MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression involved in countless biological processes and are widely studied across metazoans. Although miRNA research continues to grow, the large community of fish miRNA researchers lacks exhaustive resources consistent among species. To fill this gap, we developed FishmiRNA, an evolutionarily supported miRNA annotation and expression database for ray-finned fishes: www.fishmirna.org. The self-explanatory database contains detailed, manually curated miRNA annotations with orthology relationships rigorously established by sequence similarity and conserved syntenies, and expression data provided for each detected mature miRNA. In just few clicks, users can download the annotation and expression database in several convenient formats either in its entirety or a subset. Simple filters and Blast search options also permit the simultaneous exploration and visual comparison of expression data for up to any ten mature miRNAs across species and organs. FishmiRNA was specifically designed for ease of use to reach a wide audience.
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http://dx.doi.org/10.1093/molbev/msac004 | DOI Listing |
Cancers (Basel)
January 2025
Avantyx Pharmaceuticals, Miami, FL 33136, USA.
There are numerous ways of portraying cancer complexity based on combining multiple types of data. A common approach involves developing signatures from gene expression profiles to highlight a few key reproducible features that provide insight into cancer risk, progression, or recurrence. Normally, a selection of such features is made through relevance or significance, given a reference context.
View Article and Find Full Text PDFInt J Mol Sci
January 2025
College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China.
Salt tolerance is a critical trait for plant survival and productivity in saline environments. Development of salt tolerant crops is a practical strategy for addressing soil salinity issues. In this study, RNA-Seq analysis was performed using two wheat cultivars with contrasting salt tolerance (Neixiang188, tolerant and Barra, sensitive) at 6 h and 24 h after salinity treatment to determine the genetic variations reflected in the RNA expression patterns and identify key genes associated with salt tolerance.
View Article and Find Full Text PDFInt J Mol Sci
December 2024
Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai 264005, China.
Powdery mildew, caused by f. sp. (), is a disease that seriously harms wheat production and occurs in all wheat-producing areas around the world.
View Article and Find Full Text PDFInt J Mol Sci
December 2024
State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China.
TCP is a plant-specific transcription factor that plays an important role in plant growth and development. In this study, we used bioinformatics to identify the entire genome of the gene family in Bat, and we analyzed the expression characteristics of genes under UV-B radiation using qRT-PCR. The results were as follows: (1) 24 members of the gene family were identified in , evenly distributed on its 24 chromosomes.
View Article and Find Full Text PDFBMC Genomics
January 2025
Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China.
Background: Identification of global transcriptional events is crucial for genome annotation, as accurate annotation enhances the efficiency and comparability of genomic information across species. However, the annotation of transcripts in the cucumber genome remains to be improved, and many transcriptional events have not been well studied.
Results: We collected 1,904 high-quality public cucumber transcriptome samples from the National Center for Biotechnology Information (NCBI) to identify and annotate transcript isoforms in the cucumber genome.
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