News & Information

Plant Science Seminar co-organized by IGP

(posted on September 5th, 2019)

Plant Science Seminar will be co-organized by IGP on September 19.

Please feel free to join us!

Date: Thursday, September 19, 2019

Time: 14:00-15:00

Venue: Room 5-305, 3th Floor, Building #5, School of Science, Hokkaido University

Speaker: Dr. Noé Fernández Pozo (Marburg University, Germany)

Title: Physcomitrella patens Genomic and Bioinformatics Resources

Language: English

Abstract:

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.

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