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

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.

doi:10.1111/tpj.13940

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

Journal Article · Sun Apr 22 00:00:00 EDT 2018 · The Plant Journal

DOI:https://doi.org/10.1111/tpj.13940· OSTI ID:1616061

^[1];

^[1]; Hiss, Manuel ^[1];

^[1]; Alboresi, Alessandro ^[2]; Amirebrahimi, Mojgan ^[3]; Barry, Kerrie ^[3]; Bassi, Roberto ^[2]; Bonhomme, Sandrine ^[4]; Chen, Haodong ^[5];

^[6]; Fujita, Tomomichi ^[7]; Guyon‐Debast, Anouchka ^[4]; Lang, Daniel ^[8]; Lin, Junyan ^[3]; Lipzen, Anna ^[3]; Nogué, Fabien ^[4]; Oliver, Melvin J. ^[9]; Ponce de León, Inés ^[10]; Quatrano, Ralph S. ^[11] 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)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: 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)

Grant/Contract Number:: AC02-05CH11231; 31621001; F/ 0094/BA; 160004; 131726; DE‐899 AC02‐05CH11231

OSTI ID:: 1616061

Alternate ID(s):: OSTI ID: 1441035

Journal Information:: The Plant Journal, Vol. 95, Issue 1; ISSN 0960-7412

Publisher:: Society for Experimental BiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 50 works

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References (77)

