Lowe-Power Lab

Lowe-Power Lab

Plant Bacteriology

Datasets and Research Resources

Lowe-Power Lab YouTube Channel

Link to the channel

Seminar on Ralstonia biogeography and host range

Seminar on the physiological mechanisms that underly wilt symptoms during Ralstonia disease

FigShare

On FigShare, we release cartoons and raw data from papers. Most data is released with a CC-BY license that only requires attribution and does not restrict any reuse of the data.

KBase

We use KBase to generate organized datasets for comparative evolutionary genomics studies. We also have created public narratives that allow anyone to re-analyze Ralstonia RNAseq data from SRA.

We currate a list of useful KBase narratives on a page of our Protocols GitHub: https://github.com/lowepowerlab/protocols/blob/main/kbase.md

Interactive files to understand genetic organization of Ralstonia’s vgr-linked toxin/antitoxin clusters

These tools were built as part of our study:

Methods:

The interative synteny analysis files were created using Clinker. The documentation for Clinker can be found here

Reference: clinker & clustermap.js: Automatic generation of gene cluster comparison figures. Gilchrist, C.L.M., Chooi, Y.-H., 2020. Bioinformatics.

Synteny files organized by aux cluster

If you would like to re-analyze the files used in this dataset, the inputs are located in a repository on our FigShare (see link above)

Plasmid Maps

These plasmids are described in the linked publications. All plasmid maps are provided as read-only Benchling links. If you prefer a different cloning software, Benchlings allows exports as genbank files (.gb). If you find a broken link, or you’re looking for a vector sequence that I’ve overlooked, please email me

2018

Plasmids from: Metabolomics of tomato xylem sap during bacterial wilt reveals Ralstonia solanacearum produces abundant putrescine, a metabolite that accelerates wilt disease. Download PDF

Benchling: pKO-speC::Sm Benchling: pRCTspeC_com Benchling: pUFR80-hrcC

2017

Plasmids from: Plant-like bacterial expansins play contrasting roles in two tomato vascular pathogens. Download PDF

Benchling: pUFR80-RSc0818KO Benchling: pMiniTn7-RSc0818comp Benchling: pHN_RsExpA

2016

Plasmids from: Degradation of the plant defense signal salicylic acid protects *Ralstonia solanacearum from toxicity and enhances virulence on tobacco.* Download PDF

Benchling: pUFR80-KOnagGH Benchling: pST-KOnagAaGHAbIKL Benchling: pRCGnagGHcomp Benchling: pMiniTn7-nagAaGHAbIKL-comp Benchling: pMiniTn7-KRNP

Plasmids from: Functional identification of putrescine C- and N-hydroxylases. Download PDF

Benchling: pUFR80-2HPut

2015

Plasmids from: Hydroxycinnamic acid degradation, a broadly conserved trait, protects Ralstonia solanacearum from chemical plant defenses and contributes to root colonization and virulence. Download PDF

Benchling: pUFR80-fcsKO Benchling: pMiniTn7FcsComp

Parental Plasmids

Most of the plasmids I use frequently (e.g. pST-Blue, pUC18miniTn7t-Gm, & pRC* series for Ralstonia solanacearum GMI1000) are available online (PubMed or via manufacturers). However, I had to track down or reconstruct a few plasmid sequences. Those are listed below with original citations.

pUFR80 (Kan/sacB vector for markerless deletions)

Castañeda A, Reddy JD, El-Yacoubi B, Gabriel DW. 2005. Mutagenesis of all eight avr genes in Xanthomonas campestris pv. campestris had no detected effect on pathogenicity, but one avr gene affected race specificity. Mol Plant-Microbe Interact 18:1306-1317.

Benchling: pUFR80

pAX1-Cm, pAX1-Em, & pAX1-Gm (Chromosomal complementation of Xylella Temecula1

Matsumoto, Young, and Igo. 2009. Chromosome-based genetic complementation system for Xylella fastidiosa. Appl Env Micro 75:1679-1687.

Benchling: pAX1-Cm Benchling: pAX1-Em Benchling: pAX1-Gm