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Title: ChloroSeq, an optimized chloroplast RNA-Seq bioinformatic pipeline, reveals remodeling of the organellar transcriptome under heat stress

Abstract

Although RNA-Seq has revolutionized transcript analysis, organellar transcriptomes are rarely assessed even when present in published datasets. Here, we describe the development and application of a rapid and convenient method, ChloroSeq, to delineate qualitative and quantitative features of chloroplast RNA metabolism from strand-specific RNA-Seq datasets, including processing, editing, splicing, and relative transcript abundance. The use of a single experiment to analyze systematically chloroplast transcript maturation and abundance is of particular interest due to frequent pleiotropic effects observed in mutants that affect chloroplast gene expression and/or photosynthesis. To illustrate its utility, ChloroSeq was applied to published RNA-Seq datasets derived from Arabidopsis thaliana grown under control and abiotic stress conditions, where the organellar transcriptome had not been examined. The most appreciable effects were found for heat stress, which induces a global reduction in splicing and editing efficiency, and leads to increased abundance of chloroplast transcripts, including genic, intergenic, and antisense transcripts. Moreover, by concomitantly analyzing nuclear transcripts that encode chloroplast gene expression regulators from the same libraries, we demonstrate the possibility of achieving a holistic understanding of the nucleus-organelle system. In conclusion, ChloroSeq thus represents a unique method for streamlining RNA-Seq data interpretation of the chloroplast transcriptome and its regulators.

Authors:
 [1];  [1]; ORCiD logo [1]; ORCiD logo [1]
  1. Boyce Thompson Inst., Ithaca, NY (United States)
Publication Date:
Research Org.:
Boyce Thompson Inst., Ithaca, NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1361698
Alternate Identifier(s):
OSTI ID: 1393425
Grant/Contract Number:  
FG02-90ER20015; FG02-10ER20015
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
G3
Additional Journal Information:
Journal Volume: 6; Journal Issue: 9; Journal ID: ISSN 2160-1836
Publisher:
Genetics Society of America
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Arabidopsis thaliana; chloroplast; RNA-Seq; heat stress; transcriptome; noncoding RNAs; introns; RNA splicing; RNA editing; RNA-SEQ

Citation Formats

Castandet, Benoît, Hotto, Amber M., Strickler, Susan R., and Stern, David B. ChloroSeq, an optimized chloroplast RNA-Seq bioinformatic pipeline, reveals remodeling of the organellar transcriptome under heat stress. United States: N. p., 2016. Web. doi:10.1534/g3.116.030783.
Castandet, Benoît, Hotto, Amber M., Strickler, Susan R., & Stern, David B. ChloroSeq, an optimized chloroplast RNA-Seq bioinformatic pipeline, reveals remodeling of the organellar transcriptome under heat stress. United States. doi:10.1534/g3.116.030783.
Castandet, Benoît, Hotto, Amber M., Strickler, Susan R., and Stern, David B. Wed . "ChloroSeq, an optimized chloroplast RNA-Seq bioinformatic pipeline, reveals remodeling of the organellar transcriptome under heat stress". United States. doi:10.1534/g3.116.030783. https://www.osti.gov/servlets/purl/1361698.
@article{osti_1361698,
title = {ChloroSeq, an optimized chloroplast RNA-Seq bioinformatic pipeline, reveals remodeling of the organellar transcriptome under heat stress},
author = {Castandet, Benoît and Hotto, Amber M. and Strickler, Susan R. and Stern, David B.},
abstractNote = {Although RNA-Seq has revolutionized transcript analysis, organellar transcriptomes are rarely assessed even when present in published datasets. Here, we describe the development and application of a rapid and convenient method, ChloroSeq, to delineate qualitative and quantitative features of chloroplast RNA metabolism from strand-specific RNA-Seq datasets, including processing, editing, splicing, and relative transcript abundance. The use of a single experiment to analyze systematically chloroplast transcript maturation and abundance is of particular interest due to frequent pleiotropic effects observed in mutants that affect chloroplast gene expression and/or photosynthesis. To illustrate its utility, ChloroSeq was applied to published RNA-Seq datasets derived from Arabidopsis thaliana grown under control and abiotic stress conditions, where the organellar transcriptome had not been examined. The most appreciable effects were found for heat stress, which induces a global reduction in splicing and editing efficiency, and leads to increased abundance of chloroplast transcripts, including genic, intergenic, and antisense transcripts. Moreover, by concomitantly analyzing nuclear transcripts that encode chloroplast gene expression regulators from the same libraries, we demonstrate the possibility of achieving a holistic understanding of the nucleus-organelle system. In conclusion, ChloroSeq thus represents a unique method for streamlining RNA-Seq data interpretation of the chloroplast transcriptome and its regulators.},
doi = {10.1534/g3.116.030783},
journal = {G3},
number = 9,
volume = 6,
place = {United States},
year = {Wed Jul 06 00:00:00 EDT 2016},
month = {Wed Jul 06 00:00:00 EDT 2016}
}

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