Complex heatmaps reveal patterns and correlations in multidimensional genomic data Gu, Zuguang; Eils, Roland; Schlesner, Matthias Bioinformatics, Vol. 32, Issue 18 https://doi.org/10.1093/bioinformatics/btw313	journal	May 2016
De novo assembly and comparative analysis of the Ceratodon purpureus transcriptome Szövényi, Péter; Perroud, Pierre-François; Symeonidi, Aikaterini Molecular Ecology Resources, Vol. 15, Issue 1 https://doi.org/10.1111/1755-0998.12284	journal	June 2014
The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants Banks, J. A.; Nishiyama, T.; Hasebe, M. Science, Vol. 332, Issue 6032 https://doi.org/10.1126/science.1203810	journal	May 2011
Comprehensive Annotation of Physcomitrella patens Small RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants Coruh, Ceyda; Cho, Sung Hyun; Shahid, Saima The Plant Cell, Vol. 27, Issue 8 https://doi.org/10.1105/tpc.15.00228	journal	July 2015
Quality control and preprocessing of metagenomic datasets Schmieder, R.; Edwards, R. Bioinformatics, Vol. 27, Issue 6 https://doi.org/10.1093/bioinformatics/btr026	journal	January 2011
Desiccation sensitivity and tolerance in the moss Physcomitrella patens: assessing limits and damage Koster, Karen L.; Balsamo, Ronald A.; Espinoza, Catherine Plant Growth Regulation, Vol. 62, Issue 3 https://doi.org/10.1007/s10725-010-9490-9	journal	June 2010
Nutrient constraints on terrestrial carbon fixation: The role of nitrogen Coskun, Devrim; Britto, Dev T.; Kronzucker, Herbert J. Journal of Plant Physiology, Vol. 203 https://doi.org/10.1016/j.jplph.2016.05.016	journal	September 2016
Sexual reproduction, sporophyte development and molecular variation in the model moss Physcomitrella patens : introducing the ecotype Reute Hiss, Manuel; Meyberg, Rabea; Westermann, Jens The Plant Journal, Vol. 90, Issue 3 https://doi.org/10.1111/tpj.13501	journal	March 2017
Differential expression in RNA-seq: A matter of depth Tarazona, S.; Garcia-Alcalde, F.; Dopazo, J. Genome Research, Vol. 21, Issue 12 https://doi.org/10.1101/gr.124321.111	journal	September 2011
Transcriptome analyses provide insights into the phylogeny and adaptive evolution of the mangrove fern genus Acrostichum Zhang, Zhang; He, Ziwen; Xu, Shaohua Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep35634	journal	October 2016
Generation-Biased Gene Expression in a Bryophyte Model System Szovenyi, P.; Rensing, S. A.; Lang, D. Molecular Biology and Evolution, Vol. 28, Issue 1 https://doi.org/10.1093/molbev/msq254	journal	September 2010
Data access for the 1,000 Plants (1KP) project Matasci, Naim; Hung, Ling-Hong; Yan, Zhixiang GigaScience, Vol. 3, Issue 1 https://doi.org/10.1186/2047-217X-3-17	journal	October 2014
RNA Sequencing Analysis of the Gametophyte Transcriptome from the Liverwort, Marchantia polymorpha Sharma, Niharika; Jung, Chol-Hee; Bhalla, Prem L. PLoS ONE, Vol. 9, Issue 5 https://doi.org/10.1371/journal.pone.0097497	journal	May 2014
Fast and SNP-tolerant detection of complex variants and splicing in short reads Wu, T. D.; Nacu, S. Bioinformatics, Vol. 26, Issue 7, p. 873-881 https://doi.org/10.1093/bioinformatics/btq057	journal	February 2010
Large-scale gene expression profiling data for the model moss Physcomitrella patens aid understanding of developmental progression, culture and stress conditions Hiss, Manuel; Laule, Oliver; Meskauskiene, Rasa M. The Plant Journal, Vol. 79, Issue 3 https://doi.org/10.1111/tpj.12572	journal	July 2014
A Transcriptome Atlas of Physcomitrella patens Provides Insights into the Evolution and Development of Land Plants Ortiz-Ramírez, Carlos; Hernandez-Coronado, Marcela; Thamm, Anna Molecular Plant, Vol. 9, Issue 2 https://doi.org/10.1016/j.molp.2015.12.002	journal	February 2016
Exclusion of Na ⁺ via Sodium ATPase (PpENA1) Ensures Normal Growth of Physcomitrella patens under Moderate Salt Stress Lunde, Christina; Drew, Damian P.; Jacobs, Andrew K. Plant Physiology, Vol. 144, Issue 4 https://doi.org/10.1104/pp.106.094946	journal	June 2007
Global transcriptome analysis reveals extensive gene remodeling, alternative splicing and differential transcription profiles in non-seed vascular plant Selaginella moellendorffii Zhu, Yan; Chen, Longxian; Zhang, Chengjun BMC Genomics, Vol. 18, Issue S1 https://doi.org/10.1186/s12864-016-3266-1	journal	January 2017
Trimmomatic: a flexible trimmer for Illumina sequence data Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern Bioinformatics, Vol. 30, Issue 15 https://doi.org/10.1093/bioinformatics/btu170	journal	April 2014
