Phaseolus vulgaris
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ABSTRACT:
PROVIDER: PRJNA175395 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Metabolomics of wild and domesticated varieties of common bean (Phaseolus vulgaris)
2022-05-13 | MSV000089468 | MassIVE
Project description:Metabolomics of wild and domesticated varieties of common bean (Phaseolus vulgaris)
2022-05-13 | MSV000089468 | GNPS
Project description:We report how phosphate deficiency early rhizobia-induced genes in Phaseolus vulgaris (common bean)
2018-11-14 | GSE118968 | GEO
Project description:The goal of this study was to detemine the genes responsible of the pod indehiscence in Phaseolus vulgaris by comparing 4 accesions with total, middle and null dehiscence transcriptomes of three stages of pod develoment of Phaseolus vulgaris
2022-04-16 | GSE179985 | GEO
Project description: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 and no phasiRNAs have been identified for the legume model 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 of this organism and, particularly, new protagonists of 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 Results: We identified a set of 185 mature miRNAs, including 121 previously unpublished sequences, encoded by 307 precursors and distributed in 98 families.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, known to play crucial roles in the well-establishment of nodules, and novel miRNAs specific of the common bean suggesting a specific action of these sequences. In parallel, we identified 125 loci that potentially produce phased small RNAs and 47 of them present all the characteristics to be 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, which contribute to the broader scene 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 draw up here the probable functional regulation associated with the sRNAome and particularly in N2-fixing symbiotic nodules. Degradome sequencing from Phaseolus vulgaris seedling
2015-09-01 | E-GEOD-67432 | biostudies-arrayexpress
Project description: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 and no phasiRNAs have been identified for the legume model 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 of this organism and, particularly, new protagonists of 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, known to play crucial roles in the well-establishment of nodules, and novel miRNAs specific of the common bean suggesting a specific action of these sequences. In parallel, we identified 125 loci that potentially produce phased small RNAs and 47 of them present all the characteristics to be 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, which contribute to the broader scene 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 draw up here the probable functional regulation associated with the sRNAome and particularly in N2-fixing symbiotic nodules. Small RNA sequencing from 5 Phaseolus vulgaris tissues
2015-09-01 | E-GEOD-67409 | biostudies-arrayexpress
Project description:Comparative RNA-Seq study of expression in Phaseolus vulgaris nectaries
2018-04-10 | GSE112944 | GEO
Project description:A Phaseolus vulgaris genome-wide analysis led to identify the small RNAs (sRNA) of this agronomical important legume. It revealed newly identified P. vulgaris-specific microRNAs (miRNAs) that could be involved in the regulation of the rhizobia-symbiotic process. Generally, novel miRNAs are difficult to identify and study because they are very lowly expressed in a tissue- or cell-specific manner. We aimed to analyze sRNAs from common bean root hairs (RH), a single-cell model, induced with pure Rhizobium etli-Nod factors (NF), a unique type of signal molecule. The sequence analysis of samples from NF-induced and control libraries led to identify 132 mature miRNAs, including 63 novel miRNAs and 1984 phasiRNAs. From these, six miRNAs were significantly differentially expressed during NF-induction, including one novel miRNA: miR-RH82. A parallel degradome analysis of the same samples revealed 29 targets potentially cleaved by novel miRNAs specifically in NF-induced RH samples, however these novel miRNAs were not differentially accumulated in this tissue. This study reveals Phaseolus vulgaris-specific novel miRNA candidates and their corresponding targets that meet all criteria to be involved in the regulation of the early nodulation events.
2017-05-01 | GSE81176 | GEO
Project description:TIFY is a large plant-specific transcription factor gene family. A subgroup of TIFY genes named JAZ (Jasmonate-ZIM domain) has been identified as repressors of jasmonate (JA)-regulated transcription in Arabidopsis and other plants. JA signaling is involved in many aspects of plant growth/development and in the defense responses to biotic and abiotic stresses. Here we identified the TIFY genes (designated as PvTIFY) from the legume common bean (Phaseolus vulgaris) and functionally characterized PvTIFY10C as a transcriptional regulator. Twenty-three genes from the PvTIFY gene family were identified through whole genome sequence analysis. Most of these were induced upon methyl-JA elicitation. We selected PvTIFY10C as a representative JA-responsive PvTIFY gene for further functional analysis. Transcriptome analysis via microarray hybridization using the designed Bean Custom Array 90K was performed in transgenic roots of composite plants with modulated -RNAi-silencing or over-expression- PvTIFY10C gene expression. Data were interpreted using Mapman adapted to common bean. Microarray differential gene expression data were validated by real-time qRT-PCR expression analysis. Comparative global gene expression analysis revealed opposite regulatory changes in processes such as RNA and protein regulation, stress response and metabolism in silenced vs. over-expressing roots. These data point to transcript reprogramming -mainly repression- orchestrated by PvTIFY10C. In addition we found that several PvTIFY genes as well as genes from the JA biosynthetic pathway responded to P-deficiency. Relevant P-responsive genes that participate in carbon metabolic pathways, cell wall synthesis, lipid metabolism, transport, DNA, RNA and protein regulation, signaling, were oppositely-regulated in control vs. PvTIFY10C silenced roots. These data indicate that PvTIFY10C regulates, directly or indirectly, gene expression of some P-responsive genes something that could be mediated by JA-signaling. Our work contributed to the functional characterization of PvTIFY transcriptional regulators in common bean, an agronomically important legume. Members from the large PvTIFY gene family are important global transcriptional regulators that could participate as repressors of the JA signaling pathway. In addition we propose that the JA-signaling pathway that involves PvTIFY genes might play a role in regulating the plant response / adaptation to P-starvation.
2013-02-27 | E-GEOD-40935 | biostudies-arrayexpress
Project description:Common Bacterial Blight (CBB) is a major threat to bean crops caused by Xanthomonas citri pv. fuscans (Xcf). The pathogenicity of Xcf is known to be dependent upon a functional Type 3 Secretion System (T3SS), that allows the injection of numerous Type III Effectors (T3Es) into plant cells. We generated a transcriptomic dataset to compare the response of susceptible and resistant cultivars of Phaseolus vulgaris to the inoculation of the virulent strain Xcf CFBP4885 or its avirulent T3SS-defective hrcV mutant (CFBP13802). This dataset is a valuable resource to investigate the role of T3Es in subverting the cellular functions of bean.
2024-08-28 | GSE271236 | GEO