scholarly journals Time-course profiling of bovine alphaherpesvirus 1.1 transcriptome using multiplatform sequencing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Norbert Moldován ◽  
Gábor Torma ◽  
Gábor Gulyás ◽  
Ákos Hornyák ◽  
Zoltán Zádori ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Time Course ◽  
Splice Variants ◽  
Library Preparation ◽  
Transcription Start ◽  
Viral Mrnas ◽  
Transcript Isoforms ◽  
Oxford Nanopore ◽  
Long Read ◽  
Oxford Nanopore Technologies

AbstractLong-read sequencing (LRS) has become a standard approach for transcriptome analysis in recent years. Bovine alphaherpesvirus 1 (BoHV-1) is an important pathogen of cattle worldwide. This study reports the profiling of the dynamic lytic transcriptome of BoHV-1 using two long-read sequencing (LRS) techniques, the Oxford Nanopore Technologies MinION, and the LoopSeq synthetic LRS methods, using multiple library preparation protocols. In this work, we annotated viral mRNAs and non-coding transcripts, and a large number of transcript isoforms, including transcription start and end sites, as well as splice variants of BoHV-1. Our analysis demonstrated an extremely complex pattern of transcriptional overlaps.

scholarly journals Time-course Profiling of Bovine Herpesvirus Type 1 and Host Cell Transcriptomes using Multiplatform Sequencing

2020 ◽  
Author(s):  
Norbert Moldován ◽  
Zoltán Maróti ◽  
Gábor Torma ◽  
Gábor Gulyás ◽  
Ákos Hornyák ◽  
...  
Keyword(s):  
Host Cell ◽  
Time Course ◽  
Splice Variants ◽  
Bovine Herpesvirus ◽  
Viral Mrnas ◽  
Herpesvirus Type ◽  
Long Read ◽  
Bovine Herpesvirus Type 1 ◽  
The Impact

SUMMARYLong-read sequencing (LRS) has become a standard approach for transcriptome analysis in recent years. This technology is also used for the identification and annotation of genes of various organisms, including viruses. Bovine herpesvirus type 1 (BoHV-1) is an important pathogen of cattle worldwide. However, the transcriptome of this virus is still largely unannotated. This study reports the profiling of the dynamic lytic transcriptome of BoHV-1 using two long-read sequencing (LRS) techniques, the Oxford Nanopore Technology (ONT) MinION, and the Illumina LoopSeq synthetic LRS methods, using multiple library preparation protocols. In this work, we annotated viral mRNAs and non-coding transcripts, and a large number of transcript isoforms, including transcription start and end sites, as well as splice variants of BoHV-1. Very long polycistronic and complex viral transcripts were also detected. Our analysis demonstrated an extremely complex pattern of transcriptional overlaps formed by transcriptional read-throughs or overlapping the 5’-untranslated regions of divergently-oriented transcripts. The impact of the viral infection on the host cell transcriptome was also assessed. Our results demonstrate that genes associated with antiviral response as well as viral transcription and translation are upregulated.

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

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Balázs Kakuk ◽  
Dóra Tombácz ◽  
Zsolt Balázs ◽  
Norbert Moldován ◽  
Zsolt Csabai ◽  
...  
Keyword(s):  
Single Molecule ◽  
Splice Variants ◽  
Splice Isoforms ◽  
Short Read Sequencing ◽  
Novel Transcript ◽  
Novel Approach ◽  
Oxford Nanopore ◽  
Long Read ◽  
Polycistronic Transcripts ◽  
Oxford Nanopore Technologies

AbstractLong-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.

scholarly journals Combined Nanopore and Single-Molecule Real-Time Sequencing Survey of Human Betaherpesvirus 5 Transcriptome

2021 ◽  
Author(s):  
Balazs Kakuk ◽  
Dora Tombacz ◽  
Zsolt Balazs ◽  
Norbert Moldovan ◽  
Zsolt Csabai ◽  
...  
Keyword(s):  
Single Molecule ◽  
Splice Variants ◽  
Splice Isoforms ◽  
Short Read Sequencing ◽  
Novel Transcript ◽  
Novel Approach ◽  
Oxford Nanopore ◽  
Long Read ◽  
Polycistronic Transcripts ◽  
Oxford Nanopore Technologies

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.

