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

Abstract

Summary 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.

Detecting horizontal gene transfer with metagenomics co-barcoding sequencing

“…In this study, we developed MECOS, a new co-barcoding sequencing system to identify recent HGT events. The computational resources required for MECOS are comparable to those needed for short-reads mNGS ( 21 ). Importantly, MECOS requires only 0.1 ng high-quality DNA, which is much lower compared to the 200 ng required for short-reads mNGS ( Table 2 ).…”

Membrane-remodeling protein ESCRT-III homologs incarnate the evolution and morphogenesis of multicellular magnetotactic bacteria

“…The WGS libraries of ZJ12, ZJW7, ZJ63 and stLFR libraries of QDG1, ZJ64, QDA1 were sequenced on BGISEQ-500 platform (BGI-Qingdao, China) in 100 bp pair-end model. After performing quality trimming and filtering using SOAPnuke, the high-quality clean reads of WGS data were assembled using metaSPAdes (v3.14.1) with k-mer size from 33 to 113 by step 20, and the stLFR clean reads were assembled using Supernova (v2.1.1) as described before 67 .…”