ArticleBMC research notes2011
Comparative analysis of miRNAs and their targets across four plant species.
Article in BMC research notes, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 19 citations in OpenAlex.
- Review
- MicroRNA Profiling During Mulberry (Frontiers in plant science · 2021Article
- MiRNA-seq-based profiles of miRNAs in mulberry phloem sap provide insight into the pathogenic mechanisms of mulberry yellow dwarf disease.Scientific reports · 2018Article
- Computational Identification of MicroRNAs and Their Transcript Target(s) in Field Mustard (Iranian journal of biotechnology · 2017Article
- ASR5 is involved in the regulation of miRNA expression in rice.Plant cell reports · 2015Article
- Identification of AGO3-associated miRNAs and computational prediction of their targets in the green alga Chlamydomonas reinhardtii.Genetics · 2015Article
- The liverwort Pellia endiviifolia shares microtranscriptomic traits that are common to green algae and land plants.The New phytologist · 2015Article
- Microevolution of nematode miRNAs reveals diverse modes of selection.Genome biology and evolution · 2014Article
- Global identification of miRNAs and targets in Populus euphratica under salt stress.Plant molecular biology · 2013Article
- Identification of miRNAs and their target genes in peach (Prunus persica L.) using high-throughput sequencing and degradome analysis.PloS one · 2013Article
- Genome-wide identification of Brassica napus microRNAs and their targets in response to cadmium.Journal of experimental botany · 2012Article
- Identifying conserved and novel microRNAs in developing seeds of Brassica napus using deep sequencing.PloS one · 2012Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicroRNA (miRNA) mediated regulation of gene expression has been recognized as a major posttranscriptional regulatory mechanism also in plants. We performed a comparative analysis of miRNAs and their respective gene targets across four plant species: Arabidopsis thaliana (Ath), Medicago truncatula(Mtr), Brassica napus (Bna), and Chlamydomonas reinhardtii (Cre).
resultsmiRNAs were obtained from mirBase with 218 miRNAs for Ath, 375 for Mtr, 46 for Bna, and 73 for Cre, annotated for each species respectively. miRNA targets were obtained from available database annotations, bioinformatic predictions using RNAhybrid as well as predicted from an analysis of mRNA degradation products (degradome sequencing) aimed at identifying miRNA cleavage products. On average, and considering both experimental and bioinformatic predictions together, every miRNA was associated with about 46 unique gene transcripts with considerably variation across species. We observed a positive and linear correlation between the number miRNAs and the total number of transcripts across different plant species suggesting that the repertoire of miRNAs correlates with the size of the transcriptome of an organism. Conserved miRNA-target pairs were found to be associated with developmental processes and transcriptional regulation, while species-specific (in particular, Ath) pairs are involved in signal transduction and response to stress processes. Conserved miRNAs have more targets and higher expression values than non-conserved miRNAs. We found evidence for a conservation of not only the sequence of miRNAs, but their expression levels as well.
conclusionsOur results support the notion of a high birth and death rate of miRNAs and that miRNAs serve many species specific functions, while conserved miRNA are related mainly to developmental processes and transcriptional regulation with conservation operating at both the sequence and expression level.
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Registered trials
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.