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Comprehensive analysis of the isomiRome in the vegetative organs of the conifer Pinus pinaster under contrasting water availability

https://doi.org/10.1111/pce.13976
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/1873-3468.12746openalex-snapshot
mi RP ursuit—a pipeline for automated analyses of small RNA s in model and nonmodel plants
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Molecular study of drought response in the Mediterranean conifer Pinus pinaster Ait.: Differential transcriptomic profiling reveals constitutive water deficit‐independent drought tolerance mechanisms
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The pivotal role of small non-coding RNAs in the regulation of seed development
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Identification of cold-inducible microRNAs in plants by transcriptome analysis
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Identification of drought-induced microRNAs in rice
inferredcites →https://doi.org/10.1016/j.envexpbot.2014.05.011openalex-snapshot
The dynamic regulation of microRNAs circuits in plant adaptation to abiotic stresses: A survey on molecular, physiological and methodological aspects
inferredcites →https://doi.org/10.1016/j.febslet.2013.06.047openalex-snapshot
isomiRex: Web‐based identification of microRNAs, isomiR variations and differential expression using next‐generation sequencing datasets
inferredcites →https://doi.org/10.1016/j.freeradbiomed.2013.06.013openalex-snapshot
MitomiRs delineating the intracellular localization of microRNAs at mitochondria
inferredcites →https://doi.org/10.1016/j.gene.2009.01.006openalex-snapshot
High throughput sequencing technology reveals that the taxoid elicitor methyl jasmonate regulates microRNA expression in Chinese yew (Taxus chinensis)
inferredcites →https://doi.org/10.1016/j.gene.2014.04.039openalex-snapshot
A challenge for miRNA: multiple isomiRs in miRNAomics
inferredcites →https://doi.org/10.1016/j.tig.2012.07.005openalex-snapshot
IsomiRs – the overlooked repertoire in the dynamic microRNAome
inferredcites →https://doi.org/10.1038/nature12211openalex-snapshot
The Norway spruce genome sequence and conifer genome evolution
inferredcites →https://doi.org/10.1038/ng1791openalex-snapshot
Functions of microRNAs and related small RNAs in plants
inferredcites →https://doi.org/10.1038/nrm1488openalex-snapshot
Molecular mechanisms of translational control
inferredcites →https://doi.org/10.1038/s41598-017-16861-wopenalex-snapshot
MicroRNA-like RNAs from the same miRNA precursors play a role in cassava chilling responses
inferredcites →https://doi.org/10.1038/s41598-019-47789-yopenalex-snapshot
Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos
inferredcites →https://doi.org/10.1073/pnas.0708743105openalex-snapshot
Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs)
inferredcites →https://doi.org/10.1080/15476286.2019.1637680openalex-snapshot
miRBaseMiner, a tool for investigating miRBase content
inferredcites →https://doi.org/10.1093/bib/bbv019openalex-snapshot
Optimization of miRNA-seq data preprocessing
inferredcites →https://doi.org/10.1093/bib/bbw124openalex-snapshot
MicroRNAs and their variants in an RNA world: implications for complex interactions and diverse roles in an RNA regulatory network
inferredcites →https://doi.org/10.1093/bioinformatics/btg455openalex-snapshot
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes
inferredcites →https://doi.org/10.1093/bioinformatics/bti610openalex-snapshot
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
inferredcites →https://doi.org/10.1093/bioinformatics/btn223openalex-snapshot
PatMaN: rapid alignment of short sequences to large databases
inferredcites →https://doi.org/10.1093/bioinformatics/btn604openalex-snapshot
CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets
inferredcites →https://doi.org/10.1093/bioinformatics/bts311openalex-snapshot
