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Pipeline publication

[…] nita. We previously found that B. cereus AR156 can induce systemic resistance to Pseudomonas syringae pv. tomato DC3000 by simultaneously activating the SA and JA/ET signaling pathways via an NPR1-dependent mechanism (). The biocontrol mechanisms of B. cereus AR156 are currently unclear. To better understand the biocontrol and plant growth-promoting mechanisms of B. cereus AR156, the whole genome of the strain was determined by 454 sequencing. Total DNA was prepared as described in the GS FLX Titanium general library preparation kit (454 sequencing) and then sequenced according to the GS FLX Titanium sequencing method manual. The 239,826 generated reads were assembled into contigs using the GS de novo assembler. The genome coverage, which was based on the sequenced DNA, was found to be approximately 15.3-fold. Primer walking and PCR-based techniques were applied to close the remaining gaps. All of the manual editing steps were performed using the Consed software package (, ). Prediction of the operons in the B. cereus AR156 chromosomes was performed with an algorithm that combines intergenic distance and phylogenetic information (), and tRNAs and transfer-messenger RNAs (tmRNAs) were predicted using the ARAGORN program (); rRNA was obtained by using RNAmmer version 1.2 ()., The 5.66-Mb B. cereus AR156 genome was composed of four replicons, a circular chromosome that encodes 5,367 open reading frames (ORFs) and three plasmids, pAR460, pAR41, and pAR10. Among the 5,367 ORFs, 3,333 clusters of orthologous groups were identified. Riboswitches play a very important role in a number of cellular processes, such as regulation of gene expression, tRNA processing, and protein secretion (). The riboswitches in the B. cereus AR156 genome sequence were predicted with a method using pHMM. By applying default parameters, 36 riboswitches were identified in the B. cereus AR156 genome (eight binding S-adenosylmethionine, six specific for thiamine pyropho […]

Pipeline specifications

Software tools Newbler, Consed, ARAGORN, RNAmmer