De novo transcriptome characterization and gene expression profiling of the desiccation tolerant moss Bryum argenteum following rehydration Gao, Bei; Zhang, Daoyuan; Li, Xiaoshuang BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-1633-y	journal	January 2015
Revelation of ancestral roles of KNOX genes by a functional analysis of Physcomitrella homologues Singer, S. D.; Ashton, N. W. Plant Cell Reports, Vol. 26, Issue 12 https://doi.org/10.1007/s00299-007-0409-5	journal	August 2007
Class 1 KNOX genes are not involved in shoot development in the moss Physcomitrella patens but do function in sporophyte development Sakakibara, Keiko; Nishiyama, Tomoaki; Deguchi, Hironori Evolution & Development, Vol. 10, Issue 5 https://doi.org/10.1111/j.1525-142X.2008.00271.x	journal	September 2008
Efficient gene targeting in the moss Physcomitrella patens Schaefer, Didier G.; Zryd, Jean-Pierre The Plant Journal, Vol. 11, Issue 6 https://doi.org/10.1046/j.1365-313X.1997.11061195.x	journal	June 1997
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome Zhang, G.; Guo, G.; Hu, X. Genome Research, Vol. 20, Issue 5 https://doi.org/10.1101/gr.100677.109	journal	March 2010
Strigolactones are positive regulators of light-harvesting genes in tomato Mayzlish-Gati, Einav; LekKala, Sivarama P.; Resnick, Nathalie Journal of Experimental Botany, Vol. 61, Issue 11 https://doi.org/10.1093/jxb/erq138	journal	May 2010
COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly Liu, B.; Yuan, J.; Yiu, S. -M. Bioinformatics, Vol. 28, Issue 22 https://doi.org/10.1093/bioinformatics/bts563	journal	October 2012
Genome-Wide Analysis of Heat-Sensitive Alternative Splicing in Physcomitrella patens Chang, Chiung-Yun; Lin, Wen-Dar; Tu, Shih-Long Plant Physiology, Vol. 165, Issue 2 https://doi.org/10.1104/pp.113.230540	journal	April 2014
Catalysts of plant cell wall loosening Cosgrove, Daniel J. F1000Research, Vol. 5 https://doi.org/10.12688/f1000research.7180.1	journal	January 2016
Distinct Roles of Nitrate and Nitrite in Regulation of Expression of the Nitrate Transport Genes in the Moss Physcomitrella patens Tsujimoto, R.; Yamazaki, H.; Maeda, S. -i. Plant and Cell Physiology, Vol. 48, Issue 3 https://doi.org/10.1093/pcp/pcm019	journal	January 2007
Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation Gaidatzis, Dimos; Burger, Lukas; Florescu, Maria Nature Biotechnology, Vol. 33, Issue 7 https://doi.org/10.1038/nbt.3269	journal	June 2015
The chromatin landscape of the moss Physcomitrella patens and its dynamics during development and drought stress Widiez, Thomas; Symeonidi, Aikaterini; Luo, Chongyuan The Plant Journal, Vol. 79, Issue 1 https://doi.org/10.1111/tpj.12542	journal	June 2014
Digital Gene Expression Signatures for Maize Development Eveland, Andrea L.; Satoh-Nagasawa, Namiko; Goldshmidt, Alexander Plant Physiology, Vol. 154, Issue 3 https://doi.org/10.1104/pp.110.159673	journal	September 2010
De Novo Transcriptome Assembly of a Fern, Lygodium japonicum, and a Web Resource Database, Ljtrans DB Aya, Koichiro; Kobayashi, Masaaki; Tanaka, Junmu Plant and Cell Physiology, Vol. 56, Issue 1 https://doi.org/10.1093/pcp/pcu184	journal	December 2014
The nitrogen-potassium intersection: membranes, metabolism, and mechanism: The N-K intersection Coskun, Devrim; Britto, Dev T.; Kronzucker, Herbert J. Plant, Cell & Environment, Vol. 40, Issue 10 https://doi.org/10.1111/pce.12671	journal	January 2016
Genetic Analysis of DEFECTIVE KERNEL1 Loop Function in Three-Dimensional Body Patterning in Physcomitrella patens Demko, V.; Perroud, P. -F.; Johansen, W. PLANT PHYSIOLOGY, Vol. 166, Issue 2 https://doi.org/10.1104/pp.114.243758	journal	September 2014
Strigolactones Inhibit Caulonema Elongation and Cell Division in the Moss Physcomitrella patens Hoffmann, Beate; Proust, Hélène; Belcram, Katia PLoS ONE, Vol. 9, Issue 6 https://doi.org/10.1371/journal.pone.0099206	journal	June 2014
The Induction of Biochemical and Morphological Mutants in the Moss Physcomitrella patens Engel, Paulinus P. American Journal of Botany, Vol. 55, Issue 4 https://doi.org/10.2307/2440573	journal	April 1968
The Induction of Biochemical and Morphological Mutants in the moss Physcomitrella Patens Engel, Paulinus P. American Journal of Botany, Vol. 55, Issue 4 https://doi.org/10.1002/j.1537-2197.1968.tb07397.x	journal	April 1968
Ancestry of KNOX genes revealed by bryophyte (Physcomitrella patens) homologs Champagne, Connie E. M.; Ashton, Neil W. New Phytologist, Vol. 150, Issue 1 https://doi.org/10.1046/j.1469-8137.2001.00076.x	journal	April 2001
The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants Rensing, S. A.; Lang, D.; Zimmer, A. D. Science, Vol. 319, Issue 5859 https://doi.org/10.1126/science.1150646	journal	December 2007
