Multivariate regression tree of the diversity indices.

<p>Multivariate regression tree of the relation between standardized diversity indices and chemical parameters. The bar plots show the mean of the diversity indices at the terminal nodes. The numbers under the bar plots indicate the error and the number of samples (n) within each group. Error: 0.744.</p

Relative abundance of bacterial phyla in soil samples.

<p>Others: Acidobacteria, AD3, Armatimonadetes, Chlamydiae, Chlorobi, Elusimicrobia, Fusobacteria, GAL15 Nitrospirae, OD1, Spirochaetes, Tenericutes, Verrucomicrobia, TM6, TM7, WPS-2, WS3, WYO, and unclassified Bacteria.</p

Aggregated boosted tree (ABT).

<p>The ABT analysis show the relative influence of the principal chemical parameters for the dominant phyla in the Sossego mine.</p

Principal OTUs responsible for differences between the drainage and soil samples.

<p>Principal OTUs responsible for differences between the drainage and soil samples.</p

Chemical parameters of the drainage and soil samples, and P-values derived from the Student's t-test.

<p>Metal concentrations are expressed in mg/kg. The organic matter (OM) content is expressed in g/dm³.</p><p>* Statistically significant at 5%.</p><p>** Statistically significant at 1%.</p

Non-metric multidimensional scaling.

<p>Non-metric multidimensional scaling using the Bray-Curtis dissimilarity plots of the first two components for drainage (red) and soil (blue) samples. The stress value is 0.095.</p

Large-Scale Transcriptome Analysis of Two Sugarcane Genotypes Contrasting for Lignin Content

<div><p>Sugarcane is an important crop worldwide for sugar and first generation ethanol production. Recently, the residue of sugarcane mills, named bagasse, has been considered a promising lignocellulosic biomass to produce the second-generation ethanol. Lignin is a major factor limiting the use of bagasse and other plant lignocellulosic materials to produce second-generation ethanol. Lignin biosynthesis pathway is a complex network and changes in the expression of genes of this pathway have in general led to diverse and undesirable impacts on plant structure and physiology. Despite its economic importance, sugarcane genome was still not sequenced. In this study a high-throughput transcriptome evaluation of two sugarcane genotypes contrasting for lignin content was carried out. We generated a set of 85,151 transcripts of sugarcane using RNA-seq and <i>de novo</i> assembling. More than 2,000 transcripts showed differential expression between the genotypes, including several genes involved in the lignin biosynthetic pathway. This information can give valuable knowledge on the lignin biosynthesis and its interactions with other metabolic pathways in the complex sugarcane genome.</p></div

Transcripts of the cluster enriched for flavonoid metabolism (C16), as derived from the K-means analysis.

<p>Transcripts of the cluster enriched for flavonoid metabolism (C16), as derived from the K-means analysis.</p

Simplified scheme of the phenylpropanoid biosynthesis pathway with genes identified in sugarcane transcriptome.

<p>Pair-wise comparisons were made between both genotypes. Each heatmap represent lignin transcript sequences identified in RNA-seq. The log2 (IACSP04-627 / IACSP04-065) expression ratio values were false color-coded using a scale of -1 to 1 and indicate the genotype that showed highest expression for each transcript. The intensity of green and red indicates the degree of down- and up-regulation of the corresponding lignin gene.</p

The K-means clusters of the identified sugarcane transcripts.

<p>Each dot represents a transcript. In case of differential expressed transcripts (n = 2,162) the dot is indicated in red. Transcripts within the same ellipse belong to the same cluster (100 clusters in total), according to K-means analysis. Axis indicates the first two principal components that explain the transcription expression variability. Several clusters have a significant enrichment for certain MapMan classes (according to PageMan), how showed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134909#pone.0134909.g005" target="_blank">Fig 5</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134909#pone.0134909.t001" target="_blank">Table 1</a>.</p