Cost-effective hybrid long-short read assembly delineates alternative GC-rich Streptomyces hosts for natural product discovery  

作　　者：Elena Heng Lee Ling Tan Dillon W.P.Tay Yee Hwee Lim Lay-Kien Yang Deborah C.S.Seow Chung Yan Leong Veronica Ng Siew Bee Ng Yoganathan Kanagasundaram Fong Tian Wong Lokanand Koduru 

机构地区：[1]Molecular Engineering Laboratory,Institute of Molecular and Cell Biology(IMCB),Agency for Science,Technology and Research(A*STAR),61 Biopolis Drive,#07-06,Proteos,Singapore,138673,Singapore [2]Green Chemistry and Biocatalysis,Institute of Sustainability for Chemicals,Energy and Environment(ISCE2),Agency for Science,Technology and Research(A*STAR),8 Biomedical Grove,Neuros,#07-01,Singapore,138665,Singapore [3]Singapore Institute of Food and Biotechnology Innovation(SIFBI),Agency for Science,Technology and Research(A*STAR),31 Biopolis Way,Level 2,Nanos,Singapore,138669,Singapore

出　　处：《Synthetic and Systems Biotechnology》2023年第2期253-261,共9页合成和系统生物技术（英文）

基　　金：supported by National Research Foundation,Singapore(NRF-CRP19-2017-05-00);Agency for Science,Technology and Research(A*STAR),Singapore(#21719).

摘　　要：With the advent of rapid automated in silico identification of biosynthetic gene clusters(BGCs),genomics pre-sents vast opportunities to accelerate natural product(NP)discovery.However,prolific NP producers,Strepto-myces,are exceptionally GC-rich(>80%)and highly repetitive within BGCs.These pose challenges in sequencing and high-quality genome assembly which are currently circumvented via 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 and assembled 8 GC-rich Streptomyces genomes whose lengths range from 7.1 to 12.1 Mb with a median N50 of 8.2 Mb.Taxonomic analysis revealed previous misrepresentation among these strains and allowed us to propose a potentially new species,Streptomyces sydneybrenneri.Further comprehensive characterization of their biosynthetic,pan-genomic and antibiotic resistance features especially for molecules derived from type I polyketide synthase(PKS)BGCs reflected their potential as alternative NP hosts.Thus,the genome assemblies and insights presented here are envisioned to serve as gateway for the scientific community to expand their avenues in NP discovery.

关 键 词：Streptomyces GC-Rich Hybrid assembly Biosynthetic gene cluster(BGC) Natural product(NP)chassis Type I polyketide Synthase(PKS) 

分 类 号：S51[农业科学—作物学]