The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets
inferredcites →https://doi.org/10.1093/emboj/cdf476openalex-snapshot
MicroRNA maturation: stepwise processing and subcellular localization
inferredcites →https://doi.org/10.1093/jxb/erq237openalex-snapshot
Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa
inferredcites →https://doi.org/10.1093/jxb/ert164openalex-snapshot
Emerging roles of microRNAs in the mediation of drought stress response in plants
inferredcites →https://doi.org/10.1093/jxb/erv013openalex-snapshot
MicroRNA: a new target for improving plant tolerance to abiotic stress
inferredcites →https://doi.org/10.1093/jxb/erv103openalex-snapshot
Genome-wide analysis reveals dynamic changes in expression of microRNAs during vascular cambium development in Chinese fir, Cunninghamia lanceolata
inferredcites →https://doi.org/10.1093/molbev/msv164openalex-snapshot
Extensive Families of miRNAs and PHAS Loci in Norway Spruce Demonstrate the Origins of Complex phasiRNA Networks in Seed Plants
inferredcites →https://doi.org/10.1093/nar/gkv384openalex-snapshot
Babelomics 5.0: functional interpretation for new generations of genomic data
inferredcites →https://doi.org/10.1093/treephys/tpr122openalex-snapshot
Functional and genetic characterization of gas exchange and intrinsic water use efficiency in a full-sib family of Pinus pinaster Ait. in response to drought
inferredcites →https://doi.org/10.1101/gad.1615208openalex-snapshot
Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci
inferredcites →https://doi.org/10.1101/gr.6897308openalex-snapshot
Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa
inferredcites →https://doi.org/10.1104/pp.113.214643openalex-snapshot
A Significant Fraction of 21-Nucleotide Small RNA Originates from Phased Degradation of Resistance Genes in Several Perennial Species
inferredcites →https://doi.org/10.1111/j.1365-313x.2007.03208.xopenalex-snapshot
MicroRNAs in loblolly pine ( Pinus taeda L.) and their association with fusiform rust gall development
inferredcites →https://doi.org/10.1111/j.1469-8137.2010.03341.xopenalex-snapshot
MicroRNAs, the epigenetic memory and climatic adaptation in Norway spruce
inferredcites →https://doi.org/10.1111/j.1756-1051.2012.01516.xopenalex-snapshot
Conifer genome sizes of 172 species, covering 64 of 67 genera, range from 8 to 72 picogram
inferredcites →https://doi.org/10.1146/annurev-arplant-050312-120043openalex-snapshot
Classification and Comparison of Small RNAs from Plants
inferredcites →https://doi.org/10.1146/annurev.arplant.57.032905.105218openalex-snapshot
MicroRNAs AND THEIR REGULATORY ROLES IN PLANTS
inferredcites →https://doi.org/10.1186/1471-2164-12-367openalex-snapshot
Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing
inferredcites →https://doi.org/10.1186/1471-2164-14-233openalex-snapshot
Identification of drought-responsive and novel Populus trichocarpamicroRNAs by high-throughput sequencing and their targets using degradome analysis
inferredcites →https://doi.org/10.1186/1471-2229-12-146openalex-snapshot
Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing
inferredcites →https://doi.org/10.1186/1471-2229-8-25openalex-snapshot
Identification of novel and candidate miRNAs in rice by high throughput sequencing
inferredcites →https://doi.org/10.1186/gb-2010-11-8-r81openalex-snapshot
Multiple distinct small RNAs originate from the same microRNA precursors
inferredcites →https://doi.org/10.1186/gb-2011-12-12-r126openalex-snapshot
MicroRNAs and their isomiRs function cooperatively to target common biological pathways
inferredcites →https://doi.org/10.1186/gb-2014-15-3-r59openalex-snapshot
Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies
inferredcites →https://doi.org/10.1186/s41544-018-0003-8openalex-snapshot
Biogenesis and biological implications of isomiRs in mammals- a review
inferredcites →https://doi.org/10.1261/rna.1052008openalex-snapshot
Conifers have a unique small RNA silencing signature
