Dual isoform sequencing reveals complex transcriptomic and epitranscriptomic landscapes of a prototype baculovirus
Abstract In this study, two long-read sequencing (LRS) techniques, MinION from Oxford Nanopore Technologies and Sequel from the Pacific Biosciences, were used for the transcriptional characterization of a prototype baculovirus, Autographa californica multiple nucleopolyhedrovirus. LRS is able to rea...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2022-01-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-05457-8 |
| _version_ | 1797865126218432512 |
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| author | Gábor Torma Dóra Tombácz Norbert Moldován Ádám Fülöp István Prazsák Zsolt Csabai Michael Snyder Zsolt Boldogkői |
| author_facet | Gábor Torma Dóra Tombácz Norbert Moldován Ádám Fülöp István Prazsák Zsolt Csabai Michael Snyder Zsolt Boldogkői |
| author_sort | Gábor Torma |
| collection | DOAJ |
| description | Abstract In this study, two long-read sequencing (LRS) techniques, MinION from Oxford Nanopore Technologies and Sequel from the Pacific Biosciences, were used for the transcriptional characterization of a prototype baculovirus, Autographa californica multiple nucleopolyhedrovirus. LRS is able to read full-length RNA molecules, and thereby distinguish between transcript isoforms, mono- and polycistronic RNAs, and overlapping transcripts. Altogether, we detected 875 transcript species, of which 759 were novel and 116 were annotated previously. These RNA molecules include 41 novel putative protein coding transcripts [each containing 5′-truncated in-frame open reading frames (ORFs), 14 monocistronic transcripts, 99 polygenic RNAs, 101 non-coding RNAs, and 504 untranslated region isoforms. This work also identified novel replication origin-associated transcripts, upstream ORFs, cis-regulatory sequences and poly(A) sites. We also detected RNA methylation in 99 viral genes and RNA hyper-editing in the longer 5′-UTR transcript isoform of the canonical ORF 19 transcript. |
| first_indexed | 2024-04-09T23:02:55Z |
| format | Article |
| id | doaj.art-74d365d3689644c38060e9411fe37614 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-09T23:02:55Z |
| publishDate | 2022-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-74d365d3689644c38060e9411fe376142023-03-22T10:50:45ZengNature PortfolioScientific Reports2045-23222022-01-0112111610.1038/s41598-022-05457-8Dual isoform sequencing reveals complex transcriptomic and epitranscriptomic landscapes of a prototype baculovirusGábor Torma0Dóra Tombácz1Norbert Moldován2Ádám Fülöp3István Prazsák4Zsolt Csabai5Michael Snyder6Zsolt Boldogkői7Department of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Genetics, School of Medicine, Stanford UniversityDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedAbstract In this study, two long-read sequencing (LRS) techniques, MinION from Oxford Nanopore Technologies and Sequel from the Pacific Biosciences, were used for the transcriptional characterization of a prototype baculovirus, Autographa californica multiple nucleopolyhedrovirus. LRS is able to read full-length RNA molecules, and thereby distinguish between transcript isoforms, mono- and polycistronic RNAs, and overlapping transcripts. Altogether, we detected 875 transcript species, of which 759 were novel and 116 were annotated previously. These RNA molecules include 41 novel putative protein coding transcripts [each containing 5′-truncated in-frame open reading frames (ORFs), 14 monocistronic transcripts, 99 polygenic RNAs, 101 non-coding RNAs, and 504 untranslated region isoforms. This work also identified novel replication origin-associated transcripts, upstream ORFs, cis-regulatory sequences and poly(A) sites. We also detected RNA methylation in 99 viral genes and RNA hyper-editing in the longer 5′-UTR transcript isoform of the canonical ORF 19 transcript.https://doi.org/10.1038/s41598-022-05457-8 |
| spellingShingle | Gábor Torma Dóra Tombácz Norbert Moldován Ádám Fülöp István Prazsák Zsolt Csabai Michael Snyder Zsolt Boldogkői Dual isoform sequencing reveals complex transcriptomic and epitranscriptomic landscapes of a prototype baculovirus Scientific Reports |
| title | Dual isoform sequencing reveals complex transcriptomic and epitranscriptomic landscapes of a prototype baculovirus |
| title_full | Dual isoform sequencing reveals complex transcriptomic and epitranscriptomic landscapes of a prototype baculovirus |
| title_fullStr | Dual isoform sequencing reveals complex transcriptomic and epitranscriptomic landscapes of a prototype baculovirus |
| title_full_unstemmed | Dual isoform sequencing reveals complex transcriptomic and epitranscriptomic landscapes of a prototype baculovirus |
| title_short | Dual isoform sequencing reveals complex transcriptomic and epitranscriptomic landscapes of a prototype baculovirus |
| title_sort | dual isoform sequencing reveals complex transcriptomic and epitranscriptomic landscapes of a prototype baculovirus |
| url | https://doi.org/10.1038/s41598-022-05457-8 |
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