms
Animals, Base Composition, DNA, DNA, Mitochondrial, Reproducibility of Results, Sequence Analysis, DNA, Genomics, High-Throughput Nucleotide Sequencing

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