Event | September 19, 2019
The Graduate School of Life Science’s International Graduate Program (IGP) is organizing the 161st Plant Science Seminar. Everyone is welcome to join!
Physcomitrella patens Genomic and Bioinformatics Resources
Dr. Noé Fernández Pozo, Marburg University, Germany
Date and time
Thursday, 19 September 2019, 14:00 – 15:00
Room 5-305, 3rd Floor, Building #5, School of Science, Hokkaido University
P.patens is a model of great importance for comparative genomics and evo-devo approaches and its genomics and bioinformatics resources are under continuous development. As most genome sequencing projects, the genome sequence and annotations are improved over the years when more sequences are available and new technologies appear or become cheaper. Thereby, it is possible to accomplish better scaffolding, gap closing and predicting new gene models with better evidence. Here, we present the status of the new P.patens genome assembly and annotation with a set of bioinformatics tools to unify P.patens gene version, expression data and transcription factors. We have developed PEATmoss (https://peatmoss.online.uni-marburg.de) , a very interactive expression atlas for P.patens gene expression data with multiple visualization methods and tools such as a 3D expression cube, expression data in cartoons, bar plots, hierarchical clustering heatmap, scatterplot, differentially expressed genes detection and data downloading. The expression cube shows gene expression for the query gene and co-expressed genes, a custom list of genes or the output from BLAST, allowing multiple gene comparison and facilitating the discovery of genes of interest. Together with PEATmoss other tools were developed for bulk gene conversion and annotation and sequence downloading. This resource provides cross link annotations for P.patens genes to NCBI GenBank, Phytozome, Ensembl Plants, TAIR, PLAZA, CoGe, TAPscan and genome browsers to assist researchers when looking for gene information.
Additionally, the analysis of the sequence nucleotide polymorphisms from the expression data, shown an accumulation of somatic mutations in P.patens lab strains and lineages. These mutations could be responsible for changes on gene sequence between accessions and, for example, it could be related to the loss of fertility in some Grandsen strains.
Professor Tomomichi Fujita
Faculty of Science