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The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data


Perroud, Pierre-François; Haas, Fabian B; Hiss, Manuel; Ullrich, Kristian K; et al; Szövényi, Peter (2018). The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data. The Plant Journal, 95(1):168-182.

Abstract

High‐throughput RNA sequencing (RNA‐seq) has recently become the method of choice to define and analyze transcriptomes. For the model moss Physcomitrella patens, although this method has been used to help analyze specific perturbations, no overall reference dataset has yet been established. In the framework of the Gene Atlas project, the Joint Genome Institute selected P. patens as a flagship genome, opening the way to generate the first comprehensive transcriptome dataset for this moss. The first round of sequencing described here is composed of 99 independent libraries spanning 34 different developmental stages and conditions. Upon dataset quality control and processing through read mapping, 28 509 of the 34 361 v3.3 gene models (83%) were detected to be expressed across the samples. Differentially expressed genes (DEGs) were calculated across the dataset to permit perturbation comparisons between conditions. The analysis of the three most distinct and abundant P. patens growth stages – protonema, gametophore and sporophyte – allowed us to define both general transcriptional patterns and stage‐specific transcripts. As an example of variation of physico‐chemical growth conditions, we detail here the impact of ammonium supplementation under standard growth conditions on the protonemal transcriptome. Finally, the cooperative nature of this project allowed us to analyze inter‐laboratory variation, as 13 different laboratories around the world provided samples. We compare differences in the replication of experiments in a single laboratory and between different laboratories.

Abstract

High‐throughput RNA sequencing (RNA‐seq) has recently become the method of choice to define and analyze transcriptomes. For the model moss Physcomitrella patens, although this method has been used to help analyze specific perturbations, no overall reference dataset has yet been established. In the framework of the Gene Atlas project, the Joint Genome Institute selected P. patens as a flagship genome, opening the way to generate the first comprehensive transcriptome dataset for this moss. The first round of sequencing described here is composed of 99 independent libraries spanning 34 different developmental stages and conditions. Upon dataset quality control and processing through read mapping, 28 509 of the 34 361 v3.3 gene models (83%) were detected to be expressed across the samples. Differentially expressed genes (DEGs) were calculated across the dataset to permit perturbation comparisons between conditions. The analysis of the three most distinct and abundant P. patens growth stages – protonema, gametophore and sporophyte – allowed us to define both general transcriptional patterns and stage‐specific transcripts. As an example of variation of physico‐chemical growth conditions, we detail here the impact of ammonium supplementation under standard growth conditions on the protonemal transcriptome. Finally, the cooperative nature of this project allowed us to analyze inter‐laboratory variation, as 13 different laboratories around the world provided samples. We compare differences in the replication of experiments in a single laboratory and between different laboratories.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Systematic and Evolutionary Botany
07 Faculty of Science > Zurich-Basel Plant Science Center
08 Research Priority Programs > Evolution in Action: From Genomes to Ecosystems
Dewey Decimal Classification:580 Plants (Botany)
Uncontrolled Keywords:Plant Science, Genetics, Cell Biology
Language:English
Date:1 July 2018
Deposited On:04 Feb 2019 12:02
Last Modified:20 Oct 2019 05:57
Publisher:Wiley-Blackwell Publishing, Inc.
ISSN:0960-7412
OA Status:Closed
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1111/tpj.13940
Project Information:
  • : FunderSNSF
  • : Grant ID31003A_160004
  • : Project TitleTesting hypotheses on the evolutionary origin of the land plant sporophyte
  • : FunderSNSF
  • : Grant IDPZ00P3_131726
  • : Project TitleGene expression and the evolution of plant alternation of generations
  • : FunderH2020
  • : Grant ID675006
  • : Project TitleSE2B - Solar Energy to Biomass - Optimisation of light energy conversion in plants and microalgae

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