PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens

Abstract

Physcomitrella patens is a bryophyte model plant that is often used to study plant evolution and development. Its resources are of great importance for comparative genomics and evo-devo approaches. However, expression data from Physcomitrella patens were so far generated using different gene annotation versions and three different platforms: CombiMatrix and NimbleGen expression microarrays and RNA sequencing. The currently available P. patens expression data are distributed across three tools with different visualization methods to access the data. Here, we introduce an interactive expression atlas, Physcomitrella Expression Atlas Tool (PEATmoss), that unifies publicly available expression data for P. patens and provides multiple visualization methods to query the data in a single web-based tool. Moreover, PEATmoss includes 35 expression experiments not previously available in any other expression atlas. To facilitate gene expression queries across different gene annotation versions, and to access P. patens annotations and related resources, a lookup database and web tool linked to PEATmoss was implemented. PEATmoss can be accessed at https://peatmoss.online.uni-marburg.de

Characterisation of evolutionarily conserved key players affecting eukaryotic flagellar motility and fertility using a moss model

“…For this purpose, we analysed the nearly self‐sterile ecotype Gransden (Gd) in comparison with the highly fertile ecotype Reute (Re), using genetic and epigenetic variation data, fertility phenotyping as well as transcript profiling. Based on publicly available array data of developmental stages during sexual reproduction (Ortiz‐Ramirez et al , 2017; Fernandez‐Pozo et al , 2019) and network analyses, we generated a deletion mutant of a gene exclusively expressed in sexual reproductive organs. The mutant displays a loss of male fertility similar to that observed in Gd, and to that in human/mammal mutants of the orthologue.…”

Single Nucleotide Polymorphism Charting of P. patens Reveals Accumulation of Somatic Mutations During in vitro Culture on the Scale of Natural Variation by Selfing

“…However, P. patens gDNA samples are rare. Nevertheless, the recent publication of RNA-seq datasets (Demko et al, 2014;Frank and Scanlon, 2015;Stevenson et al, 2016;Szövényi et al, 2017;Perroud et al, 2018;Fernandez-Pozo et al, 2019) provides a source of information that can be used to detect SNPs. Due to the high number of RNA-seq samples analyzed, efficient pipeline processing is essential.…”

Global transcriptome analysis reveals circadian control of splicing events in Arabidopsis thaliana

“…Homologue sequences from A. thaliana, Capsella rubella, Solanum lycopersicum, Oryza sativa and Sorghum bicolor were identified with BLASTP and downloaded from GENBANK. Physcomitrella patens sequences were obtained from PEATMOSS PPGML DB V1.6 (Fernandez-Pozo et al, 2019). Using these sequences as input, a phylogenetic tree was reconstructed using SEAVIEW 4.7 (Gouy et al, 2010).…”