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

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

doi:10.1093/gigascience/gix049

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.

Authors

Sarah Siu Tze Mak¹, Shyam Gopalakrishnan¹, Christian Carøe^{1

2}, Chunyu Geng³, Shanlin Liu^{1

4}, Mikkel-Holger S Sinding^{1

5

6}, Lukas F K Kuderna^{7

8}, Wenwei Zhang³, Shujin Fu³, Filipe G Vieira¹, Mietje Germonpré⁹, Hervé Bocherens^{10

11}, Sergey Fedorov¹², Bent Petersen², Thomas Sicheritz-Pontén², Tomas Marques-Bonet^{7

8

13}, Guojie Zhang^{4

14}, Hui Jiang³, M Thomas P Gilbert^{1

15

16}

Affiliations

¹ Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
² DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark.
³ BGI-Shenzhen, Shenzhen 518083, China.
⁴ China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
⁵ Natural History Museum, University of Oslo, PO Box 1172 Blindern, N-0318 Oslo, Norway.
⁶ The Qimmeq Project, University of Greenland, Manutooq 1, PO Box 1061, 3905 Nuussuaq, Greenland.
⁷ Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.
⁸ CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
⁹ OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000 Brussels, Belgium.
¹⁰ Department of Geosciences, Palaeobiology, University of Tübingen, Tübingen, Germany.
¹¹ Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.
¹² Mammoth Museum, Institute of Applied Ecology of the North of the North-Eastern Federal University, ul. Kulakovskogo 48, 677980 Yakutsk, Russia.
¹³ Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain.
¹⁴ Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, Copenhagen DK-2100, Denmark.
¹⁵ Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, 6102 Perth, Australia.
¹⁶ Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway.

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.

Keywords: BGISEQ-500; Illumina HiSeq 2500; ancient DNA; comparative performance.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Base Composition
DNA / chemistry
DNA, Mitochondrial / chemistry
Genomics / methods*
Genomics / standards*
High-Throughput Nucleotide Sequencing / methods*
High-Throughput Nucleotide Sequencing / standards*
Reproducibility of Results
Sequence Analysis, DNA

Substances

DNA, Mitochondrial
DNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding