Genome analysis of two novel Pseudomonas strains exhibiting differential hypersensitivity reactions on tobacco seedlings reveals differences in nonflagellar T3SS organization and predicted effector proteins

MicrobiologyOpen
Caetanie Fometeu TchagangJames T Tambong

Abstract

Multilocus sequence analysis (MLSA) of two new biological control strains (S1E40 and S3E12) of Pseudomonas was performed to assess their taxonomic position relative to close lineages, and comparative genomics employed to investigate whether these strains differ in key genetic features involved in hypersensitivity responses (HRs). Strain S3E12, at high concentration, incites HRs on tobacco and corn plantlets while S1E40 does not. Phylogenies based on individual genes and 16S rRNA-gyrB-rpoB-rpoD concatenated sequence data show strains S1E40 and S3E12 clustering in distinct groups. Strain S3E12 consistently clustered with Pseudomonas marginalis, a bacterium causing soft rots on plant tissues. MLSA data suggest that strains S1E40 and S3E12 are novel genotypes. This is consistent with the data of genome-based DNA-DNA homology values that are below the proposed cutoff species boundary. Comparative genomics analysis of the two strains revealed major differences in the type III secretion systems (T3SS) as well as the predicted T3SS secreted effector proteins (T3Es). One nonflagellar (NF-T3SS) and two flagellar T3SSs (F-T3SS) clusters were identified in both strains. While F-T3SS clusters in both strains were relatively conserved, the N...Continue Reading

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Datasets Mentioned

BETA
BS2976
BS3265

Methods Mentioned

BETA
bioprotection
PCR
electrophoresis

Software Mentioned

BLASTp
CMG
RNAmmer
CLC Genomics Workbench
BLASTp search
R package
BLAST
FastQC
ABySS assembler
Geneious

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