Abstract
We analyzed the genome sequence of an endophytic bacterial strain Pseudomonas putida TJI51 isolated from mango bark tissues. Next generation DNA sequencing and short read de novo assembly generated the 5,805,096 bp draft genome of P. putida TJI51. Out of 6,036 protein coding genes in P. putida TJI51 sequences, 4,367 (72%) were annotated with functional specifications, while the remaining encoded hypothetical proteins. Comparative genome sequence analysis revealed that the P. putida TJI51genome contains several regions, not identified in so far sequenced P. putida genomes. Some of these regions were predicted to encode enzymes, including acetylornithine deacetylase, betaine aldehyde dehydrogenase, aldehyde dehydrogenase, benzoylformate decarboxylase, hydroxyacylglutathione hydrolase, and uroporphyrinogen decarboxylase. The genome of P. putida TJI51 contained three nonribosomal peptide synthetase gene clusters. Genome sequence analysis of P. putidaTJI51 identified this bacterium as an endophytic resident. The endophytic fitness might be linked with alginate, which facilitates bacterial colonization in plant tissues. Genome sequence analysis shed light on the presence of a diverse spectrum of metabolic activities and adaptation of this isolate to various niches.
Highlights
The genus Pseudomonas is a versatile and ecologically important group of bacteria
We isolated a number of endophytic Pseudomonas strains from dead tissues of bark, leaves and inflorescence of mango (Mangifera indica) trees grown in agricultural farms in mango growing districts in Sindh province of Pakistan (Khan et al, 2014)
Genome-wide DNA sequencing and comparative genomics were done for detailed functional characterization of this isolate
Summary
The genus Pseudomonas is a versatile and ecologically important group of bacteria. They are Gram-negative, slightly curved flagellated rods and prolific colonizers of surfaces (Clarke, 1982). Pseudomonas species have been isolated from diverse ecosystems including marine, freshwater and terrestrial environment including plants and animals sources (Achouak et al, 2000; Manaia and Moore, 2002; Liu et al, 2008). This widespread distribution is due to physiological and genetic diversity (Spiers et al, 2000). Comparative genomics of the Pseudomonas strains revealed much variability in their genome sizes, ranging from 3.7 Mbp for Pseudomonas stutzeri to 7.1 Mbp for Pseudomonas aeruginosa (Schmidt et al, 1996; Ginard et al, 1997)
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