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Filichkin SA, Hamilton M, Dharmawardhana PD, Singh SK, Sullivan C, Ben-Hur A, Reddy ASN, Jaiswal P. Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching. Front Plant Sci 2018; 9:5. [PMID: 29483921 PMCID: PMC5816337 DOI: 10.3389/fpls.2018.00005] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/03/2018] [Indexed: 05/19/2023]
Abstract
Abiotic stresses affect plant physiology, development, growth, and alter pre-mRNA splicing. Western poplar is a model woody tree and a potential bioenergy feedstock. To investigate the extent of stress-regulated alternative splicing (AS), we conducted an in-depth survey of leaf, root, and stem xylem transcriptomes under drought, salt, or temperature stress. Analysis of approximately one billion of genome-aligned RNA-Seq reads from tissue- or stress-specific libraries revealed over fifteen millions of novel splice junctions. Transcript models supported by both RNA-Seq and single molecule isoform sequencing (Iso-Seq) data revealed a broad array of novel stress- and/or tissue-specific isoforms. Analysis of Iso-Seq data also resulted in the discovery of 15,087 novel transcribed regions of which 164 show AS. Our findings demonstrate that abiotic stresses profoundly perturb transcript isoform profiles and trigger widespread intron retention (IR) events. Stress treatments often increased or decreased retention of specific introns - a phenomenon described here as differential intron retention (DIR). Many differentially retained introns were regulated in a stress- and/or tissue-specific manner. A subset of transcripts harboring super stress-responsive DIR events showed persisting fluctuations in the degree of IR across all treatments and tissue types. To investigate coordinated dynamics of intron-containing transcripts in the study we quantified absolute copy number of isoforms of two conserved transcription factors (TFs) using Droplet Digital PCR. This case study suggests that stress treatments can be associated with coordinated switches in relative ratios between fully spliced and intron-retaining isoforms and may play a role in adjusting transcriptome to abiotic stresses.
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Affiliation(s)
- Sergei A. Filichkin
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Michael Hamilton
- Department of Computer Science, Colorado State University, Fort Collins, CO, United States
| | | | - Sunil K. Singh
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Christopher Sullivan
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
| | - Asa Ben-Hur
- Department of Computer Science, Colorado State University, Fort Collins, CO, United States
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- *Correspondence: Pankaj Jaiswal,
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Naithani S, Preece J, D'Eustachio P, Gupta P, Amarasinghe V, Dharmawardhana PD, Wu G, Fabregat A, Elser JL, Weiser J, Keays M, Fuentes AMP, Petryszak R, Stein LD, Ware D, Jaiswal P. Plant Reactome: a resource for plant pathways and comparative analysis. Nucleic Acids Res 2016; 45:D1029-D1039. [PMID: 27799469 PMCID: PMC5210633 DOI: 10.1093/nar/gkw932] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/27/2016] [Indexed: 12/18/2022] Open
Abstract
Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX.
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Affiliation(s)
- Sushma Naithani
- 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Justin Preece
- 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Peter D'Eustachio
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Parul Gupta
- 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Vindhya Amarasinghe
- 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Palitha D Dharmawardhana
- 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Guanming Wu
- Ontario Institute of Cancer Research, Toronto, ON M5G 0A3, Canada.,Oregon Health & Science University, Portland, OR 97239, USA
| | - Antonio Fabregat
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | - Justin L Elser
- 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Joel Weiser
- Ontario Institute of Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Maria Keays
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | | | - Robert Petryszak
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | - Lincoln D Stein
- Ontario Institute of Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,United States Department of Agriculture - Agriculture Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Pankaj Jaiswal
- 2082 Cordley Hall, Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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