ArticleG3 (Bethesda, Md.)2016
ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress.
Article in G3 (Bethesda, Md.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Uncovering the role of the PPR protein PHOTOSYSTEM ONE BIOGENESIS FACTOR6 in splicing chloroplast group II introns.Journal of integrative plant biology · 2026Article
- A poly(A)-independent PacBio strategy for organellar transcriptome profiling.Plant physiology · 2026Article
- Library Preparation Biases Plant Virome Detection: Poly(A) mRNA Enrichment vs. rRNA Depletion in Pepper and Garlic.International journal of molecular sciences · 2026Article
- The GT1 domain of RNase J ensures RNA quality control through dsRNA binding in Arabidopsis plastids.Nucleic acids research · 2026Article
- Why "Where" Matters as Much as "How Much": Single-Cell and Spatial Transcriptomics in Plants.International journal of molecular sciences · 2025Review
- Comparative genomics uncovers organellar genome structural divergence in Caryophyllales and reveals widespread non-coding transcription in Bougainvillea glabra organellar.BMC genomics · 2025Article
- Molecular Networks Governing Plant Responses to Heat and Cold Stress.Plants (Basel, Switzerland) · 2025Review
- The chloroplast RNA-binding protein CP29A supportsProceedings of the National Academy of Sciences of the United States of America · 2025Article
- A prion-like domain is required for phase separation and chloroplast RNA processing during cold acclimation in Arabidopsis.The Plant cell · 2024Article
- Uncovering the photosystem I assembly pathway in land plants.Nature plants · 2024Article
- Response of the organellar and nuclear (post)transcriptomes of Arabidopsis to drought.Frontiers in plant science · 2023Article
- RNA Editing in Chloroplast: Advancements and Opportunities.Current issues in molecular biology · 2022Review
- Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Context-Dependent Mutation Dynamics, Not Selection, Explains the Codon Usage Bias of Most Angiosperm Chloroplast Genes.Journal of molecular evolution · 2022Article
- Does IR-loss promote plastome structural variation and sequence evolution?Frontiers in plant science · 2022Article
- CAF Proteins Help SOT1 Regulate the Stability of ChloroplastInternational journal of molecular sciences · 2021Article
- Full Length Transcriptome Highlights the Coordination of Plastid Transcript Processing.International journal of molecular sciences · 2021Article
- OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security.Plants (Basel, Switzerland) · 2021Review
- Noncoding RNA: An Insight into Chloroplast and Mitochondrial Gene Expressions.Life (Basel, Switzerland) · 2021Review
- Plant Ribonuclease J: An Essential Player in Maintaining Chloroplast RNA Quality Control for Gene Expression.Plants (Basel, Switzerland) · 2020Review
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4 authors.
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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. ChloroSeq thus represents a unique method for streamlining RNA-Seq data interpretation of the chloroplast transcriptome and its regulators.
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