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United States Department of Agriculture

Agricultural Research Service

Title: Repetitive extragenic palindromic elements within the genomes of biocontrol Pseudomonas spp.

item Hassan, Karl
item Davis, Edward
item Lim, Chee
item Breakwell, Katy
item Loper, Joyce
item Paulsen, Ian

Submitted to: Pseudomonas
Publication Type: Abstract Only
Publication Acceptance Date: 8/29/2011
Publication Date: 9/4/2011
Citation: Hassan, K., Davis, E.W., Lim, C., Breakwell, K., Loper, J.E., Paulsen, I. 2011. Repetitive extragenic palindromic elements within the genomes of biocontrol Pseudomonas spp. Pseudomonas 2011. 13th International Conference abstract book. Pg. 10.

Interpretive Summary:

Technical Abstract: Repetitive extragenic palindromic (REP) sequence elements have been identified within the genome sequences of many bacterial species, including a number of animal and plant pathogenic Pseudomonas spp. Several functions have been proposed for these sequences, e.g., binding or target sites for DNA replication machinery and integrases, mediators of mRNA stability, transcriptional termination and genomic recombination. We recently determined the complete genomic sequences of seven plant commensal Pseudomonas strains that display biocontrol properties, including two P. chlororaphis, one P. synxantha and four P. fluorescens strains. These strains display differing levels of phylogenetic relatedness, ranging from the species to species-complex and genus levels. As such, these genomes provide an ideal platform to investigate the diversity and dynamics of REP elements. REP elements were detected bioinformatically in each of the newly sequenced genomes, as well as the previously sequenced strain P. fluorescens Pf-5. A total of four distinct REP sequences were identified in these strains. One REP element was highly conserved across all strains and present at up to 1970 copies per genome. One of three secondary REP elements was also observed in most of the strains. Interestingly, only one of these secondary REP elements was linked to the phylogeny of the strains. Chromosomal sequence alignments of closely related strains demonstrated that local expansion of REP element copy number is a frequent event and an important contributor to sequence variability. Comparisons between more distantly related strains revealed that the local REP element expansion typically occurs within older, more highly conserved regions of the genome, a feature that we have exploited to detect regions that may have been acquired recently via mechanisms of lateral transfer. Together, these results revealed interesting features of the evolution and diversity of extragenic regions in Pseudomonas genomes and demonstrate the use of REP sequence analysis in genomic studies.

Last Modified: 10/19/2017
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