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

Castandet, Benoît; Hotto, Amber M.; Strickler, Susan R.; Stern, David B.

doi:10.1534/g3.116.030783

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

Journal Article · Wed Jul 06 00:00:00 EDT 2016 · G3

DOI:https://doi.org/10.1534/g3.116.030783· OSTI ID:1361698

Castandet, Benoît ^[1]; Hotto, Amber M. ^[1];

^[1];

^[1]

Boyce Thompson Inst., Ithaca, NY (United States)

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. ChloroSeq thus represents a unique method for streamlining RNA-Seq data interpretation of the chloroplast transcriptome and its regulators.

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Research Organization:: Boyce Thompson Inst., Ithaca, NY (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: FG02-90ER20015; FG02-10ER20015

OSTI ID:: 1361698

Alternate ID(s):: OSTI ID: 1393425

Journal Information:: G3, Vol. 6, Issue 9; ISSN 2160-1836

Publisher:: Genetics Society of AmericaCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 42 works

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Related Subjects

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