Long-read RNA sequencing analysis of the lytic human cytomegalovirus transcriptome

Balázs, Zsolt

doi:10.14232/phd.10113

Cited by 2 publications

(2 citation statements)

References 117 publications

(138 reference statements)

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“…Reverse transcription (RT) and PCR are inevitable cDNA library preparation steps for both NGS and thirdgeneration sequencing technologies. As discussed in our previous works 13,40,41 , both can lead to artifacts through template switching and false priming, which need to be considered during the analysis of novel TSSs and TESs. The direct sequencing of ribonucleotides with the ONT nanopore technology allows for the detection of modi ed and edited bases through the comparison of altered and canonical signals 37,42 , but this approach implies a known location of the modi cation or editing.…”

Section: Introductionmentioning

confidence: 99%

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

Torma

Tombácz

Moldován

et al. 2021

Preprint

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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.

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Section: Introductionmentioning

confidence: 99%

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

Torma

Tombácz

Moldován

et al. 2021

Preprint

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“…The PacBio Sequel™ system (PacBio, Menlo Park, CA, USA) can produce an average read length of more than 10 kb. This protocol is also called Isoform Sequencing (hereafter referred to as Iso-Seq), because by producing longer reads, the PacBio Iso-Seq technology eliminates the need for assembly, providing direct evidence for transcript isoforms of each gene [16,17]. This considerable advantage of Iso-Seq technology expands its utility to de ne alternatively spliced forms and some non-coding RNAs that can vary with cell-type, developmental stage, or stress [18].…”

Section: Introductionmentioning

confidence: 99%

Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms

Wang

et al. 2020

Preprint

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Background Miscanthus sinensis Andersson is a perennial grass that exhibits remarkable lignocellulose characteristics for sustainable bioenergy production. However, knowledge of the genetic resources of this species is relatively limited, which significantly hampers further work on its interesting biology and genetic improvement. Results In this study, through analyzing the transcriptome of mixed samples of leaves and stems using the latest PacBio Iso-Seq sequencing technology combined with Illumina HiSeq, we report the first full-length transcriptome dataset of M. sinensis with a total of 58.21 Gbp clean data. An average of 15.75 Gbp clean reads of each sample were obtained from PacBio Iso-Seq system, which doubled the data size (6.68 Gbp) obtained from the Illumina HiSeq platform. The integrated analyses of PacBio- and Illumina-based transcriptomic data uncovered 408,801 non-redundant transcripts with an average length of 1,685 bp, representing about 60% of the total number of predicted Miscanthus genes. Of those, 189,406 transcripts were commonly identified by both methods, 169,149 transcripts with an average length of 619 bp were uniquely identified by Illumina HiSeq, and 51,246 transcripts with an average length of 2,535 bp were uniquely identified by PacBio Iso-SEq. When comparing our data with genomes of four Andropogoneae species, M. sinensis showed the closest relationship with sugarcane with up to 93% mapping ratios, followed by sorghum with up to 80% mapping ratios, indicating a high conservation of orthologs in these three genomes. Furthermore, 306,228 transcripts were successfully annotated against public databases including cell wall related genes and transcript factor families, thus providing many new insights into gene functions. The PacBio Iso-Seq data also helped identify 3,898 alternative splicing events and 2,963 annotated AS isoforms within 10 function categories. Conclusions Taken together, the present study provides a rich data set of full-length transcripts that greatly enriches our understanding of M. sinensis genomic resources, thus facilitating further genetic improvement and molecular studies of the Miscanthus species.

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Long-read RNA sequencing analysis of the lytic human cytomegalovirus transcriptome

Cited by 2 publications

References 117 publications

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

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

Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms

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