ArticleInternational journal of molecular sciences2020
Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in
Article in International journal of molecular sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed, 48 citations in OpenAlex.
- High-throughput single-molecule long-read RNA sequencing analysis of tissue-specific genes and isoforms in lettuce (Lactuca sativa L.).Communications biology · 2024Article
- Single molecule real-time sequencing data sets of Hypericum perforatum L. plantlets and cell suspension cultures.Scientific data · 2024Article
- Heterologous biosynthesis of medicarpin using engineeredSynthetic and systems biotechnology · 2023Article
- Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs.International journal of molecular sciences · 2023Review
- Molecular Mechanism Underlying thePlants (Basel, Switzerland) · 2023Article
- Linking plant functional genes to rhizosphere microbes: a review.Plant biotechnology journal · 2023Review
- De novo full length transcriptome analysis of a naturally caffeine-free tea plant reveals specificity in secondary metabolic regulation.Scientific reports · 2023Article
- Full-Length RNA Sequencing Provides Insights into Goldfish Evolution under Artificial Selection.International journal of molecular sciences · 2023Article
- Design, execution, and interpretation of plant RNA-seq analyses.Frontiers in plant science · 2023Review
- Integrative analysis of Iso-Seq and RNA-seq reveals dynamic changes of alternative promoter, alternative splicing and alternative polyadenylation during Angiotensin II-induced senescence in rat primary aortic endothelial cells.Frontiers in genetics · 2023Article
- De novo full length transcriptome analysis and gene expression profiling to identify genes involved in phenylethanol glycosides biosynthesis in Cistanche tubulosa.BMC genomics · 2022Article
- Full-length transcriptome analysis of maize root tips reveals the molecular mechanism of cold stress during the seedling stage.BMC plant biology · 2022Article
- A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis.Genome biology · 2022Article
- Nanopore long-read RNAseq reveals transcriptional variations in citrus species.Frontiers in plant science · 2022Article
- Genomics and transcriptomics to protect rice (Frontiers in plant science · 2022Review
- High-quality reference transcriptome construction improves RNA-seq quantification inFrontiers in genetics · 2022Article
- Transcript Complexity and New Insights of Restorer Line in CMS-D8 Cotton Through Full-Length Transcriptomic Analysis.Frontiers in plant science · 2022Article
- Full-Length Transcriptome Sequencing Reveals Tissue-Specific Gene Expression Profile of Mangrove ClamFrontiers in physiology · 2022Article
- Functional Genomics for Plant Breeding.International journal of molecular sciences · 2021Article
- Methods for Analyzing Alternative Splicing and Its Regulation in Plants: From Gene-Specific Approaches to Transcriptome-Wide Studies.Physiologia plantarumReview
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Authors and funding
10 authors at 5 institutions in 3 countries.
Funding
Abstract
The wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding. However, identification of candidate genes from RNA-Seq studies is hampered by the lack of high-quality genome assemblies for the most stress tolerant cultivars. A more targeted solution is the reconstruction of transcriptomes to provide templates to map RNA-seq reads. Here, we sequenced transcriptomes of ten rice cultivars of three subspecies on the PacBio Sequel platform. RNA was isolated from different organs of plants grown under control and abiotic stress conditions in different environments. Reconstructed de novo reference transcriptomes resulted in 37,500 to 54,600 plant-specific high-quality isoforms per cultivar. Isoforms were collapsed to reduce sequence redundancy and evaluated, e.g., for protein completeness (BUSCO). About 40% of all identified transcripts were novel isoforms compared to the Nipponbare reference transcriptome. For the drought/heat tolerant
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