Comprehensive Genome Sequencing and Annotation of Phage BUCT609

The whole genome was sequenced using Illumina’s MiSeq sequencing platform (Thermo Fisher Scientific, United States; Kozich et al., 2013 (link)) and the low-quality sequences were filtered by Trimmomatic (V0.32) program (Bolger et al., 2014 (link)). Then, the complete genomic sequence of BUCT609 was assembled by Newbler V3.0 software (Roche, Switzerland; Zhang et al., 2012 (link)) and CLC software (QIAGEN, Germany; Liu and Di, 2020 (link)). Using the online tools RAST (https://rast.nmpdr.org/; Aziz et al., 2008 (link)) to predict the ORFs and ORF Finder (https://www.bioinformatics.org/sms2/orf_find.html; Rombel et al., 2002 (link)) to annotate the DNA sequencing result. Sequence similarity analyses and comparisons were performed using the NCBI BLAST algorithm. A phylogenetic tree of phage BUCT609 was conducted by VICTOR (https://ggdc.dsmz.de/victor.php; Meier-Kolthoff and Göker, 2017 (link)) and average nucleotide identity (ANI) analysis was analyzed by another online tool VIRIDIC (http://rhea.icbm.uni-oldenburg.de/VIRIDIC/; Moraru et al., 2020 (link)).

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Han K., Dong Y., An X., Song L., Li M., Fan H, & Tong Y. (2022). Potential application of a newly isolated phage BUCT609 infecting Stenotrophomonas maltophilia. Frontiers in Microbiology, 13, 1001237.

Publication 2022

Newbler V3.0 software CLC software

Genomic Nucleotide Orfs Phage Rast Rhea Sequence analyses

Corresponding Organization : Beijing University of Chemical Technology

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Variable analysis

independent variables

Illumina's MiSeq sequencing platform (Thermo Fisher Scientific, United States)
Trimmomatic (V0.32) program (Bolger et al., 2014)
Newbler V3.0 software (Roche, Switzerland)
CLC software (QIAGEN, Germany)
RAST online tool
ORF Finder online tool
NCBI BLAST algorithm
VICTOR (https://ggdc.dsmz.de/victor.php)
VIRIDIC (http://rhea.icbm.uni-oldenburg.de/VIRIDIC/)

dependent variables

The complete genomic sequence of BUCT609

control variables

Low-quality sequences were filtered by Trimmomatic (V0.32) program

Annotations

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