Dual Isoform Sequencing Reveals a Multifaceted Transcriptional Architecture of a Prototype Baculovirus

2021 ◽  
Author(s):  
Gábor Torma ◽  
Dóra Tombácz ◽  
Norbert Moldován ◽  
Ádám Fülöp ◽  
István Prazsák ◽  
...  
Keyword(s):  
Protein Coding ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Oxford Nanopore ◽  
The Pacific ◽  
Viral Genes ◽  
Long Read ◽  
Oxford Nanopore Technologies ◽  
Overlapping Transcripts

Abstract In this study, we used two long-read sequencing (LRS) techniques, Sequel from the Pacific Biosciences and MinION from Oxford Nanopore Technologies, for the transcriptional characterization of a prototype baculovirus, Autographacalifornica multiple nucleopolyhedrovirus. LRS is able to read full-length RNA molecules, and thereby to distinguish between transcript isoforms, mono- and polycistronic RNAs, and overlapping transcripts. Altogether, we detected 875 transcripts, of which 759 are novel and 116 have been annotated previously. These RNA molecules include 41 novel putative protein coding transcript (each containing 5’-truncated in-frame ORFs), 14 monocistronic transcripts, 99 multicistronic RNAs, 101 non-coding RNA, and 504 length isoforms. We also detected RNA methylation in 12 viral genes and RNA hyper-editing in the longer 5’-UTR transcript isoform of ORF 19 gene.

scholarly journals Microbial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing

2020 ◽  
Author(s):  
Michael Liem ◽  
Tonny Regensburg-Tuïnk ◽  
Christiaan Henkel ◽  
Hans Jansen ◽  
Herman Spaink
Keyword(s):  
Microbial Diversity ◽  
Environmental Samples ◽  
Sea Water ◽  
Flow Cells ◽  
Oxford Nanopore ◽  
Challenging Tasks ◽  
Long Read ◽  
Close Relatives ◽  
Oxford Nanopore Technologies

Abstract Objective: Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diversity in seawater from multiple locations. We compared the microbial species diversity of retrieved environmental samples from two different locations and time points.Results: With only three ONT flow cells we were able to identify thousands of organisms, including bacteriophages, from which a large part at species level. It was possible to assemble genomes from environmental samples with Flye. In several cases this resulted in >1 Mbp contigs and in the particular case of a Thioglobus singularis species it even produced a near complete genome. k-mer analysis reveals that a large part of the data represents species of which close relatives have not yet been deposited to the database. These results show that our approach is suitable for scalable genomic investigations such as monitoring oceanic biodiversity and provides a new platform for education in biodiversity.

scholarly journals Swan: a library for the analysis and visualization of long-read transcriptomes

2020 ◽  
Author(s):  
Fairlie Reese ◽  
Ali Mortazavi
Keyword(s):  
Rna Sequencing ◽  
Cell Lines ◽  
Intron Retention ◽  
Exon Skipping ◽  
Differentially Expressed ◽  
Transcript Isoforms ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Long Read

Abstract Motivation Long-read RNA-sequencing technologies such as PacBio and Oxford Nanopore have discovered an explosion of new transcript isoforms that are difficult to visually analyze using currently available tools. We introduce the Swan Python library, which is designed to analyze and visualize transcript models. Results Swan finds 4909 differentially expressed transcripts between cell lines HepG2 and HFFc6, including 279 that are differentially expressed even though the parent gene is not. Additionally, Swan discovers 285 reproducible exon skipping and 47 intron retention events not recorded in the GENCODE v29 annotation. Availability and implementation The Swan library for Python 3 is available on PyPi at https://pypi.org/project/swan-vis/ and on GitHub at https://github.com/mortazavilab/swan_vis.

scholarly journals Plasmidome analysis of carbapenem-resistant Enterobacteriaceae isolated in Vietnam

