Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome

Cui, Jiawen; Shen, Nan; Lu, Zhaogeng; Xu, Guolu; Wang, Yuyao; Jin, Biao

doi:10.1186/s13007-020-00629-x

Cited by 88 publications

(77 citation statements)

References 30 publications

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“…Additionally, sample preparation for ONT long-read sequencing does not require PCR amplification, thus reducing possible bias, although with the consequence of reduced sequencing throughput [ 1 , 2 , 7 ]. Moreover, previous work comparing Illumina and ONT quantification of gene expression assessed the existence of a high level of correlation between the quantification of transcripts for both technologies [ 8 , 9 , 10 , 11 ], confirming that results obtained with ONT RNA-seq approaches are comparable to those obtained with short-read sequencing platforms. All of these characteristics make these two long-read sequencing technologies—ONT and PacBio—very attractive and suitable options for isoform and fusion transcript discovery and de novo transcriptomic analysis [ 12 ].…”

Section: Introductionsupporting

confidence: 69%

Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon

Udaondo

Sittikankaew

Uengwetwanit

et al. 2021

Life

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With the advantages that long-read sequencing platforms such as Pacific Biosciences (Menlo Park, CA, USA) (PacBio) and Oxford Nanopore Technologies (Oxford, UK) (ONT) can offer, various research fields such as genomics and transcriptomics can exploit their benefits. Selecting an appropriate sequencing platform is undoubtedly crucial for the success of the research outcome, thus there is a need to compare these long-read sequencing platforms and evaluate them for specific research questions. This study aims to compare the performance of PacBio and ONT platforms for transcriptomic analysis by utilizing transcriptome data from three different tissues (hepatopancreas, intestine, and gonads) of the juvenile black tiger shrimp, Penaeus monodon. We compared three important features: (i) main characteristics of the sequencing libraries and their alignment with the reference genome, (ii) transcript assembly features and isoform identification, and (iii) correlation of the quantification of gene expression levels for both platforms. Our analyses suggest that read-length bias and differences in sequencing throughput are highly influential factors when using long reads in transcriptome studies. These comparisons can provide a guideline when designing a transcriptome study utilizing these two long-read sequencing technologies.

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Section: Introductionsupporting

confidence: 69%

Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon

Udaondo

Sittikankaew

Uengwetwanit

et al. 2021

Life

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“…It can read from the beginning without assembly, and obtain more transcript information, which is more conducive to comprehensive analysis. Increasing studies utilized ONT sequencers for transcriptome sequencing, such as Arabidopsis thaliana ( Cui et al, 2020 ) and Saccharomyces cerevisiae ( Jenjaroenpun et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Nanopore-based full-length transcriptome sequencing of Muscovy duck (Cairina moschata) ovary

Bai

et al. 2021

Poultry Science

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Unlike mammals, studies on mechanisms that regulate waterfowl ovulation have been rarely reported. To advance our understanding of the ovulation differences in Muscovy duck, we utilized the Oxford Nanopore Technologies ( ONT ) to generate transcriptome data from 3 groups of female duck ovaries with ovulation differences (i.e., preovulation [ PO] , consecutive ovulation [ CO ], and inconsecutive ovulation [ IO ]). In this study, the full-length transcriptome data qualitative analysis showed that a total of 24,504 nonredundant full-length transcripts were generated, 19,060 new transcripts were discovered and 14,848 novel transcripts were successfully annotated. For the quantitative analysis, differentially expressed genes ( DEGs ) between the 3 groups were identified and functional properties were characterized. CTNNB1, IGF1, FOXO3, HSPA2, PTEN and SMC4 may be potential hub genes that regulate ovulation. Adhesion-related pathway, mTOR pathway, TGF-β signaling pathway and FoxO signaling pathway have been considered as important pathways that affect follicular development and ovulation. These results provide a more complete data source of full-length transcriptome for the further study of gene expression and genetics in Muscovy duck. The hub genes and potential mechanisms that affect the ovulation of Muscovy duck have been screened out to provide a scientific basis for breeding work to improve the reproduction performance of Muscovy duck.

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“…Oxford Nanopore Technologies (ONT), a new third-generation sequencing technology, is a cost-effective and powerful method. One recent study has shown that this technology generates better quality raw data and estimates transcript levels more accurately than PacBio technology ( Cui et al, 2020 ). ONT has been broadly applied in whole genome sequencing but has rarely been used in full-length transcriptome sequencing.…”

Section: Introductionmentioning

confidence: 99%

Comparative Analyses of Full-Length Transcriptomes Reveal Gnetum luofuense Stem Developmental Dynamics

et al. 2021

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Genus Gnetum, of which the majority species are pantropical liana, have broad industrial uses including for string, nets, and paper production. Although numerous studies have investigated anatomical structures during stem development, the underlying molecular mechanisms that regulate this developmental trajectory in Gnetum species remain poorly understood. A total of 12 full-length transcriptomes were generated from four stem developmental stages of an arborescent representative of this genus, Gnetum luofuense, using Oxford Nanopore Technologies. The results of this analysis reveal a total of 24,151 alternative splicing (AS) and 134,391 alternative polyadenylation events. A remarkably dynamic pattern of AS events, especially in the case of intron retentions, was found across the four developmental stages while no dynamic pattern was found among transcript numbers with varied poly(A) sites. A total of 728 long non-coding RNAs were also detected; the number of cis-regulated target genes dramatically increased while no changes were found among trans-regulated target genes. In addition, a K-means clustering analysis of all full-length transcripts revealed that primary growth is associated with carbohydrate metabolism and fungi defense, while secondary growth is closely linked with photosynthesis, nitrogen transportation, and leaf ontogenesis. The use of weighted gene co-expression network analysis as well as differentially expressed transcripts reveals that bHLH, GRF, and MYB-related transcription factors are involved in primary growth, while AP2/ERF, MYB, NAC, PLAZ, and bZIP participate in G. luofuense stem secondary growth. The results of this study provide further evidence that Nanopore sequencing technology provides a cost-effective method for generating full-length transcriptome data as well as for investigating seed plant organ development.

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Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome

Cited by 88 publications

References 30 publications

Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon

Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon

Nanopore-based full-length transcriptome sequencing of Muscovy duck (Cairina moschata) ovary

Comparative Analyses of Full-Length Transcriptomes Reveal Gnetum luofuense Stem Developmental Dynamics

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