Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus

Clustering the difference in transcriptome response of PtQTL and PdQTL genotypes. Modulated Modularity Clustering of genes displaying a similar pattern of expression differences between genotypes from the PtQTL and PdQTL categories, at all time points. (DOCX 25 kb

In silico characterization of microRNAs-like sequences in the genome of Paracoccidioides brasiliensis

Eukaryotic cells have different mechanisms of post-transcriptional regulation. Among these mechanisms, microRNAs promote regulation of targets by cleavage or degradation of the mRNA. Fungi of the Paracoccidioides complex are the etiological agents of the main systemic mycosis of Latin America. These fungi present a plasticity to adapt and survive in different conditions, and the presence of microRNAs-like molecules could be part of the mechanisms that provide such plasticity. MicroRNAs produced by the host influence the progression of this mycosis in the lungs besides regulating targets involved in apoptosis in macrophage, activation of T and B cells and the production of cytokines. Therefore, this work analyzed the presence of regions in the genome of this fungus with a potential to encode microRNAs-like molecules. Here we show by analysis of sequence similarity the presence of 18 regions, putatively coding for microRNAs-like molecules in the Paracoccidioides brasiliensis genome. We also described the conservation of dicer and argonaut proteins and the cognate transcripts induced in the yeast parasitic phase. This work represents a starting point for the analysis of the presence of those molecules in the morphological stages of the fungus and their role in fungal development

Cell Wall Synthesis, Development of Hyphae and Metabolic Pathways Are Processes Potentially Regulated by MicroRNAs Produced Between the Morphological Stages of Paracoccidioides brasiliensis

MicroRNAs are molecules involved in post-transcriptional gene regulation. In pathogenic fungi, microRNAs have been described at different morphological stages by regulating targets involved in processes such as morphogenesis and energy production. Members of the Paracoccidioides complex are the main etiological agents of a systemic mycosis in Latin America. Fungi of the Paracoccidioides complex present a wide range of plasticity to colonize different niches. In response to environmental changes these fungi undergo a morphological switch, remodel their cellular metabolism and modulate structural cell wall components. However, the underlying mechanisms regulating the gene expression is not well understood. By using high performance sequencing and bioinformatics analyses, this work characterizes microRNAs produced by Paracoccidioides brasiliensis. Here, we demonstrated that the transcript encoding proteins involved in microRNA biogenesis were differentially expressed in each morphological stage. In addition, 49 microRNAs were identified in cDNA libraries with 44 differentially regulated among the libraries. Sixteen microRNAs were differentially regulated in comparison to the mycelium in the mycelium-to-yeast transition phase. The yeast parasitic phase revealed a complete remodeling of the expression of these small RNAs. Analyses of targets of the induced microRNAs, from the different libraries, revealed that these molecules may potentially regulate in the cell wall, by repressing genes involved in the synthesis and degradation of glucans and chitin. Furthermore, mRNAs involved in cellular metabolism and development were predicted to be regulated by microRNAs. Therefore, this work describes a putative post transcriptional regulation, mediated by microRNAs in P. brasiliensis and its influence on the adaptive processes of thermal dimorphic fungus

Growth differential related to wood structure and function of Eucalyptus spp. clones adapted to seasonal drought stress

Aim of the study: To evaluate the growth performance, wood density and anatomical features of four drought-tolerant Eucalyptus spp. clones, at 4 years, and to examine the relationships between these characteristics and some functional parameters. Area of study: The analyzed trees were from a clonal test installed in a region characterized by seasonal drought stress in central-western Brazil. Methods: Trees were felled, followed by obtaining dendrometric parameters and wood disk sampling to determine wood bulk density by x-ray densitometry, and morphometric parameters of fibers and vessels in order to evaluate the xylem hydraulic architecture. Lumen fraction (F), vessel composition (S) and hydraulic conductivity (Ks) were estimated. Results: Clone D (E. urophylla x E grandis) presented the highest growth rates, which was related to anatomical characteristics such as low relative frequency of wide vessels. High theoretical Ks does not necessarily imply higher growth rates and were related to lower wood densities. It is possible to infer that the better xylem adjustability of Eucalyptus trees in response to drought stress conditions is associated with increased vessel composition to the detriment of higher hydraulic conductivity. Research highlights: Vessel composition showed a greater variation among Eucalyptus genotypes and was positively associated with growth performance. Keywords: wood anatomy; dendrometry; X-ray densitometry; water stress; hydraulic conductivity. Abbreviations used: F: lumen fraction; S: vessel composition; Ks: theoretical xylem-specific hydraulic conductivity

Wood Quality and Pulping Process Efficiency of Elite <em>Eucalyptus</em> spp. Clones Field-Grown under Seasonal Drought Stress

The objective of the present study is to evaluate the wood quality of five elite Eucalyptus spp. clones at 4 years of age from a clonal test installed in a region of seasonal drought stress in central-western Brazil focusing on pulp production. A total of 25 trees were systematically felled and disks and logs were obtained along the trunk. Wooden disks were used for density and fiber analyses and the logs were converted into chips for application in the pulping process. For the denser genotype, clone D (E. grandis x E. urophylla x Eucalyptus tereticornis), a thicker cell wall associated to thinner fibers results in a negative effect on the fiber quality. In contrast, clone B (Eucalyptus pellita x E. grandis), which has relatively inferior pulping performance, displayed the lowest wood density associated to wider lumen and fibers. The best growth performances in response to acclimatization and adaptation to the site strongly influences the pulp productivity, which is identified as the parameter of greatest variance between genotypes, and highlighting clone E (E. grandis x E. urophylla)

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

<p>Abstract</p> <p>Background</p> <p>Benefits from high-throughput sequencing using 454 pyrosequencing technology may be most apparent for species with high societal or economic value but few genomic resources. Rapid means of gene sequence and SNP discovery using this novel sequencing technology provide a set of baseline tools for genome-level research. However, it is questionable how effective the sequencing of large numbers of short reads for species with essentially no prior gene sequence information will support contig assemblies and sequence annotation.</p> <p>Results</p> <p>With the purpose of generating the first broad survey of gene sequences in <it>Eucalyptus grandis</it>, the most widely planted hardwood tree species, we used 454 technology to sequence and assemble 148 Mbp of expressed sequences (EST). EST sequences were generated from a normalized cDNA pool comprised of multiple tissues and genotypes, promoting discovery of homologues to almost half of <it>Arabidopsis</it> genes, and a comprehensive survey of allelic variation in the transcriptome. By aligning the sequencing reads from multiple genotypes we detected 23,742 SNPs, 83% of which were validated in a sample. Genome-wide nucleotide diversity was estimated for 2,392 contigs using a modified theta (θ) parameter, adapted for measuring genetic diversity from polymorphisms detected by randomly sequencing a multi-genotype cDNA pool. Diversity estimates in non-synonymous nucleotides were on average 4x smaller than in synonymous, suggesting purifying selection. Non-synonymous to synonymous substitutions (Ka/Ks) among 2,001 contigs averaged 0.30 and was skewed to the right, further supporting that most genes are under purifying selection. Comparison of these estimates among contigs identified major functional classes of genes under purifying and diversifying selection in agreement with previous researches.</p> <p>Conclusion</p> <p>In providing an abundance of foundational transcript sequences where limited prior genomic information existed, this work created part of the foundation for the annotation of the <it>E. grandis </it>genome that is being sequenced by the US Department of Energy. In addition we demonstrated that SNPs sampled in large-scale with 454 pyrosequencing can be used to detect evolutionary signatures among genes, providing one of the first genome-wide assessments of nucleotide diversity and Ka/Ks for a non-model plant species.</p