|
Bacterial and virus strains
|
|
Escherichia coli NEB® Turbo |
NEB |
Cat# C2984 |
|
Escherichia coli BL21(DE3) |
NEB |
Cat# C2527 |
|
Escherichia coli 10-beta electrocompetent |
NEB |
Cat# C3020K |
|
Escherichia coli BL21(DE3) electrocompetent |
Millipore Sigma |
Cat# CMC0016 |
|
Chemicals, peptides, and recombinant proteins
|
| LB Broth |
Fisher |
Cat# BP1426 |
| LB Agar |
Fisher |
DF0445-07-6 |
| Spectinomycin |
Gold Bio |
Cat# S-140 |
| Kanamycin |
Gold Bio |
Cat# K-120 |
| Carbenicillin |
Gold Bio |
Cat# C-103 |
| IPTG |
Gold Bio |
Cat# I2481C |
| Klenow Fragment |
NEB |
Cat# M0212L |
|
Critical commercial assays
|
| SsoAdvanced Universal SYBR Green Supermix |
BioRad |
Cat# 1725275 |
| Promega Wizard Genomic DNA purification kit |
Promega |
Cat# A1120 |
| NEBNext Library Quant Kit |
NEB |
Cat# E7630L |
|
Deposited data
|
| Raw agarose gel image |
This paper, Mendeley Data |
doi:10.17632/89p4wdryt3.1
|
| Illumina sequencing data |
This paper, SRA |
SRA: PRJNA769066 |
| Custom python scripts |
This paper, Mendeley Data |
doi:10.17632/89p4wdryt3.1
|
|
Oligonucleotides
|
| All oligonucleotides used in this study. |
This paper. |
Table S3
|
|
Recombinant DNA
|
| All plasmids used in this study. |
This paper. |
Table S2
|
|
Software and algorithms
|
| PSI-BLAST (2.10.0+) |
NCBI |
https://blast.ncbi.nlm.nih.gov/Blast.cgi
|
| NCBI Efetch |
NCBI |
https://www.ncbi.nlm.nih.gov/books/NBK25499/
|
| Entrez Programming Utilities |
NCBI |
https://www.ncbi.nlm.nih.gov/books/NBK25501/
|
| CRISPRCasFinder (4.2.2) |
Couvin et al., 2018
|
https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index
|
| Krona |
Ondov et al., 2011
|
https://github.com/marbl/Krona
|
| WebLogo (2.8.2) |
Crooks et al., 2004
|
https://weblogo.berkeley.edu/
|
| Illumina pipeline script |
Vo et al., 2020 |
https://github.com/sternberglab/Illumina-pipeline
|
| CD-HIT |
Li et al., 2001, 2002
|
https://github.com/weizhongli/cdhit
|
| MUSCLE (v3.8.1551) |
Edgar, 2004
|
N/A |
| FastTree (version 2.1.10) |
Price et al., 2010
|
http://www.microbesonline.org/fasttree/
|
| iTOL (6.4) |
Letunic and Bork, 2021
|
https://itol.embl.de/itol.cgi
|
| HMMER 3.3.2 |
Eddy, 1995
|
http://hmmer.org/
|
| Geneious Prime® 2019.2.1 |
Biomatters |
https://www.geneious.com/
|
| Prokka (version 1.14.6) |
Seemann, 2014
|
https://github.com/tseemann/prokka
|
| DefenseFinder (v0.9, model v0.0.2) |
Tesson et al., 2021
|
https://defense-finder.mdmparis-lab.com/
|
| EasyFig |
Sullivan et al., 2011
|
https://mjsull.github.io/Easyfig/
|