The evolution of hydrophobic cell wall biopolymers: from algae to angiosperms Niklas, Karl J.; Cobb, Edward D.; Matas, Antonio J. Journal of Experimental Botany, Vol. 68, Issue 19 https://doi.org/10.1093/jxb/erx215	journal	June 2017
Strigolactone biosynthesis is evolutionarily conserved, regulated by phosphate starvation and contributes to resistance against phytopathogenic fungi in a moss, Physcomitrella patens Decker, Eva L.; Alder, Adrian; Hunn, Stefan New Phytologist, Vol. 216, Issue 2 https://doi.org/10.1111/nph.14506	journal	March 2017
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data Robinson, M. D.; McCarthy, D. J.; Smyth, G. K. Bioinformatics, Vol. 26, Issue 1 https://doi.org/10.1093/bioinformatics/btp616	journal	November 2009
Rascaf: Improving Genome Assembly with RNA Sequencing Data Song, Li; Shankar, Dhruv S.; Florea, Liliana The Plant Genome, Vol. 9, Issue 3 https://doi.org/10.3835/plantgenome2016.03.0027	journal	January 2016
HTSeq--a Python framework to work with high-throughput sequencing data Anders, S.; Pyl, P. T.; Huber, W. Bioinformatics, Vol. 31, Issue 2 https://doi.org/10.1093/bioinformatics/btu638	journal	September 2014
RNA-Seq Analysis of Sulfur-Deprived Chlamydomonas Cells Reveals Aspects of Acclimation Critical for Cell Survival González-Ballester, David; Casero, David; Cokus, Shawn The Plant Cell, Vol. 22, Issue 6 https://doi.org/10.1105/tpc.109.071167	journal	June 2010
A phenol-enriched cuticle is ancestral to lignin evolution in land plants Renault, Hugues; Alber, Annette; Horst, Nelly A. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms14713	journal	March 2017
Development and genetics in the evolution of land plant body plans Jill Harrison, C. Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 372, Issue 1713 https://doi.org/10.1098/rstb.2015.0490	journal	February 2017
The liverwort Pellia endiviifolia shares microtranscriptomic traits that are common to green algae and land plants Alaba, Sylwia; Piszczalka, Pawel; Pietrykowska, Halina New Phytologist, Vol. 206, Issue 1 https://doi.org/10.1111/nph.13220	journal	December 2014
Distinct phytochrome actions in nonvascular plants revealed by targeted inactivation of phytobilin biosynthesis Chen, Y. -R.; Su, Y. -s.; Tu, S. -L. Proceedings of the National Academy of Sciences, Vol. 109, Issue 21 https://doi.org/10.1073/pnas.1201744109	journal	May 2012
PpASCL, the Physcomitrella patens Anther-Specific Chalcone Synthase-Like Enzyme Implicated in Sporopollenin Biosynthesis, Is Needed for Integrity of the Moss Spore Wall and Spore Viability Daku, Rhys M.; Rabbi, Fazle; Buttigieg, Josef PLOS ONE, Vol. 11, Issue 1 https://doi.org/10.1371/journal.pone.0146817	journal	January 2016
A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data Zhang, Zong Hong; Jhaveri, Dhanisha J.; Marshall, Vikki M. PLoS ONE, Vol. 9, Issue 8 https://doi.org/10.1371/journal.pone.0103207	journal	August 2014
The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution Lang, Daniel; Ullrich, Kristian K.; Murat, Florent The Plant Journal, Vol. 93, Issue 3 https://doi.org/10.1111/tpj.13801	journal	January 2018
Structural modelling and transcriptional responses highlight a clade of PpKAI2-LIKE genes as candidate receptors for strigolactones in Physcomitrella patens Lopez-Obando, Mauricio; Conn, Caitlin E.; Hoffmann, Beate Planta, Vol. 243, Issue 6 https://doi.org/10.1007/s00425-016-2481-y	journal	March 2016
Siliques Are Red1 from Arabidopsis Acts as a Bidirectional Amino Acid Transporter That Is Crucial for the Amino Acid Homeostasis of Siliques Ladwig, Friederike; Stahl, Mark; Ludewig, Uwe Plant Physiology, Vol. 158, Issue 4 https://doi.org/10.1104/pp.111.192583	journal	February 2012
RNA-seq analysis identifies potential modulators of gravity response in spores of Ceratopteris (Parkeriaceae): Evidence for modulation by calcium pumps and apyrase activity Bushart, Thomas J.; Cannon, Ashley E.; ul Haque, Aeraj American Journal of Botany, Vol. 100, Issue 1 https://doi.org/10.3732/ajb.1200292	journal	January 2013
Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens Xiao, Lihong; Wang, Hui; Wan, Ping BMC Plant Biology, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2229-11-177	journal	January 2011
Constitutive auxin response in Physcomitrella reveals complex interactions between Aux/IAA and ARF proteins Lavy, Meirav; Prigge, Michael J.; Tao, Sibo eLife, Vol. 5 https://doi.org/10.7554/eLife.13325	journal	June 2016
Induction of budding on chloronemata and caulonemata of the moss, Physcomitrella patens, using isopentenyladenine Reski, R.; Abel, W. O. Planta, Vol. 165, Issue 3 https://doi.org/10.1007/BF00392232	journal	January 1985
