摘要：SummaryIn this study, six bacterial isolates with variable GC, includingEscherichia colias 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 werede novoassembled 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.Graphical abstractDisplay OmittedHighlights•Assembling and evaluating bacterial chromosome-level genomes by multiple strategies•The stLFR data can assemble chromosome sequences of different GC extremophilesMicrobiology; Microbial Genomics; Omics
