| Gene (P. fluorescens SBW25) |
serCGA |
N/A |
PFLUt39 |
Encodes tRNA-Ser(CGA) |
| Gene (P. fluorescens SBW25) |
serTGA |
N/A |
PFLUt51 |
Encodes tRNA-Ser(UGA) |
| Strain, strainbackground (P. fluorescens SBW25) |
Pseudomonas fluorescens SBW25 |
Rainey and Bailey, 1996; Silby et al., 2009
|
|
Wild type |
| Genetic reagent (P. fluorescens SBW25) |
SBW25-lacZ
|
Zhang and Rainey, 2007 |
|
Neutrally marked SBW25 for competition experiments |
| Genetic reagent (P. fluorescens SBW25) |
ΔserCGA-1 |
This work |
|
Bases 1624957–1625092, encompassing serCGA, removed. Biological replicate of ΔserCGA-2 |
| Genetic reagent (P. fluorescens SBW25) |
ΔserCGA-2 |
This work |
|
Bases 1624957–1625092, encompassing serCGA, removed. Biological replicate of ΔserCGA-1 |
| Genetic reagent (P. fluorescens SBW25) |
SBW25-eWT |
This work |
|
Wild type SBW25 that has been through the engineering process |
| Genetic reagent (P. fluorescens SBW25) |
W1-L |
This work |
|
Evolution isolate from day 13 of lineage W1 (founded by SBW25) |
| Genetic reagent (P. fluorescens SBW25) |
W3-L |
This work |
|
Evolution isolate from day 13 of lineage W3 (founded by SBW25-eWT) |
| Genetic reagent (P. fluorescens SBW25) |
M1-L |
This work |
|
Evolution isolate from day 13 of lineage M1 (founded by ΔserCGA-1) |
| Genetic reagent (P. fluorescens SBW25) |
M2-L |
This work |
|
Evolution isolate from day 13 of lineage M2 (founded by ΔserCGA-1) |
| Genetic reagent (P. fluorescens SBW25) |
M2-Lop |
This work |
|
Second evolution isolate from day 13 of lineage M2 (founded by ΔserCGA-1) |
| Genetic reagent (P. fluorescens SBW25) |
M3-L |
This work |
|
Evolution isolate from day 13 of lineage M3 (founded by ΔserCGA-2) |
| Genetic reagent (P. fluorescens SBW25) |
M4-L |
This work |
|
Evolution isolate from day 13 of lineage M4 (founded by ΔserCGA-2) |
| Recombinant DNA reagent |
pSXn (plasmid) |
Owen and Ackerley, 2011; Frederic Bertels |
|
pSX with one copy of a 38 bp direct repeat removed |
| Recombinant DNA reagent |
pSXn-CGA (plasmid) |
This work |
|
pSXn carrying serCGA
|
| Recombinant DNA reagent |
pSXn-TGA (plasmid) |
This work |
|
pSXn carrying serTGA
|
| Commercial assay or kit |
DNeasy Blood and Tissue Kit |
Qiagencat. no. 69506 |
|
|
| Commercial assay or kit |
NextSeq 550 Output v2.5 kit |
Illuminacat.no. 20024904 |
|
|
| Commercial assay or kit |
TRIzol Max Bacterial RNA isolation kit |
Life Technologiescat.no. 16096040 |
|
|
| Commercial assay or kit |
DNA 7500 kit |
Agilent Technologies |
|
|
| Software, algorithm |
GtRNAdb 2.0 |
Chan and Lowe, 2016 |
|
https://www.gtrnadb.ucsc.edu |
| Software, algorithm |
tRNAscan-SE 2.0 |
Chan and Lowe, 2019 |
|
https://www.lowelab.ucsc.edu/tRNAscan-SE/ |
| Software, algorithm |
BLASTp |
Altschul et al., 1990 |
|
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins |
| Software, algorithm |
Gen5 |
BioTek |
|
https://www.biotek.com/ |
| Software, algorithm |
Geneious v11.1.4 |
Geneious |
|
https://www.geneious.com/home/ |
| Software, algorithm |
breseq v0.33.2 |
Deatherage et al., 2014a; Deatherage and Barrick, 2014b
|
|
https://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing |
| Software, algorithm |
R v3.6.0 |
R Foundation for Statistical Computing, 2013 |
|
https://www.r-project.org/ |
| Other |
SuperScript III reverse transcriptase |
ThermoFisher Scientific cat.no.18080093 |
|
|
| Other |
T4 RNA ligase 2 |
New England BioLabs cat.no. M0239L |
|
Also known as T4 Rnl2 |
| Other |
Phusion |
ThermoFisher Scientific cat.no.M0531S |
|
|
| Other |
5% Mini-PROTEANTBE Gels |
Bio-Rad Laboratories cat.no.4565015 |
|
|
