The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data
Abstract
Summary 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 ( DEG s) 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 allowedmore »
- Authors:
-
[1];
[1];
[1];
[6];
more »
- University of Marburg (Germany)
- University of Verona (Italy)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Université Paris-Saclay, Versailles (France)
- Peking University, Beijing (China)
- University of Birmingham (United Kingdom)
- Hokkaido University, Sapporo (Japan)
- Helmholtz Zentrum München, Neuherberg (Germany)
- University of Missouri, Columbia, MO (United States)
- Clemente Estable Biological Research Institute, Montevideo (Uruguay)
- Washington University, St. Louis, MO (United States)
- Max Planck Institute for Plant Breeding Research, Köln (Germany)
- University of Freiburg (Germany)
- University of Zurich (Switzerland)
- HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
- University of Marburg (Germany); University of Freiburg (Germany)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Natural Science Foundation of China (NSFC); German Federal and State Governments; UK Leverhulme Trust; Swiss National Science Foundation (SNSF)
- OSTI Identifier:
- 1616061
- Alternate Identifier(s):
- OSTI ID: 1441035
- Grant/Contract Number:
- AC02-05CH11231; 31621001; F/ 0094/BA; 160004; 131726; DE‐899 AC02‐05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- The Plant Journal
- Additional Journal Information:
- Journal Volume: 95; Journal Issue: 1; Journal ID: ISSN 0960-7412
- Publisher:
- Society for Experimental Biology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; developmental stag; differential expression; Physcomitrella patens; RNA-seq; stress; transcriptome analysis
Citation Formats
Perroud, Pierre‐François, Haas, Fabian B., Hiss, Manuel, Ullrich, Kristian K., Alboresi, Alessandro, Amirebrahimi, Mojgan, Barry, Kerrie, Bassi, Roberto, Bonhomme, Sandrine, Chen, Haodong, Coates, Juliet C., Fujita, Tomomichi, Guyon‐Debast, Anouchka, Lang, Daniel, Lin, Junyan, Lipzen, Anna, Nogué, Fabien, Oliver, Melvin J., Ponce de León, Inés, Quatrano, Ralph S., Rameau, Catherine, Reiss, Bernd, Reski, Ralf, Ricca, Mariana, Saidi, Younousse, Sun, Ning, Szövényi, Péter, Sreedasyam, Avinash, Grimwood, Jane, Stacey, Gary, Schmutz, Jeremy, and Rensing, Stefan A. The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data. United States: N. p., 2018.
Web. doi:10.1111/tpj.13940.
Perroud, Pierre‐François, Haas, Fabian B., Hiss, Manuel, Ullrich, Kristian K., Alboresi, Alessandro, Amirebrahimi, Mojgan, Barry, Kerrie, Bassi, Roberto, Bonhomme, Sandrine, Chen, Haodong, Coates, Juliet C., Fujita, Tomomichi, Guyon‐Debast, Anouchka, Lang, Daniel, Lin, Junyan, Lipzen, Anna, Nogué, Fabien, Oliver, Melvin J., Ponce de León, Inés, Quatrano, Ralph S., Rameau, Catherine, Reiss, Bernd, Reski, Ralf, Ricca, Mariana, Saidi, Younousse, Sun, Ning, Szövényi, Péter, Sreedasyam, Avinash, Grimwood, Jane, Stacey, Gary, Schmutz, Jeremy, & Rensing, Stefan A. The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data. United States. https://doi.org/10.1111/tpj.13940
Perroud, Pierre‐François, Haas, Fabian B., Hiss, Manuel, Ullrich, Kristian K., Alboresi, Alessandro, Amirebrahimi, Mojgan, Barry, Kerrie, Bassi, Roberto, Bonhomme, Sandrine, Chen, Haodong, Coates, Juliet C., Fujita, Tomomichi, Guyon‐Debast, Anouchka, Lang, Daniel, Lin, Junyan, Lipzen, Anna, Nogué, Fabien, Oliver, Melvin J., Ponce de León, Inés, Quatrano, Ralph S., Rameau, Catherine, Reiss, Bernd, Reski, Ralf, Ricca, Mariana, Saidi, Younousse, Sun, Ning, Szövényi, Péter, Sreedasyam, Avinash, Grimwood, Jane, Stacey, Gary, Schmutz, Jeremy, and Rensing, Stefan A. Sun .
"The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data". United States. https://doi.org/10.1111/tpj.13940. https://www.osti.gov/servlets/purl/1616061.
@article{osti_1616061,
title = {The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data},
author = {Perroud, Pierre‐François and Haas, Fabian B. and Hiss, Manuel and Ullrich, Kristian K. and Alboresi, Alessandro and Amirebrahimi, Mojgan and Barry, Kerrie and Bassi, Roberto and Bonhomme, Sandrine and Chen, Haodong and Coates, Juliet C. and Fujita, Tomomichi and Guyon‐Debast, Anouchka and Lang, Daniel and Lin, Junyan and Lipzen, Anna and Nogué, Fabien and Oliver, Melvin J. and Ponce de León, Inés and Quatrano, Ralph S. and Rameau, Catherine and Reiss, Bernd and Reski, Ralf and Ricca, Mariana and Saidi, Younousse and Sun, Ning and Szövényi, Péter and Sreedasyam, Avinash and Grimwood, Jane and Stacey, Gary and Schmutz, Jeremy and Rensing, Stefan A.},
abstractNote = {Summary 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 ( DEG s) 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.},
doi = {10.1111/tpj.13940},
journal = {The Plant Journal},
number = 1,
volume = 95,
place = {United States},
year = {Sun Apr 22 00:00:00 EDT 2018},
month = {Sun Apr 22 00:00:00 EDT 2018}
}
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