Shedding some light over the floral metabolism by Arum Lily (Zantedeschia aethiopica) Spathe de novo transcriptome assembly

Zantedeschia aethiopica is an evergreen perennial plant cultivated worldwide and commonly used for ornamental and medicinal purposes including the treatment of bacterial infections. However, the current understanding of molecular and physiological mechanisms in this plant is limited, in comparison to other non-model plants. In order to improve understanding of the biology of this botanical species, RNA-Seq technology was used for transcriptome assembly and characterization. Following Z. aethiopica spathe tissue RNA extraction, high-throughput RNA sequencing was performed with the aim of obtaining both abundant and rare transcript data. Functional profiling based on KEGG Orthology (KO) analysis highlighted contigs that were involved predominantly in genetic information (37%) and metabolism (34%) processes. Predicted proteins involved in the plant circadian system, hormone signal transduction, secondary metabolism and basal immunity are described here. In silico screening of the transcriptome data set for antimicrobial peptide (AMP) – encoding sequences was also carried out and three lipid transfer proteins (LTP) were identified as potential AMPs involved in plant defense. Spathe predicted protein maps were drawn, and suggested that major plant efforts are expended in guaranteeing the maintenance of cell homeostasis, characterized by high investment in carbohydrate, amino acid and energy metabolism as well as in genetic information

In silico analysis of Eucalyptus thioredoxins

The Eucalyptus Genome Sequencing Project (FORESTs), an initiative from the Brazilian ONSA consortium (Organization for Nucleotide Sequencing and Analysis), has achieved the sequencing of 123.889 EST clones from 18 different cDNA libraries. We have investigated the FORESTs data set to identify EST clusters potentially encoding thioredoxins (TRX). Two types of thioredoxin families described in plants, chloroplastic (TRXm/f/x/y) and cytosolic (TRXh), have been found in the transcriptome. Putative typical TRXs have been identified in fifteen clusters, four m-type, seven h-type, two f-type, one cluster for each x/y-types and one putative homologue of the TDX gene from Arabidopsis thaliana. One cluster presents an atypical active site WCMPS, different from the conserved WCGPC present in the other 15 clusters, and corresponds to a subgroup of cytosolic thioredoxins. Except in specific libraries from callus, roots, seedlings and wood tissues, thioredoxin deduced ESTs are found in all remaining libraries. According to the calculated frequencies of ESTs, chloroplastic thioredoxins are preferentially present in green tissues such as leaves whilst cytoplasmic thioredoxins are more general but demonstrate elevated frequencies in seedlings and flower tissues. TRX frequency patterns in the Eucalyptus transcriptome seem to indicate a good coherence with data from Arabidopsis thaliana gene expression

Categorization of <i>Z. aethiopica</i> spathe transcriptome into KEGG biological categories.

<p>A. Total KEGG biological categories contigs distribution; B. Metabolism biological category distribution of contigs percentage.</p

Lipid Transfer Proteins structural analysis.

<p>A. Multiple alignment of LTPs here identified. Conserved residues are green highlighted and the cysteine residues are in yellow. Final three-dimensional structures of LTPs with ligands before and after 50 ns of molecular dynamics are illustrated at B. Za-LTP1 + Oleic acid initial; C. Za-LTP1 + Oleic acid final; D. Za-LTP2 + Palmitoleic acid initial; E. Za-LTP2 + Palmitoleic acid final; F. Za-LTP3 + Alpha-Linoleic acid intial and G. Za-LTP3 + Alpha-linoleic acid final.</p

Secondary Metabolism Pathways for <i>Zantedeschia aethiopica</i> assigned by KEGG Orthology (KO).

<p>Secondary Metabolism Pathways for <i>Zantedeschia aethiopica</i> assigned by KEGG Orthology (KO).</p

Final molecular dynamics scores for <i>Zantedeschia aethiopica</i> lipid transfer protein (LTP) docking with lipid ligands.

a<p>Data generated by comparing the structure at 0 ns and 50 ns.</p>b<p>The RMSD evolution along the time is available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090487#pone.0090487.s014" target="_blank">Figure S14</a>.</p>c<p>Excluding the polyproline tail, this value is reduced to 4.117.</p

Sequencing and assembly of <i>Zantedeschia aethiopica</i> transcriptome using Illumina HiSeq 2000.

<p>Sequencing and assembly of <i>Zantedeschia aethiopica</i> transcriptome using Illumina HiSeq 2000.</p

Plant-pathogen interaction basal immunity expression at <i>Z. aethiopica</i> spathe.

<p>e. expression; +u. ubiquitination; +p. phosphorylation; -p. dephosphorilation; x. dissociation; →. activation; ——. direct effect; –. inhibition. Molecules identified in this study are highlighted with grey shadow.</p