Populations_Fitness_Data

Results of competition experiments designed to estimate the fitness of evolving E. coli populations relative to their common ancesto

Clones_Growth_Data

Results of growth assays of ancestor and evolved clones in four experimental environment

Clones_Fitness_Data

Results of competition experiments designed to estimate fitness of evolved E. coli clones relative to their common ancesto

DRYAD-luscombe-reanalysis

This file contains all data, python, and R scripts needed to replicate our analysis of synonymous substitutions in a long-term evolution experiment at 40,000 generations

Xanthomonas citri - 36 strain concatenated genome alignment (gaps +/- 20nt removed) FASTA format, Contains recombination

A FASTA format multiple sequence alignment used for phylogenetic reconstruction. The alignment was constructed by concatenating blocks from a whole genome multiple alignment using the IAPAR 306 strain to order blocks. Gap-containing columns and 20 nt surrounding gap-containing columns were removed. The alignment contains regions of recombination and the distibution of A pathotype strains is reduced to only those containing recombination event 16

Xanthomonas citri - 44 strain PhyML phylogeny SYM model

A maximum likelihood phylogenetic tree constructed with PhyML from the genome alignment of 44 strains of Xanthomonas citri. Regions of recombination were removed from the alignment as well as gap-containing columns and +/- 20bp from a gap-containing column. The evolutionary model used was SYM, as chosen with jModeltest 2.1.7

Xanthomonas citri - 44 strain concatenated genome alignment (recombination, gaps +/- 20nt removed) FASTA format

A FASTA format multiple sequence alignment used for phylogenetic reconstruction. The alignment was constructed by concatenating blocks from a whole genome multiple alignment using the IAPAR 306 strain to order blocks. Regions of recombination detected using RDP were removed, as were gap-containing columns and 20 nt surrounding gap-containing columns

Xanthomonas citri - 36 strain PhyML phylogeny GTR model, Reduced A-strain distribution, Contains recombination

A maximum likelihood phylogenetic tree constructed with PhyML from the genome alignment of 36 strains of Xanthomonas citri. The alignment contains regions of recombination and the distibution of A pathotype strains is reduced to only those containing recombination Event 16. The evolutionary model used was GTR

Xanthomonas citri - 44 strain Mugsy genome alignment

A multiple genome alignment of 44 strains of Xanthomonas citri output from the Mugsy genome alignment softwar

RNase J depletion leads to massive changes in mRNA abundance in <i>Helicobacter pylori</i>

<p>Degradation of RNA as an intermediate message between genes and corresponding proteins is important for rapid attenuation of gene expression and maintenance of cellular homeostasis. This process is controlled by ribonucleases that have different target specificities. In the bacterial pathogen <i>Helicobacter pylori</i>, an exo- and endoribonuclease RNase J is essential for growth. To explore the role of RNase J in <i>H. pylori</i>, we identified its putative targets at a global scale using next generation RNA sequencing. We found that strong depletion for RNase J led to a massive increase in the steady-state levels of non-rRNAs. mRNAs and RNAs antisense to open reading frames were most affected with over 80% increased more than 2-fold. Non-coding RNAs expressed in the intergenic regions were much less affected by RNase J depletion. Northern blotting of selected messenger and non-coding RNAs validated these results. Globally, our data suggest that RNase J of <i>H. pylori</i> is a major RNase involved in degradation of most cellular RNAs.</p