1995年至2016年间从法国牛肉制品中分离出的75个大肠杆菌基因组的混合组装。
Hybrid Assembly from 75 E. coli Genomes Isolated from French Bovine Food Products between 1995 and 2016.
作者信息
Jaudou Sandra, Tran Mai-Lan, Vorimore Fabien, Fach Patrick, Delannoy Sabine
机构信息
Pathogenic E. coli Unit, Laboratory for Food Safety, Anses, Maisons-Alfort, France.
IdentyPath Genomics Platform, Laboratory for Food Safety, Anses, Maisons-Alfort, France.
出版信息
Microbiol Resour Announc. 2023 Mar 16;12(3):e0109522. doi: 10.1128/mra.01095-22. Epub 2023 Feb 1.
Abstract
Here, we report the complete (or near-complete) genome sequences of 75 Escherichia coli isolates, including 71 -positive E. coli isolates, isolated in France between 1995 and 2016 from food of bovine origin. Genomes were assembled using a combination of long- and short-read sequencing.
摘要
在此，我们报告了75株大肠杆菌分离株的完整（或近乎完整）基因组序列，其中包括71株阳性大肠杆菌分离株，这些分离株于1995年至2016年间在法国从牛源食品中分离得到。基因组通过长读长和短读长测序相结合的方法进行组装。
相似文献
1
Hybrid Assembly from 75 E. coli Genomes Isolated from French Bovine Food Products between 1995 and 2016.
Microbiol Resour Announc. 2023 Mar 16;12(3):e0109522. doi: 10.1128/mra.01095-22. Epub 2023 Feb 1.
2
A high-throughput multiplexing and selection strategy to complete bacterial genomes.
Gigascience. 2021 Dec 9;10(12). doi: 10.1093/gigascience/giab079.
3
Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes.
Microb Genom. 2019 Sep;5(9). doi: 10.1099/mgen.0.000294. Epub 2019 Aug 30.
4
Completion of draft bacterial genomes by long-read sequencing of synthetic genomic pools.
BMC Genomics. 2020 Jul 29;21(1):519. doi: 10.1186/s12864-020-06910-6.
5
Pathogenomes of Atypical Non-shigatoxigenic NSF/SF O157:H7/NM: Comprehensive Phylogenomic Analysis Using Closed Genomes.
Front Microbiol. 2020 Apr 15;11:619. doi: 10.3389/fmicb.2020.00619. eCollection 2020.
6
Outcome of Different Sequencing and Assembly Approaches on the Detection of Plasmids and Localization of Antimicrobial Resistance Genes in Commensal .
Microorganisms. 2021 Mar 14;9(3):598. doi: 10.3390/microorganisms9030598.
7
Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing.
Microb Genom. 2024 May;10(5). doi: 10.1099/mgen.0.001246.
8
Toxigenic properties and stx phage characterization of Escherichia coli O157 isolated from animal sources in a developing country setting.
BMC Microbiol. 2018 Aug 31;18(1):98. doi: 10.1186/s12866-018-1235-3.
9
Occurrence, virulence genes and antibiotic resistance of Escherichia coli O157 isolated from raw bovine, caprine and ovine milk in Greece.
Food Microbiol. 2009 Dec;26(8):865-71. doi: 10.1016/j.fm.2009.06.002. Epub 2009 Jun 10.
10
Comparative Genomics and Characterization of Hybrid Shigatoxigenic and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains.
PLoS One. 2015 Aug 27;10(8):e0135936. doi: 10.1371/journal.pone.0135936. eCollection 2015.
引用本文的文献
1
Exploring Long-Read Metagenomics for Full Characterization of Shiga Toxin-Producing in Presence of Commensal .
Microorganisms. 2023 Aug 9;11(8):2043. doi: 10.3390/microorganisms11082043.
2
Combination of whole genome sequencing and supervised machine learning provides unambiguous identification of -positive Shiga toxin-producing .
Front Microbiol. 2023 May 12;14:1118158. doi: 10.3389/fmicb.2023.1118158. eCollection 2023.
本文引用的文献
1
Time- and memory-efficient genome assembly with Raven.
Nat Comput Sci. 2021 May;1(5):332-336. doi: 10.1038/s43588-021-00073-4. Epub 2021 May 20.
2
Evaluation of high molecular weight DNA extraction methods for long-read sequencing of Shiga toxin-producing Escherichia coli.
PLoS One. 2022 Jul 13;17(7):e0270751. doi: 10.1371/journal.pone.0270751. eCollection 2022.
3
metaFlye: scalable long-read metagenome assembly using repeat graphs.
Nat Methods. 2020 Nov;17(11):1103-1110. doi: 10.1038/s41592-020-00971-x. Epub 2020 Oct 5.
4
Performance of neural network basecalling tools for Oxford Nanopore sequencing.
Genome Biol. 2019 Jun 24;20(1):129. doi: 10.1186/s13059-019-1727-y.
5
NanoPack: visualizing and processing long-read sequencing data.
Bioinformatics. 2018 Aug 1;34(15):2666-2669. doi: 10.1093/bioinformatics/bty149.
6
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.
PLoS Comput Biol. 2017 Jun 8;13(6):e1005595. doi: 10.1371/journal.pcbi.1005595. eCollection 2017 Jun.
7
Canu: scalable and accurate long-read assembly via adaptive -mer weighting and repeat separation.
Genome Res. 2017 May;27(5):722-736. doi: 10.1101/gr.215087.116. Epub 2017 Mar 15.
8
Fast and accurate de novo genome assembly from long uncorrected reads.
Genome Res. 2017 May;27(5):737-746. doi: 10.1101/gr.214270.116. Epub 2017 Jan 18.
9
NCBI prokaryotic genome annotation pipeline.
Nucleic Acids Res. 2016 Aug 19;44(14):6614-24. doi: 10.1093/nar/gkw569. Epub 2016 Jun 24.
10
Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
PLoS One. 2014 Nov 19;9(11):e112963. doi: 10.1371/journal.pone.0112963. eCollection 2014.
Zotero 插件