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

Genome Features of the Endophytic Actinobacterium <i>Micromonospora lupini</i> Strain Lupac 08: On the Process of Adaptation to an Endophytic Life Style?

<div><p>Endophytic microorganisms live inside plants for at least part of their life cycle. According to their life strategies, bacterial endophytes can be classified as “obligate” or “facultative”. Reports that members of the genus <i>Micromonospora,</i> Gram-positive Actinobacteria, are normal occupants of nitrogen-fixing nodules has opened up a question as to what is the ecological role of these bacteria in interactions with nitrogen-fixing plants and whether it is in a process of adaptation from a terrestrial to a facultative endophytic life. The aim of this work was to analyse the genome sequence of <i>Micromonospora lupini</i> Lupac 08 isolated from a nitrogen fixing nodule of the legume <i>Lupinus angustifolius</i> and to identify genomic traits that provide information on this new plant-microbe interaction. The genome of <i>M. lupini</i> contains a diverse array of genes that may help its survival in soil or in plant tissues, while the high number of putative plant degrading enzyme genes identified is quite surprising since this bacterium is not considered a plant-pathogen. Functionality of several of these genes was demonstrated <i>in vitro</i>, showing that Lupac 08 degraded carboxymethylcellulose, starch and xylan. In addition, the production of chitinases detected <i>in vitro</i>, indicates that strain Lupac 08 may also confer protection to the plant. <i>Micromonospora</i> species appears as new candidates in plant-microbe interactions with an important potential in agriculture and biotechnology. The current data strongly suggests that a beneficial effect is produced on the host-plant.</p></div

Secretion system genes present in the genome of <i>M. lupini</i> Lupac 08.

<p>TAT, twin-arginine translocation; X, corresponds to the annotation gene numbers given in parenthesis.</p><p>Secretion system genes present in the genome of <i>M. lupini</i> Lupac 08.</p

Plant growth promotion and biological control features of <i>M. lupini</i> Lupac 08.

<p>(A) Siderophore, (B) indole-3-acetic acid [a, negative control <i>E. coli</i> DH5α; b, Lupac 08] and pectinase production (D) by <i>M. lupini</i> strain Lupac 08;. (C) Plant growth promoting effect of <i>M. lupini</i> Lupac 08 on clover plantlets. a) control; b) inoculated with <i>Rhizobium</i> sp. E11; c) co-inoculated with <i>Rhizobium</i> sp. E11 and <i>M. lupini</i> Lupac 08.</p

Circular representation of <i>Micromonospora lupini</i> Lupac 08.

<p>Circles displayed from the outside in: 1. Cellulose-binding genes in black, chitin-binding genes in red, lectin genes in lavender blue; 2. Genome coordinates; 3. MW; 4. GC% (linear range between 65 and 80%); 5. Regions of genome plasticity according to the RGP_Finder method (Mage platform) based on synteny breaks between the query genome (Lupac 08) and close genomes (<i>Micromonospora aurantiaca</i> ATCC 27029^T, <i>Micromonospora</i> sp. L5 and <i>Verrucosispora maris</i> AB-18-032^T) correlated with HGT features (tRNA hotspot, DNA repeats, mobility genes), and compositional bias and GC deviation computation. C1 to C15 indicate the position of the 15 clusters of genes coding for secondary metabolites of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108522#pone-0108522-t004" target="_blank">Table 4</a>.</p

MAUVE alignment of the genome sequences of <i>Micromonospora lupini</i> Lupac 08, <i>Micromonospora</i> sp. L5, <i>Micromonospora aurantiaca</i> ATCC 27029^T and <i>Micromonospora</i> sp. ATCC 39149.

<p>When boxes have the same colour, this indicates syntenic regions. Boxes below the horizontal line indicate inverted regions. Rearrangements are shown by coloured lines. Scale is in nucleotides.</p

Genome Features of the Endophytic Actinobacterium <i>Micromonospora lupini - Figure 1 </i> Strain Lupac 08: On the Process of Adaptation to an Endophytic Life Style?

<p>. <b>Neighbour-joining tree based on 16S rRNA gene sequences showing the relationship of </b><b><i>Micromonospora</i></b><b> species and other members of the family </b><b><i>Micromonosporaceae</i></b><b>.</b> Strains isolated from plant related sources are indicated by a green arrow.</p