Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content
文献类型： 外文期刊
作者： Zhang, Zhidong 1 ; Liu, Guilin 3 ; Chen, Yao 1 ; Xue, Weizhen 3 ; Ji, Qianyue 3 ; Xu, Qiwu 3 ; Zhang, He 3 ; Fan, Guangyi 3 ;
作者机构： 1.Nanjing Tech Univ, Coll Biotechnol & Pharmaceut Engn, Nanjing 211816, Peoples R China
2.Xinjiang Acad Agr Sci, Inst Appl Microbiol, Xinjiang Key Lab Special Environm Microbiol, Urumqi 830091, Xinjiang, Peoples R China
3.BGI Shenzhen, BGI Qingdao, Qingdao 266555, Shandong, Peoples R China
4.Nanjing Normal Univ, Sch Food Sci & Pharmaceut Engn, Nanjing 210023, Peoples R China
5.Nanjing Tech Univ, Sch Pharmaceut Sci, Nanjing 211816, Peoples R China
6.Nanjing Tech Univ, Coll Food Sci & Light Ind, Nanjing 211816, Peoples R China
7.BGI Shenzhen, Shenzhen 518083, Guangdong, Peoples R China
8.BGI Shenzhen, Qingdao Europe Adv Inst Life Sci, Qingdao 266555, Shandong, Peoples R China
9.Univ Copenhagen, Dept Biol, Lab Genom & Mol Biomed, Univ Pk 13, DK-2100 Copenhagen, Denmark
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
页码：
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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