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Grünberger F, Ferreira-Cerca S, Grohmann D. Nanopore sequencing of RNA and cDNA molecules in Escherichia coli. RNA (NEW YORK, N.Y.) 2022; 28:400-417. [PMID: 34906997 PMCID: PMC8848933 DOI: 10.1261/rna.078937.121] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/29/2021] [Indexed: 05/09/2023]
Abstract
High-throughput sequencing dramatically changed our view of transcriptome architectures and allowed for ground-breaking discoveries in RNA biology. Recently, sequencing of full-length transcripts based on the single-molecule sequencing platform from Oxford Nanopore Technologies (ONT) was introduced and is widely used to sequence eukaryotic and viral RNAs. However, experimental approaches implementing this technique for prokaryotic transcriptomes remain scarce. Here, we present an experimental and bioinformatic workflow for ONT RNA-seq in the bacterial model organism Escherichia coli, which can be applied to any microorganism. Our study highlights critical steps of library preparation and computational analysis and compares the results to gold standards in the field. Furthermore, we comprehensively evaluate the applicability and advantages of different ONT-based RNA sequencing protocols, including direct RNA, direct cDNA, and PCR-cDNA. We find that (PCR)-cDNA-seq offers improved yield and accuracy compared to direct RNA sequencing. Notably, (PCR)-cDNA-seq is suitable for quantitative measurements and can be readily used for simultaneous and accurate detection of transcript 5' and 3' boundaries, analysis of transcriptional units, and transcriptional heterogeneity. In summary, based on our comprehensive study, we show nanopore RNA-seq to be a ready-to-use tool allowing rapid, cost-effective, and accurate annotation of multiple transcriptomic features. Thereby nanopore RNA-seq holds the potential to become a valuable alternative method for RNA analysis in prokaryotes.
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Affiliation(s)
- Felix Grünberger
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Biochemistry Centre Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
- Institute for Biochemistry, Genetics and Microbiology, Regensburg Center for Biochemistry, Biochemistry III, University of Regensburg, 93053 Regensburg, Germany
| | - Dina Grohmann
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Biochemistry Centre Regensburg, University of Regensburg, 93053 Regensburg, Germany
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
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2
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Singh D, Yi SV. On the origin and evolution of SARS-CoV-2. Exp Mol Med 2021; 53:537-547. [PMID: 33864026 PMCID: PMC8050477 DOI: 10.1038/s12276-021-00604-z] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/06/2021] [Accepted: 03/10/2021] [Indexed: 12/27/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the ongoing global outbreak of a coronavirus disease (herein referred to as COVID-19). Other viruses in the same phylogenetic group have been responsible for previous regional outbreaks, including SARS and MERS. SARS-CoV-2 has a zoonotic origin, similar to the causative viruses of these previous outbreaks. The repetitive introduction of animal viruses into human populations resulting in disease outbreaks suggests that similar future epidemics are inevitable. Therefore, understanding the molecular origin and ongoing evolution of SARS-CoV-2 will provide critical insights for preparing for and preventing future outbreaks. A key feature of SARS-CoV-2 is its propensity for genetic recombination across host species boundaries. Consequently, the genome of SARS-CoV-2 harbors signatures of multiple recombination events, likely encompassing multiple species and broad geographic regions. Other regions of the SARS-CoV-2 genome show the impact of purifying selection. The spike (S) protein of SARS-CoV-2, which enables the virus to enter host cells, exhibits signatures of both purifying selection and ancestral recombination events, leading to an effective S protein capable of infecting human and many other mammalian cells. The global spread and explosive growth of the SARS-CoV-2 population (within human hosts) has contributed additional mutational variability into this genome, increasing opportunities for future recombination.
