2025/10/07 by Maureen Berg, Taylor Reiter, Joanne Emerson +2 · 1 voice · 1 citation
Environmental Science · Biochemistry, Genetics and Molecular Biology · #Bacteriophages and microbial interactions #Genomics and Phylogenetic Studies #Plant and Fungal Interactions Research
paper · pdf · doi:10.1093/nargab/lqaf163
Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but struggle to assemble complicated genome regions (e.g. repeats) compared to long-read sequence assemblies. Accurate metagenome assembly is especially challenging in diverse environments, such as soil, and long-read sequencing has been shown to improve assembly. Here, we use metagenomic data with paired long-read and short-read sequences to identify specific factors that impact genome assembly and assess their relative importance in a natural soil community. Our analysis suggests that low coverage and high sequence diversity are the two main factors leading to misassemblies in short-read data, and many of these "missed" regions tend to be variable parts of the genome, such as integrated viruses or defense system islands. Taken together, our results demonstrate that short-read metagenomes can possibly underestimate the diversity of these genome regions and that long-read sequencing can complement short-read metagenomes by improving assembly contiguity and the recovery of variable regions.