dc.contributor.author | Mak, Sarah S.T. | |
dc.contributor.author | Gopalakrishnan, Shyam | |
dc.contributor.author | Carøe, Christian | |
dc.contributor.author | Geng, Chunyu | |
dc.contributor.author | Liu, Shanlin | |
dc.contributor.author | Sinding, Mikkel Holger Strander | |
dc.contributor.author | Kuderna, Lukas FK | |
dc.contributor.author | Zhang, Wenwei | |
dc.contributor.author | Fu, Shujin | |
dc.contributor.author | Vieira, Filipe G. | |
dc.contributor.author | Germonpre, Mietje | |
dc.contributor.author | Bocherens, Hervé | |
dc.contributor.author | Fedorov, Sergey | |
dc.contributor.author | Petersen, Bent | |
dc.contributor.author | Sicheritz-Pontén, Thomas | |
dc.contributor.author | Marques-Bonet, Tomas | |
dc.contributor.author | Zhang, Guojie | |
dc.contributor.author | Jiang, Hui | |
dc.contributor.author | Gilbert, Marcus Thomas Pius | |
dc.date.accessioned | 2018-08-24T11:57:24Z | |
dc.date.available | 2018-08-24T11:57:24Z | |
dc.date.created | 2018-01-30T10:50:49Z | |
dc.date.issued | 2017 | |
dc.identifier.citation | GigaScience. 2017, 6 (8), 1-13. | nb_NO |
dc.identifier.issn | 2047-217X | |
dc.identifier.uri | http://hdl.handle.net/11250/2559247 | |
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. | nb_NO |
dc.language.iso | eng | nb_NO |
dc.publisher | Oxford University Press (OUP) | nb_NO |
dc.rights | Navngivelse 4.0 Internasjonal | * |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/deed.no | * |
dc.title | Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing | nb_NO |
dc.type | Journal article | nb_NO |
dc.type | Peer reviewed | nb_NO |
dc.description.version | publishedVersion | nb_NO |
dc.source.pagenumber | 1-13 | nb_NO |
dc.source.volume | 6 | nb_NO |
dc.source.journal | GigaScience | nb_NO |
dc.source.issue | 8 | nb_NO |
dc.identifier.doi | 10.1093/gigascience/gix049 | |
dc.identifier.cristin | 1555949 | |
dc.description.localcode | © 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. | nb_NO |
cristin.unitcode | 194,31,10,0 | |
cristin.unitname | Institutt for naturhistorie | |
cristin.ispublished | true | |
cristin.fulltext | original | |
cristin.qualitycode | 1 | |