{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Heng E"],"funding":["Agency for Science, Technology and Research","National Research Foundation Singapore","Institute of Molecular and Cell Biology"],"pagination":["253-261"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10060144"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["8(2)"],"pubmed_abstract":["With the advent of rapid automated <i>in silico</i> identification of biosynthetic gene clusters (BGCs), genomics presents vast opportunities to accelerate natural product (NP) discovery. However, prolific NP producers, <i>Streptomyces</i>, are exceptionally GC-rich (>80%) and highly repetitive within BGCs. These pose challenges in sequencing and high-quality genome assembly which are currently circumvented <i>via</i> intensive sequencing. Here, we outline a more cost-effective workflow using multiplex Illumina and Oxford Nanopore sequencing with hybrid long-short read assembly algorithms to generate high quality genomes. Our protocol involves subjecting long read-derived assemblies to up to 4 rounds of polishing with short reads to yield accurate BGC predictions. We successfully sequenced"],"journal":["Synthetic and systems biotechnology"],"pubmed_title":["Cost-effective hybrid long-short read assembly delineates alternative GC-rich <i>Streptomyces</i> hosts for natural product discovery."],"pmcid":["PMC10060144"],"funding_grant_id":["21719","NRF-CRP19-2017-05-00"],"pubmed_authors":["Yang LK","Kanagasundaram Y","Leong CY","Koduru L","Tay DWP","Seow DCS","Heng E","Lim YH","Wong FT","Ng V","Ng SB","Tan LL"],"additional_accession":[]},"is_claimable":false,"name":"Cost-effective hybrid long-short read assembly delineates alternative GC-rich <i>Streptomyces</i> hosts for natural product discovery.","description":"With the advent of rapid automated <i>in silico</i> identification of biosynthetic gene clusters (BGCs), genomics presents vast opportunities to accelerate natural product (NP) discovery. However, prolific NP producers, <i>Streptomyces</i>, are exceptionally GC-rich (>80%) and highly repetitive within BGCs. These pose challenges in sequencing and high-quality genome assembly which are currently circumvented <i>via</i> intensive sequencing. Here, we outline a more cost-effective workflow using multiplex Illumina and Oxford Nanopore sequencing with hybrid long-short read assembly algorithms to generate high quality genomes. Our protocol involves subjecting long read-derived assemblies to up to 4 rounds of polishing with short reads to yield accurate BGC predictions. We successfully sequenced","dates":{"release":"2023-01-01T00:00:00Z","publication":"2023 Jun","modification":"2026-07-15T01:27:11.334Z","creation":"2025-02-19T02:23:02.243Z"},"accession":"S-EPMC10060144","cross_references":{"pubmed":["37007277"],"doi":["10.1016/j.synbio.2023.03.001"]}}