We added 24 new genes into the initial model based on operon predictions for WH8102 [ 30] (see Additional file 6).
Previous approaches use cut-offs on operon lengths [ 27], or the distance between two adjacent genes [ 28, 29] e.g. the Gene Gap Method [ 30].
Successful PCR amplifications yielded amplicons that were approximately the expected size of rRNA operons based on the lengths of related Pantoea spp. rRNA operons (region that spans complete 23S, 5S, and 16S sequences; Pantoea ananatis LMG20103, NC_013956.2 average: 5.2 kb, range: 5.1 5.4 kb; Pantoea vagans C9-1, NC_014562.1 average: 5.2 kb, range: 5.0 5.3 kb).
We evaluated the operon prediction accuracy using two methods: one was based on adjacent operon pairs, and the other on the entire operon structure using all the gene pairs of a known operon.
This was then followed by a more operon-specific analysis, based on the operon data by Janga et al. [ 11].
Based on the operon clade membership, we could thus discern the evolutionary history of each operon copy in relation to the species-level genome phylogeny using a parsimony framework that selected the operon evolutionary history that minimized the number of evolutionary events (operon duplication, loss, or horizontal transfer).
Book ratings are based on the sentence length, the word length and how difficult the words are.
Based on the operon organization table, 694 hypothetical genes with unknown function were categorized into multiple-gene operons with validated co-expression with adjacent genes (Additional file 3).
Based on the operon prediction, disruptions in 74 of the 550 essential genes are likely to have a polar effect on downstream genes present in the same operon (Additional file 1: Table S1).
