Ontology highlight
ABSTRACT:
PROVIDER: PRJNA429665 | ENA |
REPOSITORIES: ENA
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Project description:We report how phosphate deficiency early rhizobia-induced genes in Phaseolus vulgaris (common bean)
2018-11-14 | GSE118968 | GEO
Project description:Metabolomics of wild and domesticated varieties of common bean (Phaseolus vulgaris)
2022-05-13 | MSV000089468 | MassIVE
Project description:Common bean (Phaseolus vulgaris L.) is the most consumed grain legume in developing countries in Latin America and Sub-Saharan Africa1. Like other legumes, common bean seeds are rich in protein, carbohydrates, fibers and other health-promoting phenolic compounds thus being vital for food security and income source for local small farmers2. Seed quality traits depend on accumulation of various storage molecules during the seed development (SD) process and influenced by the genotype and adaptive changes to environment3. Concerning common bean, there is still a lack of a deeper molecular knowledge of SD that is hampering the development of new biotech approaches for seed trait modulation and could timely address challenges of agriculture or industry. Our present work aims to unravel the molecular mechanisms underlying SD using a proteomic approach. To achieve this goal, we characterized SD in terms biomass, seed length and weight in the genotype SER16, one of the most promissory drought-resistant release of the CIAT-CGIAR. Seed samples were collected at the 4 main SD stages: Late-Embryogenesis (10 days after anthesis, d.a.a.), Early (20 d.a.a.) and Late Maturation (30 d.a.a.) and Desiccation (40 d.a.a.). The analysis of bean proteome was conducted using a gel-free proteomic analysis (LC-MS/MS) under the scope of EU-FP7-PRIME-XS project. A total of 410 unique proteins were differentially expressed throughout the 4 major seed development stages, in which most of the identified proteins belong in the ‘protein metabolism’ (31,98%) functional category, that includes synthesis, regulation, folding. Other functional categories are represented such as carbohydrate and lipid metabolism (11,26%) and stress/defense and redox metabolism (11,04%). We identified 93 proteins were unique to the first (10-20 d.a.a.), 22 to the second (20-30 d.a.a.) and 40 to the last (30-40 d.a.a.) phase transition, reflecting the major biological processes occurring at this specific seed developmental stage. This study will contribute to reveal key metabolic pathways and mechanisms with potential role in modulating common bean seed development and quality traits.
2018-01-05 | PXD002254 | Pride
Project description:Arthrobacter chlorophenolicus A6 is a 4-chlorophenol degrading soil bacterium with high phyllosphere colonization capacity. Till now the genetic basis for the phyllosphere competency of Arthrobacter or other pollutant-degrading bacteria is uncertain. We investigated global gene expression profile of A. chlorophenolicus grown in the phyllosphere of common bean (Phaseolus vulgaris) compared to growth on agar surfaces. We designed transcriptome arrays and investigated which genes had different transcript levels in the phyllosphere of common bean (Phaseolus vulgaris) as compared to agar surfaces. Since water availability is considered an important factor in phyllosphere survival and activity, we included both high and low relative humidity treatments for the phyllosphere-grown cells. In addition, we determined the expression profile under pollutant exposure by the inclusion of two agar surface treatments, i.e. with and without 4-chlorophenol.
2013-06-21 | E-GEOD-48198 | biostudies-arrayexpress
Project description:To understand the molecular basis for differences of common bean wild-type and mutant in sulphur amino acid content, transcripts were profiled at four developmental stages of seeds from wild-type SARC1 and major seed storage protein-deficient line SMARC1N-PN1 using a CustomArray 90K array. Microarray data confirmed that transcripts of storage and sulphur-rich proteins and sulphur-metabolism related genes were differentially expressed between the lines. The common bean (Phaseolus vulgaris) mutant line, SMARC1N-PN1 and its wild type, SARC1 used in the microarray experiment were grown in the field in London, ON, in 2009. Four developmental stages of seeds, based on fresh seed weight, were harvested. The stages of seeds used are Stage IV M-bM-^@M-^S cotyledon, 25 mg seed weight; Stage V M-bM-^@M-^S cotyledon, 50 mg seed weight; Stage VI M-bM-^@M-^S maturation, 150 mg seed weight, corresponding to the most active phase of reserve accumulation; and Stage VIII M-bM-^@M-^S maturation, 380 mg seed weight, corresponding to the onset of desiccation, were harvested for total RNA extraction. Four biological replicates for Stage IV and V and 3 biological replicates for Stage VI and VIII.
2012-11-06 | E-GEOD-34233 | biostudies-arrayexpress
Project description:Arthrobacter chlorophenolicus A6 is a 4-chlorophenol degrading soil bacterium with high phyllosphere colonization capacity. Till now the genetic basis for the phyllosphere competency of Arthrobacter or other pollutant-degrading bacteria is uncertain. We investigated global gene expression profile of A. chlorophenolicus grown in the phyllosphere of common bean (Phaseolus vulgaris) compared to growth on agar surfaces.
2013-06-21 | GSE48198 | GEO
Project description:Dry bean (Phaseolus vulgaris L.) seeds are a rich source of dietary zinc, especially for people consuming plant-based diets. Within P. vulgaris there is at least two-fold variation in seed Zn concentration. Genetic studies have revealed seed Zn differences to be controlled by a single gene in two closely related navy bean genotypes, Albion and Voyager. In this study, these two genotypes were grown under controlled fertilization conditions and the Zn concentration of various plant parts were determined. The two genotypes had similar levels of Zn in their leaves and pods but Voyager had 52% more Zn in its seeds than Albion. RNA was sequence from developing pods of both genotypes. Transcriptome analysis of these genotypes identified 27,198 genes in the developing bean pods, representing 86% of the genes in the P. vulgaris genome (v 1.0 DOE-JGI and USDA-NIFA). Expression was detected in 18,438 genes. A relatively small number of genes (381) were differentially expressed between Albion and Voyager. Differentially expressed genes included three genes potentially involved in Zn transport, including zinc-regulated transporter, iron regulated transporter like (ZIP), zinc-induced facilitator (ZIF) and heavy metal associated (HMA) family genes. In addition 12,118 SNPs were identified between the two genotypes. Of the gene families related to Zn and/or Fe transport, eleven genes were found to contain SNPs between Albion and Voyager.
2015-03-24 | GSE67121 | 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