Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest

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 quantificatio...

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Autores principales:	Anthony Bayega, Spyros Oikonomopoulos, Maria-Eleni Gregoriou, Konstantina T. Tsoumani, Antonis Giakountis, Yu Chang Wang, Kostas D. Mathiopoulos, Jiannis Ragoussis
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6c207f6e60fd436084be6381858ad281
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spelling	oai:doaj.org-article:6c207f6e60fd436084be6381858ad2812021-12-02T14:28:00ZNanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest10.1038/s41598-021-86753-72045-2322https://doaj.org/article/6c207f6e60fd436084be6381858ad2812021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-86753-7https://doaj.org/toc/2045-2322Abstract 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.Anthony BayegaSpyros OikonomopoulosMaria-Eleni GregoriouKonstantina T. TsoumaniAntonis GiakountisYu Chang WangKostas D. MathiopoulosJiannis RagoussisNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Anthony Bayega Spyros Oikonomopoulos Maria-Eleni Gregoriou Konstantina T. Tsoumani Antonis Giakountis Yu Chang Wang Kostas D. Mathiopoulos Jiannis Ragoussis Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest
description	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.
format	article
author	Anthony Bayega Spyros Oikonomopoulos Maria-Eleni Gregoriou Konstantina T. Tsoumani Antonis Giakountis Yu Chang Wang Kostas D. Mathiopoulos Jiannis Ragoussis
author_facet	Anthony Bayega Spyros Oikonomopoulos Maria-Eleni Gregoriou Konstantina T. Tsoumani Antonis Giakountis Yu Chang Wang Kostas D. Mathiopoulos Jiannis Ragoussis
author_sort	Anthony Bayega
title	Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest
title_short	Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest
title_full	Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest
title_fullStr	Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest
title_full_unstemmed	Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest
title_sort	nanopore long-read rna-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/6c207f6e60fd436084be6381858ad281
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Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest

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