Combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome

Abstract Long-read sequencing (LRS), a powerful novel approach, is able to read full-length transcripts and confers a major advantage over the earlier gold standard short-read sequencing in the efficiency of identifying for example polycistronic transcripts and transcript isoforms, including transcr...

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Autores principales:	Balázs Kakuk, Dóra Tombácz, Zsolt Balázs, Norbert Moldován, Zsolt Csabai, Gábor Torma, Klára Megyeri, Michael Snyder, Zsolt Boldogkői
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e5ae7a377ae74350a2bdba4034307c60
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spelling	oai:doaj.org-article:e5ae7a377ae74350a2bdba4034307c602021-12-02T18:30:51ZCombined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome10.1038/s41598-021-93593-y2045-2322https://doaj.org/article/e5ae7a377ae74350a2bdba4034307c602021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-93593-yhttps://doaj.org/toc/2045-2322Abstract Long-read sequencing (LRS), a powerful novel approach, is able to read full-length transcripts and confers a major advantage over the earlier gold standard short-read sequencing in the efficiency of identifying for example polycistronic transcripts and transcript isoforms, including transcript length- and splice variants. In this work, we profile the human cytomegalovirus transcriptome using two third-generation LRS platforms: the Sequel from Pacific BioSciences, and MinION from Oxford Nanopore Technologies. We carried out both cDNA and direct RNA sequencing, and applied the LoRTIA software, developed in our laboratory, for the transcript annotations. This study identified a large number of novel transcript variants, including splice isoforms and transcript start and end site isoforms, as well as putative mRNAs with truncated in-frame ORFs (located within the larger ORFs of the canonical mRNAs), which potentially encode N-terminally truncated polypeptides. Our work also disclosed a highly complex meshwork of transcriptional read-throughs and overlaps.Balázs KakukDóra TombáczZsolt BalázsNorbert MoldovánZsolt CsabaiGábor TormaKlára MegyeriMichael SnyderZsolt BoldogkőiNature 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 Balázs Kakuk Dóra Tombácz Zsolt Balázs Norbert Moldován Zsolt Csabai Gábor Torma Klára Megyeri Michael Snyder Zsolt Boldogkői Combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome
description	Abstract Long-read sequencing (LRS), a powerful novel approach, is able to read full-length transcripts and confers a major advantage over the earlier gold standard short-read sequencing in the efficiency of identifying for example polycistronic transcripts and transcript isoforms, including transcript length- and splice variants. In this work, we profile the human cytomegalovirus transcriptome using two third-generation LRS platforms: the Sequel from Pacific BioSciences, and MinION from Oxford Nanopore Technologies. We carried out both cDNA and direct RNA sequencing, and applied the LoRTIA software, developed in our laboratory, for the transcript annotations. This study identified a large number of novel transcript variants, including splice isoforms and transcript start and end site isoforms, as well as putative mRNAs with truncated in-frame ORFs (located within the larger ORFs of the canonical mRNAs), which potentially encode N-terminally truncated polypeptides. Our work also disclosed a highly complex meshwork of transcriptional read-throughs and overlaps.
format	article
author	Balázs Kakuk Dóra Tombácz Zsolt Balázs Norbert Moldován Zsolt Csabai Gábor Torma Klára Megyeri Michael Snyder Zsolt Boldogkői
author_facet	Balázs Kakuk Dóra Tombácz Zsolt Balázs Norbert Moldován Zsolt Csabai Gábor Torma Klára Megyeri Michael Snyder Zsolt Boldogkői
author_sort	Balázs Kakuk
title	Combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome
title_short	Combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome
title_full	Combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome
title_fullStr	Combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome
title_full_unstemmed	Combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome
title_sort	combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/e5ae7a377ae74350a2bdba4034307c60
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Combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome

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