Abstract
Burkholderia sp. strain SJ98 has the chemotactic activity towards nitroaromatic and chloronitroaromatic compounds. Recently our group published draft genome of strain SJ98. In this study, we further sequence and annotate the genome of stain SJ98 to exploit the potential of this bacterium. We specifically annotate its chemotaxis genes and methyl accepting chemotaxis proteins. Genome of Burkholderia sp. SJ98 was annotated using PGAAP pipeline that predicts 7,268 CDSs, 52 tRNAs and 3 rRNAs. Our analysis based on phylogenetic and comparative genomics suggest that Burkholderia sp. YI23 is closest neighbor of the strain SJ98. The genes involved in the chemotaxis of strain SJ98 were compared with genes of closely related Burkholderia strains (i.e. YI23, CCGE 1001, CCGE 1002, CCGE 1003) and with well characterized bacterium E. coli K12. It was found that strain SJ98 has 37 che genes including 19 methyl accepting chemotaxis proteins that involved in sensing of different attractants. Chemotaxis genes have been found in a cluster along with the flagellar motor proteins. We also developed a web resource that provides comprehensive information on strain SJ98 that includes all analysis data (http://crdd.osdd.net/raghava/genomesrs/burkholderia/).
Highlights
The genus Burkholderia was created in 1992 and presently contains nearly 72 well-characterized species isolated from a wide range of ecological niches including soil, water, human, plant and clinical samples [1,2,3]
SJ98 and further characterized as Burkholderia sp. strain SJ98) was isolated from a pesticide contaminated soil sample from Assam agricultural fields, India by using an enrichment technique developed by Samanta et al (2000) ‘chemotactic enrichment technique’ [7]
To determine the arrangement of the contigs in the genome of strain SJ98, these 15 contigs were aligned to the genome of Burkholderia sp
Summary
The genus Burkholderia was created in 1992 and presently contains nearly 72 well-characterized species isolated from a wide range of ecological niches including soil, water, human, plant and clinical samples [1,2,3]. The ecological versatility of the genus Burkholderia has been attributed to two main factors: i) contain an array of insertion sequences and ii) it is metabolically robust due to its large coding capacity [4]. They evolve by increasing their genome size and changing the gene order in the genome [5]. Tran et al, (2008) has reported that chemotaxis of Geobacter spp. involves numerous chemoreceptors and chemotaxis like gene clusters involved in diverse set of signaling function as well as in chemotaxis [15]
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