ReviewMolecular genetics and genomics : MGG2015
The application of RNA-seq to the comprehensive analysis of plant mitochondrial transcriptomes.
Review in Molecular genetics and genomics : MGG, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
22 citing papers in PubMed.
- Codon usage bias and selective constraints in Gentianales mitogenomes.BMC genomics · 2026Article
- Systematic identification of reference genes for qRT-PCR ofFrontiers in plant science · 2023Article
- Evolution of mitochondrial RNA editing in extant gymnosperms.The Plant journal : for cell and molecular biology · 2022Article
- Article
- Differentially Expressed Genes Shared by Two Distinct Cytoplasmic Male Sterility (CMS) Types ofCells · 2020Article
- Shared up-regulation and contrasting down-regulation of gene expression distinguish desiccation-tolerant from intolerant green algae.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Article
- Mitochondrial genome and transcriptome analysis of five alloplasmic male-sterile lines in Brassica juncea.BMC genomics · 2019Article
- High Level of Conservation of Mitochondrial RNA Editing Sites Among FourG3 (Bethesda, Md.) · 2019Article
- TheRNA (New York, N.Y.) · 2018Article
- Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0.BMC bioinformatics · 2018Article
- Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria.Plant molecular biology · 2018Article
- Toxicity ofPeerJ · 2018Article
- The Role of Non-Coding RNAs in Cytoplasmic Male Sterility in Flowering Plants.International journal of molecular sciences · 2017Review
- Non-coding RNA may be associated with cytoplasmic male sterility in Silene vulgaris.Journal of experimental botany · 2017Article
- Stable Internal Reference Genes for Normalizing Real-Time Quantitative PCR inFrontiers in plant science · 2017Article
- Article
- ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress.G3 (Bethesda, Md.) · 2016Article
- Selection and Validation of Appropriate Reference Genes for Quantitative Real-Time PCR Analysis of Gene Expression in Lycoris aurea.Frontiers in plant science · 2016Article
- High transcript abundance, RNA editing, and small RNAs in intergenic regions within the massive mitochondrial genome of the angiosperm Silene noctiflora.BMC genomics · 2015Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We review current studies of plant mitochondrial transcriptomes performed by RNA-seq, highlighting methodological challenges unique to plant mitochondria. We propose ways to improve read mapping accuracy and sensitivity such as modifying a reference genome at RNA editing sites, using splicing- and ambiguity-competent aligners, and masking chloroplast- or nucleus-derived sequences. We also outline modified RNA-seq methods permitting more accurate detection and quantification of partially edited sites and the identification of transcription start sites on a genome-wide scale. The application of RNA-seq goes beyond genome-wide determination of transcript levels and RNA maturation events, and emerges as an elegant resource for the comprehensive identification of editing, splicing, and transcription start sites. Thus, improved RNA-seq methods customized for plant mitochondria hold tremendous potential for advancing our understanding of plant mitochondrial evolution and cyto-nuclear interactions in a broad array of plant species.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.