Journal
GIGASCIENCE
Volume 6, Issue 8, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/gigascience/gix049
Keywords
ancient DNA; BGISEQ-500; Illumina HiSeq 2500; comparative performance
Categories
Funding
- ERC Consolidator Grant [681396]
- Marie Sklodowska-Curie Actions [H2020-MSCA-ETN-643063]
- Danish Council for Independent Research [4005-00107 Wine-ometrics]
- Qimmeq project
- Velux Foundations
- Aage og Johanne Louis-Hansens Fond
- China National GeneBank
- BGI-Shenzhen China
- FPI fellowship [BFU2014-55090-P]
- MINECO [BFU2014-55090-P, BFU2015-6215-ERC, U01MH106874]
- Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya
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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 (delta S; slightly lower for the BGISEQ-500, P = 0.011) and the background rate of difference from the reference genome (theta; 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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