Wolbachia in Neotropical terrestrial isopods.

Despite Wolbachia being widespread among terrestrial isopods, studies on this symbiotic relationship are still incipient in the Neotropical region. The aims of the present study were to investigate the presence and prevalence of Wolbachia in natural populations of terrestrial isopod species in South America, and to analyze the diversity and phylogenetic relationships of Wolbachia strains. A total of 1172 individuals representing 11 families and 35 species were analyzed. We observed distinct evolutionary scenarios according to the geographical origins of the species: strains harbored by most of the introduced species belong to the Oniclade in supergroup B and are identical to those found in their original ecozone (i.e. Palearctic). On the other hand, the strains found in native Neotropical terrestrial isopods showed low prevalence, high diversity and none of them belonged to the Oniclade, although most belonged to supergroup B. The dynamics of infection in Neotropical species seems to be the result of several events of loss and acquisition of the bacteria, which refutes the hypothesis of an ancestral acquisition of Wolbachia in Oniscidea. The presence of strains from supergroups A and F was also detected for the first time in terrestrial isopods, revealing a Wolbachia diversity previously unknown for this group of host.

Identification of microRNAs from Eugenia uniflora by high-throughput sequencing and bioinformatics analysis.

BACKGROUND: microRNAs or miRNAs are small non-coding regulatory RNAs that play important functions in the regulation of gene expression at the post-transcriptional level by targeting mRNAs for degradation or inhibiting protein translation. Eugenia uniflora is a plant native to tropical America with pharmacological and ecological importance, and there have been no previous studies concerning its gene expression and regulation. To date, no miRNAs have been reported in Myrtaceae species. RESULTS: Small RNA and RNA-seq libraries were constructed to identify miRNAs and pre-miRNAs in Eugenia uniflora. Solexa technology was used to perform high throughput sequencing of the library, and the data obtained were analyzed using bioinformatics tools. From 14,489,131 small RNA clean reads, we obtained 1,852,722 mature miRNA sequences representing 45 conserved families that have been identified in other plant species. Further analysis using contigs assembled from RNA-seq allowed the prediction of secondary structures of 25 known and 17 novel pre-miRNAs. The expression of twenty-seven identified miRNAs was also validated using RT-PCR assays. Potential targets were predicted for the most abundant mature miRNAs in the identified pre-miRNAs based on sequence homology. CONCLUSIONS: This study is the first large scale identification of miRNAs and their potential targets from a species of the Myrtaceae family without genomic sequence resources. Our study provides more information about the evolutionary conservation of the regulatory network of miRNAs in plants and highlights species-specific miRNAs.

Identification of novel soybean microRNAs involved in abiotic and biotic stresses.

BACKGROUND: Small RNAs (19-24 nt) are key regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in eukaryotes. Current studies have demonstrated that microRNAs (miRNAs) act in several plant pathways associated with tissue proliferation, differentiation, and development and in response to abiotic and biotic stresses. In order to identify new miRNAs in soybean and to verify those that are possibly water deficit and rust-stress regulated, eight libraries of small RNAs were constructed and submitted to Solexa sequencing. RESULTS: The libraries were developed from drought-sensitive and tolerant seedlings and rust-susceptible and resistant soybeans with or without stressors. Sequencing the library and subsequent analyses detected 256 miRNAs. From this total, we identified 24 families of novel miRNAs that had not been reported before, six families of conserved miRNAs that exist in other plants species, and 22 families previously reported in soybean. We also observed the presence of several isomiRNAs during our analyses. To validate novel miRNAs, we performed RT-qPCR across the eight different libraries. Among the 11 miRNAs analyzed, all showed different expression profiles during biotic and abiotic stresses to soybean. The majority of miRNAs were up-regulated during water deficit stress in the sensitive plants. However, for the tolerant genotype, most of the miRNAs were down regulated. The pattern of miRNAs expression was also different for the distinct genotypes submitted to the pathogen stress. Most miRNAs were down regulated during the fungus infection in the susceptible genotype; however, in the resistant genotype, most miRNAs did not vary during rust attack. A prediction of the putative targets was carried out for conserved and novel miRNAs families. CONCLUSIONS: Validation of our results with quantitative RT-qPCR revealed that Solexa sequencing is a powerful tool for miRNA discovery. The identification of differentially expressed plant miRNAs provides molecular evidence for the possible involvement of miRNAs in the process of water deficit- and rust-stress responses.