Next Generation Sequencing and Transcriptome Analysis Predicts Biosynthetic Pathway of Sennosides from Senna (Cassia angustifolia Vahl.), a Non-Model Plant with Potent Laxative Properties Rama Reddy, Nagaraja Reddy; Mehta, Rucha Harishbhai; Soni, Palak Harendrabhai PLOS ONE, Vol. 10, Issue 6 https://doi.org/10.1371/journal.pone.0129422	journal	June 2015
Analyses of transcriptome sequences reveal multiple ancient large‐scale duplication events in the ancestor of Sphagnopsida (Bryophyta) Devos, Nicolas; Szövényi, Péter; Weston, David J. New Phytologist, Vol. 211, Issue 1 https://doi.org/10.1111/nph.13887	journal	February 2016
De novo assembly and characterization of the transcriptome in the desiccation-tolerant moss Syntrichia caninervis Gao, Bei; Zhang, Daoyuan; Li, Xiaoshuang BMC Research Notes, Vol. 7, Issue 1 https://doi.org/10.1186/1756-0500-7-490	journal	January 2014
Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens O’Donoghue, Martin-Timothy; Chater, Caspar; Wallace, Simon Journal of Experimental Botany, Vol. 64, Issue 12 https://doi.org/10.1093/jxb/ert190	journal	August 2013
Strigolactones and the control of plant development: lessons from shoot branching Waldie, Tanya; McCulloch, Hayley; Leyser, Ottoline The Plant Journal, Vol. 79, Issue 4 https://doi.org/10.1111/tpj.12488	journal	April 2014
The Transcriptional Response to DNA-Double-Strand Breaks in Physcomitrella patens Kamisugi, Yasuko; Whitaker, John W.; Cuming, Andrew C. PLOS ONE, Vol. 11, Issue 8 https://doi.org/10.1371/journal.pone.0161204	journal	August 2016
The Moss Physcomitrella patens: A Novel Model System for Plant Development and Genomic Studies Cove, D. J.; Perroud, P. -F.; Charron, A. J. Cold Spring Harbor Protocols, Vol. 2009, Issue 2 https://doi.org/10.1101/pdb.emo115	journal	February 2009
Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis Lister, Ryan; O'Malley, Ronan C.; Tonti-Filippini, Julian Cell, Vol. 133, Issue 3 https://doi.org/10.1016/j.cell.2008.03.029	journal	May 2008
Alternate Modes of Photosynthate Transport in the Alternating Generations of Physcomitrella patens Regmi, Kamesh C.; Li, Lin; Gaxiola, Roberto A. Frontiers in Plant Science, Vol. 8 https://doi.org/10.3389/fpls.2017.01956	journal	November 2017
The Sequence Alignment/Map format and SAMtools Li, H.; Handsaker, B.; Wysoker, A. Bioinformatics, Vol. 25, Issue 16 https://doi.org/10.1093/bioinformatics/btp352	journal	June 2009
How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? Schurch, Nicholas J.; Schofield, Pietá; Gierliński, Marek RNA, Vol. 22, Issue 6 https://doi.org/10.1261/rna.053959.115	journal	March 2016
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Love, Michael I.; Huber, Wolfgang; Anders, Simon Genome Biology, Vol. 15, Issue 12 https://doi.org/10.1186/s13059-014-0550-8	journal	December 2014
Day Length and Temperature Strongly Influence Sexual Reproduction and Expression of a Novel MADS-Box Gene in the Moss Physcomitrella patens Hohe, A.; Rensing, S. A.; Mildner, M. Plant Biology, Vol. 4, Issue 5 https://doi.org/10.1055/s-2002-35440	journal	September 2002
PpASCL, a moss ortholog of anther-specific chalcone synthase-like enzymes, is a hydroxyalkylpyrone synthase involved in an evolutionarily conserved sporopollenin biosynthesis pathway Colpitts, Che C.; Kim, Sung Soo; Posehn, Sarah E. New Phytologist, Vol. 192, Issue 4 https://doi.org/10.1111/j.1469-8137.2011.03858.x	journal	August 2011
Feedback-Regulation of Strigolactone Biosynthetic Genes and Strigolactone-Regulated Genes in Arabidopsis Mashiguchi, Kiyoshi; Sasaki, Eriko; Shimada, Yukihisa Bioscience, Biotechnology, and Biochemistry, Vol. 73, Issue 11 https://doi.org/10.1271/bbb.90443	journal	November 2009
How Embryophytic is the Biosynthesis of Phenylpropanoids and their Derivatives in Streptophyte Algae? de Vries, Jan; de Vries, Sophie; Slamovits, Claudio H. Plant and Cell Physiology, Vol. 58, Issue 5 https://doi.org/10.1093/pcp/pcx037	journal	March 2017
Emerging Functions of Nodulin-Like Proteins in Non-Nodulating Plant Species Denancé, Nicolas; Szurek, Boris; Noël, Laurent D. Plant and Cell Physiology, Vol. 55, Issue 3 https://doi.org/10.1093/pcp/pct198	journal	January 2014
Role of the Extensin Superfamily in Primary Cell Wall Architecture Lamport, Derek T. A.; Kieliszewski, Marcia J.; Chen, Yuning Plant Physiology, Vol. 156, Issue 1 https://doi.org/10.1104/pp.110.169011	journal	March 2011

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

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