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Affiliation(s)
- Devika Singh
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Soojin V Yi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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Jain M, Olsen HE, Akeson M, Abu-Shumays R. Adaptation of Human Ribosomal RNA for Nanopore Sequencing of Canonical and Modified Nucleotides. Methods Mol Biol 2021; 2298:53-74. [PMID: 34085238 DOI: 10.1007/978-1-0716-1374-0_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Historically, RNA has been sequenced as cDNA copies derived from reverse transcription of cellular RNA followed by PCR amplification. Recently, RNA sequencing using nanopores has emerged as an alternative. Using this technology, individual cellular RNA strands are read directly as they are driven through nanoscale pores by an applied voltage. The speed of translocation is regulated by a helicase that is loaded onto each RNA strand by an adapter that also facilitates capture by the nanopore electric field. Here we describe a technique for adapting human ribosomal RNA subunits for nanopore sequencing. Using this strategy, a single Oxford Nanopore MinION run delivered 470,907 sequence reads of which 396,048 aligned to ribosomal RNA, with 28S, 18S, 5.8S, and 5S coverage of 6053, 369,472, 16,058, and 4465 reads, respectively. Example alignments that reveal putative nucleotide modifications are provided.
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Affiliation(s)
- Miten Jain
- Biomolecular Engineering Department and Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Hugh E Olsen
- Biomolecular Engineering Department and Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Mark Akeson
- Biomolecular Engineering Department and Genomics Institute, University of California, Santa Cruz, CA, USA.
| | - Robin Abu-Shumays
- Biomolecular Engineering Department and Genomics Institute, University of California, Santa Cruz, CA, USA.
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Xu L, Seki M. Recent advances in the detection of base modifications using the Nanopore sequencer. J Hum Genet 2020; 65:25-33. [PMID: 31602005 PMCID: PMC7087776 DOI: 10.1038/s10038-019-0679-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/22/2019] [Accepted: 09/26/2019] [Indexed: 12/29/2022]
Abstract
DNA and RNA modifications have important functions, including the regulation of gene expression. Existing methods based on short-read sequencing for the detection of modifications show difficulty in determining the modification patterns of single chromosomes or an entire transcript sequence. Furthermore, the kinds of modifications for which detection methods are available are very limited. The Nanopore sequencer is a single-molecule, long-read sequencer that can directly sequence RNA as well as DNA. Moreover, the Nanopore sequencer detects modifications on long DNA and RNA molecules. In this review, we mainly focus on base modification detection in the DNA and RNA of mammals using the Nanopore sequencer. We summarize current studies of modifications using the Nanopore sequencer, detection tools using statistical tests or machine learning, and applications of this technology, such as analyses of open chromatin, DNA replication, and RNA metabolism.
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Affiliation(s)
- Liu Xu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
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Rapid, Unbiased PRRSV Strain Detection Using MinION Direct RNA Sequencing and Bioinformatics Tools. Viruses 2019; 11:v11121132. [PMID: 31817886 PMCID: PMC6950593 DOI: 10.3390/v11121132] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
Prompt detection and effective control of porcine reproductive and respiratory syndrome virus (PRRSV) during outbreaks is important given its immense adverse impact on the swine industry. However, the diagnostic process can be challenging due to the high genetic diversity and high mutation rate of PRRSV. A diagnostic method that can provide more detailed genetic information about pathogens is urgently needed. In this study, we evaluated the ability of Oxford Nanopore MinION direct RNA sequencing to generate a PRRSV whole genome sequence and detect and discriminate virus at the strain-level. A nearly full length PRRSV genome was successfully generated from raw sequence reads, achieving an accuracy of 96% after consensus genome generation. Direct RNA sequencing reliably detected the PRRSV strain present with an accuracy of 99.9% using as few as 5 raw sequencing reads and successfully differentiated multiple co-infecting strains present in a sample. In addition, PRRSV strain information was obtained from clinical samples containing 104 to 106 viral copies or more within 6 hours of sequencing. Overall, direct viral RNA sequencing followed by bioinformatic analysis proves to be a promising approach for identification of the viral strain or strains involved in clinical infections, allowing for more precise prevention and control strategies during PRRSV outbreaks.
