类T4噬菌体RB3、RB5、RB6、RB7、RB9、RB10、RB27、RB33、RB55、RB59和RB68的全基因组序列
Complete Genome Sequences of T4-Like Bacteriophages RB3, RB5, RB6, RB7, RB9, RB10, RB27, RB33, RB55, RB59, and RB68.
作者信息
Yaung Stephanie J, Esvelt Kevin M, Church George M
机构信息
Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts, USA.
出版信息
Genome Announc. 2015 Jan 2;3(1):e01122-14. doi: 10.1128/genomeA.01122-14.
Abstract
T4-like bacteriophages have been explored for phage therapy and are model organisms for phage genomics and evolution. Here, we describe the sequencing of 11 T4-like phages. We found a high nucleotide similarity among the T4, RB55, and RB59; RB32 and RB33; and RB3, RB5, RB6, RB7, RB9, and RB10 phages.
摘要
类T4噬菌体已被用于噬菌体治疗研究，并且是噬菌体基因组学和进化的模式生物。在此，我们描述了11种类T4噬菌体的测序情况。我们发现T4、RB55和RB59；RB32和RB33；以及RB3、RB5、RB6、RB7、RB9和RB10噬菌体之间存在高度的核苷酸相似性。
相似文献
1
Complete Genome Sequences of T4-Like Bacteriophages RB3, RB5, RB6, RB7, RB9, RB10, RB27, RB33, RB55, RB59, and RB68.
Genome Announc. 2015 Jan 2;3(1):e01122-14. doi: 10.1128/genomeA.01122-14.
2
Sinorhizobium meliloti Phage ΦM9 Defines a New Group of T4 Superfamily Phages with Unusual Genomic Features but a Common T=16 Capsid.
J Virol. 2015 Nov;89(21):10945-58. doi: 10.1128/JVI.01353-15. Epub 2015 Aug 26.
3
The diversity and evolution of the T4-type bacteriophages.
Res Microbiol. 2003 May;154(4):259-67. doi: 10.1016/S0923-2508(03)00069-X.
4
Genomic, proteomic and bioinformatic analysis of two temperate phages in Roseobacter clade bacteria isolated from the deep-sea water.
BMC Genomics. 2017 Jun 27;18(1):485. doi: 10.1186/s12864-017-3886-0.
5
Bacteriophages of the Urinary Microbiome.
J Bacteriol. 2018 Mar 12;200(7). doi: 10.1128/JB.00738-17. Print 2018 Apr 1.
6
Analysis of whole genome sequencing for the Escherichia coli O157:H7 typing phages.
BMC Genomics. 2015 Apr 8;16(1):271. doi: 10.1186/s12864-015-1470-z.
7
Functional and comparative genome analysis of novel virulent actinophages belonging to Streptomyces flavovirens.
BMC Microbiol. 2017 Mar 3;17(1):51. doi: 10.1186/s12866-017-0940-7.
8
The genome of the pseudo T-even bacteriophages, a diverse group that resembles T4.
J Mol Biol. 1997 Mar 28;267(2):237-49. doi: 10.1006/jmbi.1996.0867.
9
Comparative genomic analysis of three lytic Lactococcus garvieae phages, novel phages with genome architecture linking the 936 phage species of Lactococcus lactis.
Mar Genomics. 2019 Dec;48:100696. doi: 10.1016/j.margen.2019.100696. Epub 2019 Jul 10.
10
A selective barrier to horizontal gene transfer in the T4-type bacteriophages that has preserved a core genome with the viral replication and structural genes.
Mol Biol Evol. 2006 Sep;23(9):1688-96. doi: 10.1093/molbev/msl036. Epub 2006 Jun 16.
引用本文的文献
1
Phage Therapy for Mosquito Larval Control: a Proof-of-Principle Study.
mBio. 2022 Dec 20;13(6):e0301722. doi: 10.1128/mbio.03017-22. Epub 2022 Nov 29.
2
Suggestion for a new bacteriophage genus for the Klebsiella pneumoniae phage vB_KpnS-Carvaje.
Curr Genet. 2022 Aug;68(3-4):393-406. doi: 10.1007/s00294-022-01242-2. Epub 2022 Jun 6.
3
Temporal Stability and Genetic Diversity of 48-Year-Old T-Series Phages.
mSystems. 2021 Feb 16;6(1):e00990-20. doi: 10.1128/mSystems.00990-20.
4
The Odd "RB" Phage-Identification of Arabinosylation as a New Epigenetic Modification of DNA in T4-Like Phage RB69.
Viruses. 2018 Jun 8;10(6):313. doi: 10.3390/v10060313.
5
Metagenomic Analysis of Dairy Bacteriophages: Extraction Method and Pilot Study on Whey Samples Derived from Using Undefined and Defined Mesophilic Starter Cultures.
Appl Environ Microbiol. 2017 Sep 15;83(19). doi: 10.1128/AEM.00888-17. Print 2017 Oct 1.
6
Genome Sequence of the Enterohemorrhagic Escherichia coli Bacteriophage UFV-AREG1.
Genome Announc. 2016 Oct 13;4(5):e00412-16. doi: 10.1128/genomeA.00412-16.
7
Bacteriophages and phage-inspired nanocarriers for targeted delivery of therapeutic cargos.
Adv Drug Deliv Rev. 2016 Nov 15;106(Pt A):45-62. doi: 10.1016/j.addr.2016.03.003. Epub 2016 Mar 17.
本文引用的文献
1
CRISPR/Cas9-mediated phage resistance is not impeded by the DNA modifications of phage T4.
PLoS One. 2014 Jun 2;9(6):e98811. doi: 10.1371/journal.pone.0098811. eCollection 2014.
2
Trimmomatic: a flexible trimmer for Illumina sequence data.
Bioinformatics. 2014 Aug 1;30(15):2114-20. doi: 10.1093/bioinformatics/btu170. Epub 2014 Apr 1.
3
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement.
PLoS One. 2010 Jun 25;5(6):e11147. doi: 10.1371/journal.pone.0011147.
4
Phage host range and efficiency of plating.
Methods Mol Biol. 2009;501:141-9. doi: 10.1007/978-1-60327-164-6_14.
5
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Genome Res. 2008 May;18(5):821-9. doi: 10.1101/gr.074492.107. Epub 2008 Mar 18.
6
Identifying bacterial genes and endosymbiont DNA with Glimmer.
Bioinformatics. 2007 Mar 15;23(6):673-9. doi: 10.1093/bioinformatics/btm009. Epub 2007 Jan 19.
7
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W686-9. doi: 10.1093/nar/gki366.
8
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402. doi: 10.1093/nar/25.17.3389.
Zotero 插件