inferredcites →https://doi.org/10.1261/rna.895308openalex-snapshot
Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana
inferredcites →https://doi.org/10.1371/journal.pone.0020220openalex-snapshot
Pre-microRNA and Mature microRNA in Human Mitochondria
inferredcites →https://doi.org/10.1371/journal.pone.0046991openalex-snapshot
Genome-Wide Identification of Reverse Complementary microRNA Genes in Plants
inferredcites →https://doi.org/10.1371/journal.pone.0081452openalex-snapshot
Deciphering Small Noncoding RNAs during the Transition from Dormant Embryo to Germinated Embryo in Larches (Larix leptolepis)
inferredcites →https://doi.org/10.3389/fphys.2015.00286openalex-snapshot
Role of bioinformatics in establishing microRNAs as modulators of abiotic stress responses: the new revolution
inferredcites →https://doi.org/10.3389/fphys.2017.00674openalex-snapshot
In Silico Analysis of Small RNAs Suggest Roles for Novel and Conserved miRNAs in the Formation of Epigenetic Memory in Somatic Embryos of Norway Spruce
inferredcites →https://doi.org/10.3389/fpls.2015.00949openalex-snapshot
isomiRs: Increasing Evidences of isomiRs Complexity in Plant Stress Functional Biology
inferredcites →https://doi.org/10.3389/fpls.2017.02200openalex-snapshot
Characterization and Function of MicroRNA∗s in Plants
inferredcites →https://doi.org/10.3389/fpls.2018.01881openalex-snapshot
Plant IsomiR Atlas: Large Scale Detection, Profiling, and Target Repertoire of IsomiRs in Plants
inferredcites →https://doi.org/10.6084/m9.figshare.12328979openalex-snapshot
Pinus pinaster drought response transcriptome (PpDR transcriptome)

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.4837256openalex-extracted
Physiological and Molecular Response to Drought in Somatic Plants from Pinus Radiata Embryonal Masses Induced at High Temperatures
inferred← citeshttps://doi.org/10.1007/124_2023_75openalex-snapshot
Regulatory Roles of Small RNAs in Forest Trees
inferred← citeshttps://doi.org/10.1007/978-3-030-93390-6_5openalex-snapshot
Maritime Pine Genomics in Focus
inferred← citeshttps://doi.org/10.1007/978-3-030-93390-6_9openalex-snapshot
Functional Genomics of Mediterranean Pines
inferred← citeshttps://doi.org/10.1016/j.plaphy.2025.109886openalex-snapshot
Physiological and molecular response to drought in somatic plants from Pinus radiata embryonal masses induced at high temperatures
inferred← citeshttps://doi.org/10.1038/s41598-022-09163-3openalex-snapshot
MicroRNA-mediated post-transcriptional regulation of Pinus pinaster response and resistance to pinewood nematode
inferred← citeshttps://doi.org/10.1111/ppl.14516openalex-snapshot
Comprehensive analysis of hairpin small RNAs involved in resistance and pathogenesis during wheat–Puccinia triticina interactions
inferred← citeshttps://doi.org/10.32717/0131-0062-2026-79-6-19openalex-snapshot
PHYSIOLOGICAL MECHANISMS OF THE INFLUENCE OF THE SPECTRAL COMPOSITION OF LED LIGHTING ON THE FORMATION OF THE PHOTOSYNTHETIC APPARATUS OF TOMATO AND CUCUMBER SEEDLINGS
inferred← citeshttps://doi.org/10.3389/fpls.2022.857611openalex-snapshot
miR160 Interacts in vivo With Pinus pinaster AUXIN RESPONSE FACTOR 18 Target Site and Negatively Regulates Its Expression During Conifer Somatic Embryo Development
inferred← citeshttps://doi.org/10.3390/ijms23031111openalex-snapshot
Cryo-Treatment Enhances the Embryogenicity of Mature Somatic Embryos via the lncRNA–miRNA–mRNA Network in White Spruce
inferred← citeshttps://doi.org/10.3390/ijms241914655openalex-snapshot
The miRNA-mRNA Regulatory Modules of Pinus massoniana Lamb. in Response to Drought Stress
inferred← citeshttps://doi.org/10.3390/plants10030504openalex-snapshot
Small Non-Coding RNAs at the Crossroads of Regulatory Pathways Controlling Somatic Embryogenesis in Seed Plants
inferred← citeshttps://doi.org/10.3390/plants12050982openalex-snapshot
Dynamic Regulation of Grapevine’s microRNAs in Response to Mycorrhizal Symbiosis and High Temperature
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