ArticleBMC genomics2015
Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 48 citations in OpenAlex.
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- Small but big player: the important role of microRNAs in legume crops.Molecular genetics and genomics : MGG · 2026Review
- The RNAome landscape of tomato during arbuscular mycorrhizal symbiosis reveals an evolving RNA layer symbiotic regulatory network.Plant communications · 2023Article
- The identification of conserved sequence features of co-translationally decayed mRNAs and upstream open reading frames in angiosperm transcriptomes.Plant direct · 2023Article
- Small RNA Sequencing Revealed that miR4415, a Legume-Specific miRNA, was Involved in the Cold Acclimation ofFrontiers in genetics · 2022Article
- Argonaute5 and its associated small RNAs modulate the transcriptional response during the rhizobia-Frontiers in plant science · 2022Article
- Review
- MicroRNAs expression dynamics reveal post-transcriptional mechanisms regulating seed development in Phaseolus vulgaris L.Horticulture research · 2021Article
- Investigation into the miRNA/5' isomiRNAs function and drought-mediated miRNA processing in rice.Functional & integrative genomics · 2020Article
- Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants.Genome research · 2020Article
- Identification of miRNAs linked to peanut nodule functional processes.Journal of biosciences · 2020Article
- Small RNAs from the plant pathogenic fungus Sclerotinia sclerotiorum highlight host candidate genes associated with quantitative disease resistance.Molecular plant pathology · 2019Article
- Stress-responsive miRNAome of Glycine max (L.) Merrill: molecular insights and way forward.Planta · 2019Review
- Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development.BMC genomics · 2019Article
- Diff isomiRs: Large-scale detection of differential isomiRs for understanding non-coding regulated stress omics in plants.Scientific reports · 2019Article
- Genome-wide discovery of tissue-specific miRNAs in clusterbean (Cyamopsis tetragonoloba) indicates their association with galactomannan biosynthesis.Plant biotechnology journal · 2018Article
- The MicroRNA319d/TCP10 Node Regulates the Common Bean - Rhizobia Nitrogen-Fixing Symbiosis.Frontiers in plant science · 2018Article
- The legume miR1514a modulates a NAC transcription factor transcript to trigger phasiRNA formation in response to drought.Journal of experimental botany · 2017Article
- Small RNAs Derived from the T-DNA ofFrontiers in plant science · 2017Article
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMiRNAs 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.
resultsWe 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.
conclusionsWe 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.