Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing

Background: MiRNAs and phasiRNAs are negative regulators of gene expression. These small RNAs have been extensively studied in plant model species but only 10 mature microRNAs are present in miRBase version 21, the most used miRNA database, and no phasiRNAs have been identified for the model legume Phaseolus vulgaris. Thanks to the recent availability of the first version of the common bean genome, degradome data and small RNA libraries, we are able to present here a catalog of the microRNAs and phasiRNAs for this organism and, particularly, we suggest new protagonists in the symbiotic nodulation events.Results: We identified a set of 185 mature miRNAs, including 121 previously unpublished sequences, encoded by 307 precursors and distributed in 98 families. Degradome data allowed us to identify a total of 181 targets for these miRNAs. We reveal two regulatory networks involving conserved miRNAs: those known to play crucial roles in the establishment of nodules, and novel miRNAs present only in common bean, suggesting a specific role for these sequences. In addition, we identified 125 loci that potentially produce phased small RNAs, with 47 of them having all the characteristics of being triggered by a total of 31 miRNAs, including 14 new miRNAs identified in this study.Conclusions: We provide here a set of new small RNAs that contribute to the broader knowledge of the sRNAome of Phaseolus vulgaris. Thanks to the identification of the miRNA targets from degradome analysis and the construction of regulatory networks between the mature microRNAs, we present here the probable functional regulation associated with the sRNAome and, particularly, in N2-fixing symbiotic nodules.Peer reviewedBiochemistry and Molecular Biolog

Single-spore extraction for genetic analyses of arbuscular mycorrhizal fungi

International audienceBiomass of arbuscular mycorrhizal fungi (AMF, Glomeromycota) is often only available in small quantities as these fungi are obligate biotrophs and many species are difficult to cultivate under controlled conditions. Here, I describe a simple, efficient approach to produce crude extracts from single or a small number of spores that can be used for genotyping AMF

Triplet Imaging by Modulated Excitation

We present a functional imaging method based on triplet state kinetics. The triplet state of many known fluorophores show a triplet lifetime typically in the order of ~10e-6 – 10e-3 s, 3-6 orders of magnitude longer than the associated fluorescence singlet lifetime. As a consequence triplet state sensing is more exposed to the microenvironment of fluorophores and can be used as a functional molecular antenna. Using an adaptive modulated excitation scheme, these long living triplet state dynamics are accessible by standard CCD detector technology. We built an imaging setup allowing extraction of triplet lifetime maps. Effective correction of the competitive bleaching component is achieved by simultaneous monitoring of bleaching. The signal processing is based on a linear regressor analysis enabling extraction of the triplet state lifetime. As a first proof of principle, we investigated oxygen as a triplet state quencher on a sample of Tetramethylrhodamine (TMR) printed on a glass cover slide by soft lithography. First bioassays will be presented indicating the high potential for functional and metabolic imaging in life cell applications

The microRNA miR171h modulates arbuscular mycorrhizal colonization of <i>Medicago truncatula</i> by targeting NSP2

International audienc

Stable Inactivation of MicroRNAs in Medicago truncatula Roots

International audienceMicroRNAs are key regulators in the development processes or stress responses in plants. In the last decade, several conserved or non-conserved microRNAs have been identified in Medicago truncatula. Different strategies leading to the inactivation of microRNAs in plants have been described. Here, we propose a protocol for an effective inactivation of microRNAs using a STTM strategy in M. truncatula transgenic roots