2021/07/09 by Sébastien Carrère, Jérôme Verdier, Pascal Gamas · 1 voice · 98 citations
Agricultural and Biological Sciences · #Biology #Computational biology #Gene #Gene Annotation #Gene expression #Genetics #Genome #Genomics #Legume Nitrogen Fixing Symbiosis #Medicago #Medicago truncatula #Plant pathogens and resistance mechanisms #Soybean genetics and cultivation #Transcriptome
paper · pdf · doi:10.1093/pcp/pcab110
published in Plant and Cell Physiology 62(9), 1494-1500 (Oxford University Press)
openalex publication_date 2021/07/09 · openalex created_date 2021/07/19 · openalex updated_date 2026/08/06
Although RNA sequencing (RNAseq) has been becoming the main transcriptomic approach in the model legume Medicago truncatula, there is currently no genome-wide gene expression atlas covering the whole set of RNAseq data published for this species. Nowadays, such a tool is highly valuable to provide a global view of gene expression in a wide range of conditions and tissues/organs. Here, we present MtExpress, a gene expression atlas that compiles an exhaustive set of published M. truncatula RNAseq data (https://medicago.toulouse.inrae.fr/MtExpress). MtExpress makes use of recent releases of M. truncatula genome sequence and annotation, as well as up-to-date tools to perform mapping, quality control, statistical analysis and normalization of RNAseq data. MtExpress combines semi-automated pipelines with manual re-labeling and organization of samples to produce an attractive and user-friendly interface, fully integrated with other available Medicago genomic resources. Importantly, MtExpress is highly flexible, in terms of both queries, e.g. allowing searches with gene names and orthologous gene IDs from Arabidopsis and other legume species, and outputs, to customize visualization and redirect gene study to relevant Medicago webservers. Thanks to its semi-automated pipeline, MtExpress will be frequently updated to follow the rapid pace of M. truncatula RNAseq data publications, as well as the constant improvement of genome annotation. MtExpress also hosts legacy GeneChip expression data originally stored in the Medicago Gene Expression Atlas, as a very valuable and complementary resource.