For all these analyses, we estimated for each data set the best-fitting nucleotide model and the gene phylogeny using the available options on Datamonkey.
Thus, we used a phylogeny built from all the available nucleotide sequences on NCBI extracted on the 30th of November 2006.
Primers for polymerase chain reaction (PCR) amplification were designed based on the available nucleotide sequence of GalDH of the P. fluorescens genome using DNASIS MAX software (DNASIS version 3.0, Hitachi Software Engineering Co., Ltd., Tokyo, Japan).
Following PCR of these regions, the pathogen species present can be identified subsequently by sequencing of the amplified DNA followed by phylogenetic analysis using widely available nucleotide databases [ 18].
Using publicly available nucleotide databases, 19 sugarcane miRNA precursors and one new sorghum miRNA precursor were identified and classified into 14 families.
In addition, complete or partial amino acid sequences, signal peptides, and open reading frames from the available nucleotides of the unigenes were deduced using ExPASy (http://www.expasy.org).org
Using all publicly available nucleotide databases, 682 miRNAs were identified in 155 diverse plant species.
Furthermore, we provide computational and/or experimental evidence for the conservation of 6 newly found Arabidopsis miRNA homologs (miR158, miR391, miR824, miR825, miR827 and miR840) and 2 small RNAs (small-85 and small-87) in Brassica spp. Using all publicly available nucleotide databases, 682 miRNAs were identified in 155 diverse plant species.
The outbreak reference genome was compared to all the MDR-Aci genome sequences that were publically available in May 2013, using the Average Nucleotide Identity (ANI) approach to identify the closest genome-sequenced strain [ 20, 21].
AmpC nucleotide sequences retrieved from the 23 AmpC-positive isolates were analyzed to determine their relationship to other pAmpC genes available in GenBank database using the BLAST nucleotide algorithm (http://www.ncbi.nlm.nih.gov/).nih.gov/
