Supporting data for "Comparative performance of the BGISEQ-500 vs Illumina sequencing platforms for palaeogenomic sequencing"

Dataset type: Genomic
Data released on June 27, 2017

Mak SST; Gopalakrishnan S; Caroe C; Geng C; Liu S; Sinding MS; K Kuderna LF; Zhang W; Fu S; Vieira FG; Germonpré M; Bocherens H; Fedorov S; Petersen B; Sicheritz-Ponten T; Marques-Bonet T; Zhang G; Jiang H; Gilbert MTP (2017): Supporting data for "Comparative performance of the BGISEQ-500 vs Illumina sequencing platforms for palaeogenomic sequencing" GigaScience Database. http://dx.doi.org/10.5524/100303

DOI10.5524/100303

Ancient DNA research has been revolutionised 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 eight historic and ancient dog and wolf samples.
The data generated was 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 (p=0.309), and sequence clonality (p=0.093). Small significant differences were found in single strand DNA damage rate (δS, slight 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 PCR 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 three of the samples with overall very low levels of endogenous DNA.
Although we acknowledge our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent 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.

Additional details

Read the peer-reviewed publication(s):

(PubMed: 28854615)

Additional information:

http://www.erda.dk/public/archives/YXJjaGl2ZS1zajh4ZTQ=/published-archive.html

Accessions (data generated as part of this study):

ENA: PRJEB21089





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
CN19219612grey wolfgray wolfCanis lupus Description:DNA extracted from historic wolf hide
Alternative names:CN 1921
Environmental medium:Hide
...
+
CN2149612grey wolfgray wolfCanis lupus Description:DNA extracted from historic wolf hide
Alternative names:CN 214
Environmental medium:Hide
...
+
FRC9612grey wolfgray wolfCanis lupus Description:DNA extracted from archaeological wolf...
Alternative names:FRC
Environmental medium:Cartilage
...
+
L9612grey wolfgray wolfCanis lupus Description:DNA extracted from archaeological wolf...
Alternative names:L
Environmental medium:Liver
...
+
M19612grey wolfgray wolfCanis lupus Description:DNA extracted from archaeological wolf...
Alternative names:M1
Environmental medium:Muscle
...
+
MGUH_VP_33329612grey wolfgray wolfCanis lupus Description:DNA extracted from archaeological wolf...
Alternative names:P84
Environmental medium:Humerus
...
+
NKA_1950x29069615dogsdogCanis lupus familiaris Description:DNA extracted from archaeological dog ...
Alternative names:P83
Environmental medium:Canine tooth
...
+
ZMK_350/19829615dogsdogCanis lupus familiaris Description:DNA extracted from archaeological dog ...
Alternative names:P79
Environmental medium:Tibia
...
+
Displaying 1-8 of 8 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
CN1921Tabular dataTEXT0.58 KB2017-06-20
CN1921Tabular dataTEXT0.58 KB2017-06-20
CN1921Tabular dataUNKNOWN49.04 KB2017-06-20
CN1921Tabular dataTEXT0.3 KB2017-06-20
CN1921OtherUNKNOWN25.07 KB2017-06-20
CN1921Tabular dataTEXT495.98 KB2017-06-20
CN1921Tabular dataTEXT1.42 KB2017-06-20
CN1921Tabular dataTEXT24.04 KB2017-06-20
CN1921Tabular dataUNKNOWN6.65 KB2017-06-20
CN1921TextUNKNOWN7.32 KB2017-06-20
Displaying 1-10 of 216 File(s).
Funding body Awardee Award ID Comments
ERC Consolidator Grant MTP Gilbert 681396 Extinction Genomics
Marie Skłodowska-Curie Actions MTP Gilbert H2020-MSCA-ETN-643063 Microwine
Danish Council for Independent Research MTP Gilbert 4005-00107 Wine-ometrics
Ministerio de Economía y Competitividad LFK Kuderna BFU2014-55090-P FPI fellowship
Ministerio de Economía y Competitividad T Marques-Bonet BFU2015-6215-ERC U01 MH106874
Ministerio de Economía y Competitividad T Marques-Bonet BFU2014-55090-P MENCO
Marie Skłodowska-Curie Actions S Gopalakrishnan H2020-MSCA-IF-2014 655732 Wherewolf

Protocols.io:

Date Action
June 27, 2017 Dataset publish
October 2, 2017 Manuscript Link added : 10.1093/gigascience/gix049
November 9, 2022 Manuscript Link updated : 10.1093/gigascience/gix049
May 23, 2023 External Link updated : https://www.protocols.io/widgets/doi?uri=dx.doi.org/10.17504/protocols.io.iajcacn
May 23, 2023 External Link updated : https://www.protocols.io/widgets/doi?uri=dx.doi.org/10.17504/protocols.io.iabcaan
May 23, 2023 External Link updated : https://www.protocols.io/widgets/doi?uri=dx.doi.org/10.17504/protocols.io.iadcaa6
May 23, 2023 External Link updated : https://www.protocols.io/widgets/doi?uri=dx.doi.org/10.17504/protocols.io.iadcaa6
May 23, 2023 External Link removed : https://www.protocols.io/widgets/protocol/bgiseq-500-library-construction-protocol-iamcac6