Long-Read Sequencing Revealed an Extensive Transcript Complexity in Herpesviruses

Tombácz, Dóra; Balázs, Zsolt; Csabai, Zsolt; Snyder, M; Boldogkői, Zsolt

doi:10.3389/fgene.2018.00259

Cited by 21 publications

(14 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…5'-truncated transcripts with in-frame ORFs It has recently been shown in several viruses that the transcripts containing 5'-truncated in-frame ORFs within larger canonical ORFs -of which they share stop codons -are much more common than it has previously been thought [21,22,34]. Here we demonstrate the same phenomenon in ASFV transcripts ( Fig.2a).…”

Section: Novel Putative Protein-coding Genessupporting

confidence: 79%

Combined short and long-read sequencing reveals a complex transcriptomic architecture of African swine fever virus

Torma

Tombácz

Csabai

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

African swine fever virus (ASFV) is a large DNA virus belonging to the Asfarviridae family. Despite its agricultural importance, little is known about the fundamental molecular mechanisms of this pathogen. Understanding of genetic regulation provides new insights into the virus pathogenicity, which can help prevent epidemics. Short-read sequencing (SRS) is able to produce a huge amount of high-precision sequencing reads for transcriptomic profiling, but it is inefficient for the comprehensive annotation of transcriptomes. Long-read sequencing (LRS) is able to overcome some of the limitations of SRS, but they also have drawbacks, such as low-coverage and high error rate. The limitations of the two approaches can be surmounted by the combined use of these techniques. In this study, we used Illumina SRS and Oxford Nanopore Technologies LRS platforms with multiple library preparation methods (amplified and direct cDNA sequencings and native RNA sequencing) for constructing the transcriptomic atlas of ASFV. This work identified a large number of novel genes, transcripts and RNA isoforms, and annotated the precise termini of previously described RNA molecules. In contrast to the current view that the ASFV transcripts are monocistronic, we detected a significant extent of polycistronism. A multifaceted meshwork of transcriptional overlaps is also discovered.

show abstract

Section: Novel Putative Protein-coding Genessupporting

confidence: 79%

Combined short and long-read sequencing reveals a complex transcriptomic architecture of African swine fever virus

Torma

Tombácz

Csabai

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…We also identified several fusion genes with relatively long introns spanning the gene boundaries. Additionally, a large number of low-abundance transcript isoforms, including splice and length variants were identified in this and also in other studies 14 . Whether these molecules have functional significance, or they are merely the result of transcriptional noise remains to be ascertained.…”

Section: Resultssupporting

confidence: 72%

Demand for Multiplatform and Meta-analytic Approaches in Transcriptome Profiling

Tombácz

Torma

Gulyás

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

In a recent article, Depledge and colleagues reported a study of the herpes simplex virus type 1 (HSV-1) transcriptome using direct RNA sequencing (dRNA-Seq) on nanopore arrays. The authors provided a useful dataset on full-length viral and host RNA molecules. In this study, we reanalyzed the published dataset and compared it with data generated by our group and others. Our comparative study clearly demonstrated the need for multiplatform and meta-analytic approaches for transcriptome profiling to obtain reliable results.

show abstract

“…Third generation sequencing platforms may have a direct impact on the RNA-seq field. Long read technologies perform better in the determination of unknown transcript abundance in single celled organisms (Tombácz et al, 2018), full-length splice isoforms with alternative splicing (Xu et al, 2017) and co-transcription of genes in a polycistronic fashion (Tardaguila et al, 2018). It is clear that there are obvious advantages to long read sequencing in reducing the difficult reassembly and loss of contextual information associated with short read sequencing.…”

Section: Metatranscriptomicsmentioning

confidence: 99%

The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach

2020

View full text Add to dashboard Cite

Lactic Acid Bacteria (LAB) have long been recognized as having a significant impact ranging from commercial to health domains. A vast amount of research has been carried out on these microbes, deciphering many of the pathways and components responsible for these desirable effects. However, a large proportion of this functional information has been derived from a reductionist approach working with pure culture strains. This provides limited insight into understanding the impact of LAB within intricate systems such as the gut microbiome or multi strain starter cultures. Whole genome sequencing of strains and shotgun metagenomics of entire systems are powerful techniques that are currently widely used to decipher function in microbes, but they also have their limitations. An available genome or metagenome can provide an image of what a strain or microbiome, respectively, is potentially capable of and the functions that they may carry out. A top-down, multi-omics approach has the power to resolve the functional potential of an ecosystem into an image of what is being expressed, translated and produced. With this image, it is possible to see the real functions that members of a system are performing and allow more accurate and impactful predictions of the effects of these microorganisms. This review will discuss how technological advances have the potential to increase the yield of information from genomics, transcriptomics, proteomics and metabolomics. The potential for integrated omics to resolve the role of LAB in complex systems will also be assessed. Finally, the current software approaches for managing these omics data sets will be discussed.

show abstract

Long-Read Sequencing Revealed an Extensive Transcript Complexity in Herpesviruses

Cited by 21 publications

References 51 publications

Combined short and long-read sequencing reveals a complex transcriptomic architecture of African swine fever virus

Combined short and long-read sequencing reveals a complex transcriptomic architecture of African swine fever virus

Demand for Multiplatform and Meta-analytic Approaches in Transcriptome Profiling

The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach

Contact Info

Product

Resources

About