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Krause M, Niazi AM, Labun K, Torres Cleuren YN, Müller FS, Valen E. tailfindr: alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing. RNA (NEW YORK, N.Y.) 2019; 25:1229-1241. [PMID: 31266821 PMCID: PMC6800471 DOI: 10.1261/rna.071332.119] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/25/2019] [Indexed: 05/02/2023]
Abstract
Polyadenylation at the 3'-end is a major regulator of messenger RNA and its length is known to affect nuclear export, stability, and translation, among others. Only recently have strategies emerged that allow for genome-wide poly(A) length assessment. These methods identify genes connected to poly(A) tail measurements indirectly by short-read alignment to genetic 3'-ends. Concurrently, Oxford Nanopore Technologies (ONT) established full-length isoform-specific RNA sequencing containing the entire poly(A) tail. However, assessing poly(A) length through base-calling has so far not been possible due to the inability to resolve long homopolymeric stretches in ONT sequencing. Here we present tailfindr, an R package to estimate poly(A) tail length on ONT long-read sequencing data. tailfindr operates on unaligned, base-called data. It measures poly(A) tail length from both native RNA and DNA sequencing, which makes poly(A) tail studies by full-length cDNA approaches possible for the first time. We assess tailfindr's performance across different poly(A) lengths, demonstrating that tailfindr is a versatile tool providing poly(A) tail estimates across a wide range of sequencing conditions.
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Affiliation(s)
- Maximilian Krause
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
| | - Adnan M Niazi
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
| | - Kornel Labun
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
| | - Yamila N Torres Cleuren
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
| | - Florian S Müller
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
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Cao Y, Li J, Chu X, Liu H, Liu W, Liu D. Nanopore sequencing: a rapid solution for infectious disease epidemics. SCIENCE CHINA. LIFE SCIENCES 2019; 62:1101-1103. [PMID: 31372817 PMCID: PMC7089317 DOI: 10.1007/s11427-019-9596-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 07/13/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Ying Cao
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- Research Group of Computer Virology, Center for Bacteria and Virus Resources and Application, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jing Li
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Chu
- Bureau of Major R&D Programs, Chinese Academy of Sciences, Beijing, 100864, China
| | - Haizhou Liu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- Research Group of Computer Virology, Center for Bacteria and Virus Resources and Application, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Wenjun Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Di Liu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
- Research Group of Computer Virology, Center for Bacteria and Virus Resources and Application, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Warwick-Dugdale J, Solonenko N, Moore K, Chittick L, Gregory AC, Allen MJ, Sullivan MB, Temperton B. Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands. PeerJ 2019; 7:e6800. [PMID: 31086738 PMCID: PMC6487183 DOI: 10.7717/peerj.6800] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/14/2019] [Indexed: 01/18/2023] Open
Abstract
Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in host culturing and a lack of reference genomes and 'universal' gene markers to facilitate community surveys. Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution, but their assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. Such features also challenge assembly across genomic islands containing niche-defining genes that drive ecological speciation. These populations and features may be successfully captured by single-virus genomics and fosmid-based approaches, at least in abundant taxa, but at considerable cost and technical expertise. Here we established a low-cost, low-input, high throughput alternative sequencing and informatics workflow to improve viral metagenomic assemblies using short-read and long-read technology. The 'VirION' (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. We then then applied VirION to the first metagenome from a natural viral community from the Western English Channel. In comparison to a short-read only approach, VirION: (i) increased number and completeness of assembled viral genomes; (ii) captured abundant, highly microdiverse virus populations, and (iii) captured more and longer genomic islands. Together, these findings suggest that VirION provides a high throughput and cost-effective alternative to fosmid and single-virus genomic approaches to more comprehensively explore viral communities in nature.
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Affiliation(s)
- Joanna Warwick-Dugdale
- Plymouth Marine Laboratory, Plymouth, Devon, United Kingdom
- School of Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Natalie Solonenko
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Karen Moore
- School of Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Lauren Chittick
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Ann C. Gregory
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Michael J. Allen
- Plymouth Marine Laboratory, Plymouth, Devon, United Kingdom
- School of Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States of America
| | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, Devon, United Kingdom
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