2020 ◽  
Author(s):  
Aki Hirabayashi ◽  
Koji Yahara ◽  
Satomi Mitsuhashi ◽  
So Nakagawa ◽  
Tadashi Imanishi ◽  
...  
Keyword(s):  
Carbapenem Resistance ◽  
Genomic Epidemiology ◽  
Carbapenem Resistant ◽  
Oxford Nanopore ◽  
Carbapenemase Gene ◽  
Long Read ◽  
Severe Infections ◽  
Oxford Nanopore Technologies ◽  
Carbapenem Resistant Enterobacteriaceae

Carbapenem-resistant Enterobacteriaceae (CRE) represent a serious threat to public health due to limited management of severe infections and high mortality. The rate of resistance of Enterobacteriaceae isolates to major antimicrobials, including carbapenems, is much higher in Vietnam than in Western countries, but the reasons remain unknown due to the lack of genomic epidemiology research. A previous study suggested that carbapenem resistance genes, such as the carbapenemase gene bla NDM-1 , spread via plasmids among Enterobacteriaceae in Vietnam. In this study, we performed detection and molecular characterization of bla NDM-1 -carrying plasmids in CRE isolated in Vietnam, and identified several possible cases of horizontal transfer of plasmids both within and among species of bacteria. Twenty-five carbapenem-resistant isolates from Enterobacteriaceae clinically isolated in a reference medical institution in Hanoi were sequenced on Illumina short-read sequencers, and 12 isolates harboring bla NDM-1 were sequenced on an Oxford Nanopore Technologies long-read sequencer to obtain complete plasmid sequences. Most of the plasmids co-carried genes conferring resistance to clinically relevant antimicrobials, including third-generation cephalosporins, aminoglycosides, and fluoroquinolones, in addition to bla NDM-1 , leading to multidrug resistance of their bacterial hosts. These results provide insight into the genetic basis of CRE in Vietnam, and could help control nosocomial infections.

scholarly journals Microbial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing

2020 ◽  
Author(s):  
Michael Liem ◽  
A.J.G. Regensburg-Tuïnk ◽  
C.V. Henkel ◽  
H.P. Spaink
Keyword(s):  
Microbial Diversity ◽  
Environmental Samples ◽  
Sea Water ◽  
Flow Cells ◽  
Oxford Nanopore ◽  
Challenging Tasks ◽  
Long Read ◽  
Close Relatives ◽  
Oxford Nanopore Technologies

Abstract Objective Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diversity in seawater from multiple locations. We compared the microbial species diversity of retrieved environmental samples from two different locations and time points. Results With only three ONT flow cells we were able to identify thousands of organisms, including bacteriophages, from which a large part at species level. It was possible to assemble genomes from environmental samples with Flye. In several cases this resulted in >1 Mbp contigs and in the particular case of a Thioglobus singularis species it even produced a near complete genome. k-mer analysis reveals that a large part of the data represents species of which close relatives have not yet been deposited to the database. These results show that our approach is suitable for scalable genomic investigations such as monitoring oceanic biodiversity and provides a new platform for education in biodiversity.

scholarly journals Updated Genome Sequence for the Probiotic Bacterium Bifidobacterium animalis subsp. lactis BB-12

2021 ◽  
Vol 10 (27) ◽  
Author(s):  
Kristian Jensen ◽  
Kosai Al-Nakeeb ◽  
Anna Koza ◽  
Ahmad A. Zeidan
Keyword(s):  
Genome Sequence ◽  
Probiotic Bacterium ◽  
Content Type ◽  
Short Read Sequencing ◽  
Bifidobacterium Animalis ◽  
Oxford Nanopore ◽  
Hybrid Genome ◽  
Long Read ◽  
Sequencing Platforms ◽  
Oxford Nanopore Technologies

The genome of Bifidobacterium animalis subsp. lactis BB-12 was sequenced using Oxford Nanopore Technologies long-read and Illumina short-read sequencing platforms. A hybrid genome assembly approach was used to construct an updated complete genome sequence for BB-12 containing 1,944,152 bp, with a G+C content of 60.5% and 1,615 genes.

Sign in / Sign up

Export Citation Format

Share Document