ArticleScientific reports2021
Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 23 citations in OpenAlex.
- NanoPrePro: a fully equipped, fast, and memory-efficient preprocessor for nanopore transcriptomic sequencing.Briefings in bioinformatics · 2026Article
- Two-way transcriptome approach for the identification of common gene targets across four insect orders and its validation in Oxycarenus laetus.Scientific reports · 2025Article
- DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.Genome biology · 2025Article
- A case for absolute gene expression estimates in microbiome studies using metatranscriptomics.The ISME journal · 2025Article
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- AdvancingPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Merging short and stranded long reads improves transcript assembly.PLoS computational biology · 2023Article
- Hemin availability induces coordinated DNA methylation and gene expression changes inmSystems · 2023Article
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- An Introduction to Nanopore Sequencing: Past, Present, and Future Considerations.Micromachines · 2023Review
- Current challenges and best practices for cell-free long RNA biomarker discovery.Biomarker research · 2022Review
- Improved Nanopore full-length cDNA sequencing by PCR-suppression.Frontiers in genetics · 2022Article
- Direct Full-Length RNA Sequencing Reveals an Important Role of Epigenetics During Sexual Reversal in Chinese Soft-Shelled Turtle.Frontiers in cell and developmental biology · 2022Article
- Transcriptome Analysis for Identification of Genes Related to Growth and Development, Digestion and Detoxification, Olfaction in the Litchi Stink BugFrontiers in physiology · 2021Article
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The olive fruit fly, Bactrocera oleae, is the most important pest for the olive fruit but lacks adequate transcriptomic characterization that could aid in molecular control approaches. We apply nanopore long-read RNA-seq with internal RNA standards allowing absolute transcript quantification to analyze transcription dynamics during early embryo development for the first time in this organism. Sequencing on the MinION platform generated over 31 million reads. Over 50% of the expressed genes had at least one read covering its entire length validating our full-length approach. We generated a de novo transcriptome assembly and identified 1768 new genes and a total of 79,810 isoforms; a fourfold increase in transcriptome diversity compared to the current NCBI predicted transcriptome. Absolute transcript quantification per embryo allowed an insight into the dramatic re-organization of maternal transcripts. We further identified Zelda as a possible regulator of early zygotic genome activation in B. oleae and provide further insights into the maternal-to-zygotic transition. These data show the utility of long-read RNA in improving characterization of non-model organisms that lack a fully annotated genome, provide potential targets for sterile insect technic approaches, and provide the first insight into the transcriptome landscape of the developing olive fruit fly embryo.
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