Background: MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulation of eukaryotic gene expression and are involved in many aspects of plant development. Although several prediction tools are available for metazoan genomes, the number of tools dedicated to plants is relatively limited.
Results: Here, we present miRkwood, a user-friendly tool for the identification of miRNAs in plant genomes using small RNA sequencing data. Deep-sequencing data of Argonaute associated small RNAs showed that miRkwood is able to identify a large diversity of plant miRNAs and limits false positive predictions. Moreover, it outperforms current tools such as ShortStack and contrary to ShortStack, miRkwood provides a quality score allowing users to rank miRNA predictions.
Conclusion: miRkwood is a very efficient tool for the annotation of miRNAs in plant genomes. It is available as a web server, as a standalone version, as a docker image and as a Galaxy tool: http://bioinfo.cristal.univ-lille.fr/mirkwood.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6599362 | PMC |
| http://dx.doi.org/10.1186/s12864-019-5913-9 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Expanding the human gut microbiome atlas of Africa.
Nature
January 2025
Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
Population studies provide insights into the interplay between the gut microbiome and geographical, lifestyle, genetic and environmental factors. However, low- and middle-income countries, in which approximately 84% of the world's population lives, are not equitably represented in large-scale gut microbiome research. Here we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,801 women from Burkina Faso, Ghana, Kenya and South Africa.
View Article and Find Full Text PDFNon-additive dosage-dependent effects of TaGS3 gene editing on grain size and weight in wheat.
Theor Appl Genet
January 2025
Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA.
Loss-of-function mutations induced by CRISPR-Cas9 in the TaGS3 gene homoeologs show non-additive dosage-dependent effects on grain size and weight and have potential utility for increasing grain yield in wheat. The grain size in cereals is one of the component traits contributing to yield. Previous studies showed that loss-of-function (LOF) mutations in GS3, encoding Gγ subunit of the multimeric G protein complex, increase grain size and weight in rice.
View Article and Find Full Text PDFChromosome-level genome assembly of the sweet potato rot nematode Ditylenchus destructor.
Sci Data
January 2025
Shaanxi Key Laboratory of Plant Nematology, Bio-Agriculture Institute of Shaanxi, Xi'an, China.
Ditylenchus destructor, commonly known as the potato rot nematode, is a significant plant-parasitic pathogen affecting over 120 plant species globally. Effective control measures for D. destructor are limited, underscoring the need a high-quality reference genome to understand its pathogenic mechanisms.
View Article and Find Full Text PDFThe atypical proteome of mitochondria from mature pollen grains.
Curr Biol
January 2025
Department of Plant Physiology, UPSC, Umeå University, 90187 Umeå, Sweden. Electronic address:
To propagate their genetic material, flowering plants rely on the production of large amounts of pollen grains that are capable of germinating on a compatible stigma. Pollen germination and pollen tube growth are thought to be extremely energy-demanding processes. This raises the question of whether mitochondria from pollen grains are specifically tuned to support this developmental process.
View Article and Find Full Text PDFGenome-wide identification of the bZIP family in Eutrema salsugineum and functional analysis of EsbZIP51 in regulating salt tolerance.
Plant Physiol Biochem
January 2025
Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China. Electronic address:
The halophyte Eutrema salsugineum is naturally distributed in saline-alkali soil and has been proposed as a model plant for understanding plant salt tolerance. As one of the largest and most diverse TF families, basic leucine zipper motif (bZIP) TFs perform robust functions in plant growth and environmental response, however the generalized information of EsbZIP genes and its regulatory role in salt tolerance has not been systematically studied to date. Here, we identified and characterized the bZIP members in E.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!