Comparative Performance of the MGISEQ-2000 and Illumina X-Ten Sequencing Platforms for Paleogenomics

Kongyang Zhu; Panxin Du; Jianxue Xiong; Xiaoying Ren; Chang Sun; Yichen Tao; Yi Ding; Yiran Xu; Hailiang Meng; Chuan-Chao Wang; Shao-Qing Wen

doi:10.3389/fgene.2021.745508

Comparative Performance of the MGISEQ-2000 and Illumina X-Ten Sequencing Platforms for Paleogenomics

Front Genet. 2021 Oct 4:12:745508. doi: 10.3389/fgene.2021.745508. eCollection 2021.

Authors

Kongyang Zhu¹, Panxin Du², Jianxue Xiong², Xiaoying Ren³, Chang Sun², Yichen Tao², Yi Ding³, Yiran Xu², Hailiang Meng², Chuan-Chao Wang¹, Shao-Qing Wen^{2

3}

Affiliations

¹ State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China.
² MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.
³ Institute of Archaeological Science, Fudan University, Shanghai, China.

Abstract

The MGISEQ-2000 sequencer is widely used in various omics studies, but the performance of this platform for paleogenomics has not been evaluated. We here compare the performance of MGISEQ-2000 with the Illumina X-Ten on ancient human DNA using four samples from 1750BCE to 60CE. We found there were only slight differences between the two platforms in most parameters (duplication rate, sequencing bias, θ, δS, and λ). MGISEQ-2000 performed well on endogenous rate and library complexity although X-Ten had a higher average base quality and lower error rate. Our results suggest that MGISEQ-2000 and X-Ten have comparable performance, and MGISEQ-2000 can be an alternative platform for paleogenomics sequencing.

Keywords: BGI tech; MGISEQ-2000; ancient DNA; paleogenomics; population genetics.