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

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  • dc.contributor.author Mak, Sarah Siu Tzeca
  • dc.contributor.author Gopalakrishnan, Shyamca
  • dc.contributor.author Carøe, Christianca
  • dc.contributor.author Geng, Chunyuca
  • dc.contributor.author Liu, Shanlinca
  • dc.contributor.author Sinding, Mikkel Holger S.ca
  • dc.contributor.author Kuderna, Lukas, 1989-ca
  • dc.contributor.author Zhang, Wenweica
  • dc.contributor.author Fu, Shujinca
  • dc.contributor.author Vieira, Filipe Garrettca
  • dc.contributor.author Germonpré, Mietjeca
  • dc.contributor.author Bocherens, Hervéca
  • dc.contributor.author Fedorov, Sergey E.ca
  • dc.contributor.author Petersen, Bentca
  • dc.contributor.author Sicheritz-Ponten, Thomasca
  • dc.contributor.author Marquès i Bonet, Tomàs, 1975-ca
  • dc.contributor.author Zhang, Guojieca
  • dc.contributor.author Jiang, Huica
  • dc.contributor.author Gilbert, M Thomasca
  • dc.date.accessioned 2018-04-05T17:37:03Z
  • dc.date.available 2018-04-05T17:37:03Z
  • dc.date.issued 2017
  • dc.description.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.
  • dc.description.sponsorship The authors would like to acknowledge the ERC Consolidator Grant (681396 - Extinction Genomics), the Marie Skłodowska-Curie Actions (H2020-MSCA-ETN-643063 “Microwine”), Danish Council for Independent Research (4005-00107 Wine-ometrics), the Qimmeq project, funded by The Velux Foundations and Aage og Johanne Louis-Hansens Fond, China National GeneBank, and BGI-Shenzhen China for funding. L.F.K.K is supported by an FPI fellowship associated with BFU2014-55090-P (FEDER), T.M.B. is supported by MINECO BFU2014-55090-P (FEDER) and BFU2015-6215-ERC, a U01 MH106874 grant, and the Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding MS et al. Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. Gigascience. 2017 Aug 1;6(8):1-13. DOI: 10.1093/gigascience/gix049
  • dc.identifier.doi http://dx.doi.org/10.1093/gigascience/gix049
  • dc.identifier.issn 2047-217X
  • dc.identifier.uri http://hdl.handle.net/10230/34298
  • dc.language.iso eng
  • dc.publisher Oxford University Pressca
  • dc.relation.ispartof Gigascience. 2017 Aug 1;6(8):1-13
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/681396
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/643063
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2014-55090-P
  • dc.rights © The Author 2017. Published by Oxford University Press. 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.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword BGISEQ-500
  • dc.subject.keyword Illumina HiSeq 2500
  • dc.subject.keyword Ancient DNA
  • dc.subject.keyword Comparative performance
  • dc.title Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencingca
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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