Genome-Guided Discovery of Natural Products through Multiplexed Low-Coverage Whole-Genome Sequencing of Soil Actinomycetes on Oxford Nanopore Flongle

Abstract

Short-read sequencing of GC-rich genomes such as those from actinomycetes results in a fragmented genome assembly and truncated biosynthetic gene clusters (often 10 to >100 kb long), which hinders our ability to understand the biosynthetic potential of a given strain and predict the molecules that can be produced. The current study demonstrates that contiguous DNA assemblies, suitable for analysis of BGCs, can be obtained through low-coverage, multiplexed sequencing on Flongle, which provides a new low-cost workflow ($30 to 40 per strain) for sequencing actinomycete strain libraries.

Improved Assembly of Metagenome-Assembled Genomes and Viruses in Tibetan Saline Lake Sediment by HiFi Metagenomic Sequencing

“…Due to the high diversity of core genes and relatively high GC content across the PKS/NRPS regions, most novel BGCs could not be extracted efficiently by NGS methods ( 60 ). Long-read technologies, such as Nanopore and PacBio sequencing, have been successfully applied to the analysis of soil and animal gut metagenomes to identify BGCs ( 31 , 61 ). Interestingly, under the ‘HiFi’ assembly strategy, HiFiasm-meta performed best both in virus and BGC detection, suggesting that this recently designed tool was the most suitable for assembling high-fidelity long reads.…”

Uncovering Genomic Features and Biosynthetic Gene Clusters in Endophytic Bacteria from Roots of the Medicinal Plant Alkanna tinctoria Tausch as a Strategy To Identify Novel Biocontrol Bacteria

“…Inference of bioactive molecules like antifungals and other secondary metabolites via the prediction of BGCs has limitations as well. Annotation of genomes and prediction of BGCs with bioinformatic tools like antiSMASH might depend on the completeness and contiguity of genomes ( 41 – 43 ). Moreover, the use of short-read sequencing platforms like Illumina, which nowadays is a popular and cost-effective technology, tends to produce fragmented genome assemblies.…”

Comparative genomics unravels a rich set of biosynthetic gene clusters with distinct evolutionary trajectories across fungal species farmed by termites

“…To identify putative BGCs, we uploaded genomes to antiSMASH fungal version (v7.0) 38 with default parameters (Tables S5 and S6). BGCs were deemed incomplete if they were positioned close to the edge of a contig 48,49 . To reduce the complexity of the BGC dataset, GenBank files from the fungiSMASH analysis were assigned to biosynthetic gene cluster families (GCFs; i.e., families of BGCs that share a similar organization and likely code for the biosynthesis of the same or similar compounds) through a pairwise distance analysis using the BiG-SCAPE network prediction software 50 , with default settings (Tables S7 and S8).…”