Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content

文献类型： 外文期刊

第一作者： Zhang, Zhidong

作者： Zhang, Zhidong;Chen, Yao;Zhang, Zhidong;Liu, Guilin;Xue, Weizhen;Ji, Qianyue;Xu, Qiwu;Zhang, He;Fan, Guangyi;Chen, Jianwei;Huang, He;Huang, He;Jiang, Ling;Fan, Guangyi;Chen, Jianwei;Chen, Jianwei;Chen, Jianwei

作者机构：

期刊名称：ISCIENCE （ 影响因子：4.447； 五年影响因子：4.452 ）

ISSN：

年卷期： 2021 年 24 卷 3 期

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收录情况： SCI

摘要： In this study, six bacterial isolates with variable GC, including Escherichia coli as mesophilic reference strain, were selected to compare hybrid assembly strategies based on next-generation sequencing (NGS) of short reads, single-tube long-fragment reads (stLFR) sequencing, and Oxford Nanopore Technologies (ONT) sequencing platforms. We obtained the complete genomes using the hybrid assembler Unicycler based on the NGS and ONT reads; others were de novo assembled using NGS, stLFR, and ONT reads by using different strategies. The contiguity, accuracy, completeness, sequencing costs, and DNA material requirements of the investigated strategies were compared systematically. Although all sequencing data could be assembled into accurate whole-genome sequences, the stLFR sequencing data yield a scaffold with more contiguity with more completeness of gene function than NGS sequencing assemblies. Our research provides a low-cost chromosome-level genome assembly strategy for large-scale sequencing of extremophile genomes with different GC contents.

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