Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing

Zhao, Liangzhen; Zhang, Hangxiao; Kohnen, Markus V.; Prasad, Kasavajhala V.  S.  K.; Gu, Lianfeng; Reddy, Anireddy S.  N.

doi:10.3389/fgene.2019.00253

Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing

Journal Article · Thu Mar 21 04:00:00 EDT 2019 · Frontiers in Genetics

DOI:https://doi.org/10.3389/fgene.2019.00253· OSTI ID:1611512

Zhao, Liangzhen ^[1]; Zhang, Hangxiao ^[2]; Kohnen, Markus V. ^[2]; Prasad, Kasavajhala V. S. K. ^[3]; Gu, Lianfeng ^[2]; Reddy, Anireddy S. N. ^[3]

Fujian Agricultural and Forestry Univ., Fuzhou (China); DOE/OSTI
Fujian Agricultural and Forestry Univ., Fuzhou (China)
Colorado State Univ., Fort Collins, CO (United States)

Nanopore sequencing from Oxford Nanopore Technologies (ONT) and Pacific BioSciences (PacBio) single-molecule real-time (SMRT) long-read isoform sequencing (Iso-Seq) are revolutionizing the way transcriptomes are analyzed. These methods offer many advantages over most widely used high-throughput short-read RNA sequencing (RNA-Seq) approaches and allow a comprehensive analysis of transcriptomes in identifying full-length splice isoforms and several other post-transcriptional events. In addition, direct RNA-Seq provides valuable information about RNA modifications, which are lost during the PCR amplification step in other methods. Here, we present a comprehensive summary of important applications of these technologies in plants, including identification of complex alternative splicing (AS), full-length splice variants, fusion transcripts, and alternative polyadenylation (APA) events. Furthermore, we discuss the impact of the newly developed nanopore direct RNA-Seq in advancing epitranscriptome research in plants. Additionally, we summarize computational tools for identifying and quantifying full-length isoforms and other co/post-transcriptional events and discussed some of the limitations with these methods. Sequencing of transcriptomes using these new single-molecule long-read methods will unravel many aspects of transcriptome complexity in unprecedented ways as compared to previous short-read sequencing approaches. Analysis of plant transcriptomes with these new powerful methods that require minimum sample processing is likely to become the norm and is expected to uncover novel co/post-transcriptional gene regulatory mechanisms that control biological outcomes during plant development and in response to various stresses.

View Accepted Manuscript (DOE)

Research Organization:: Colorado State Univ., Fort Collins, CO (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: SC0010733

OSTI ID:: 1611512

Journal Information:: Frontiers in Genetics, Journal Name: Frontiers in Genetics Vol. 10; ISSN 1664-8021

Publisher:: FrontiersCopyright Statement

Country of Publication:: United States

Language:: English

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Full-length transcriptome sequences and splice variants obtained by a combination of sequencing platforms applied to different root tissues of Salvia miltiorrhiza and tanshinone biosynthesis Xu, Zhichao; Peters, Reuben J.; Weirather, Jason The Plant Journal, Vol. 82, Issue 6 https://doi.org/10.1111/tpj.12865	journal	May 2015
Diversity of Sea Star-Associated Densoviruses and Transcribed Endogenous Viral Elements of Densovirus Origin Jackson, Elliot W.; Wilhelm, Roland C.; Johnson, Mitchell R. Journal of Virology, Vol. 95, Issue 1 https://doi.org/10.1128/jvi.01594-20	journal	December 2020
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Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis Weirather, Jason L.; de Cesare, Mariateresa; Wang, Yunhao F1000Research, Vol. 6 https://doi.org/10.12688/f1000research.10571.2	journal	January 2017
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Additional file 10 of PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response Liu, Xiaojie; Li, Xiaoshuang; Wen, Xuejing figshare https://doi.org/10.6084/m9.figshare.13578831.v1	dataset	January 2021
Additional file 11 of PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response Liu, Xiaojie; Li, Xiaoshuang; Wen, Xuejing figshare https://doi.org/10.6084/m9.figshare.13578834.v1	image	January 2021
Additional file 12 of PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response Liu, Xiaojie; Li, Xiaoshuang; Wen, Xuejing figshare https://doi.org/10.6084/m9.figshare.13578837	image	January 2021
Additional file 13 of PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response Liu, Xiaojie; Li, Xiaoshuang; Wen, Xuejing figshare https://doi.org/10.6084/m9.figshare.13578840	image	January 2021
Additional file 14 of PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response Liu, Xiaojie; Li, Xiaoshuang; Wen, Xuejing figshare https://doi.org/10.6084/m9.figshare.13578843	dataset	January 2021
Additional file 15 of PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response Liu, Xiaojie; Li, Xiaoshuang; Wen, Xuejing figshare https://doi.org/10.6084/m9.figshare.13578846	dataset	January 2021
Additional file 16 of PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response Liu, Xiaojie; Li, Xiaoshuang; Wen, Xuejing figshare https://doi.org/10.6084/m9.figshare.13578849	dataset	January 2021
Additional file 2 of PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response Liu, Xiaojie; Li, Xiaoshuang; Wen, Xuejing figshare https://doi.org/10.6084/m9.figshare.13578855.v1	dataset	January 2021
Additional file 3 of PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response Liu, Xiaojie; Li, Xiaoshuang; Wen, Xuejing figshare https://doi.org/10.6084/m9.figshare.13578858.v1	dataset	January 2021
Additional file 4 of PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response Liu, Xiaojie; Li, Xiaoshuang; Wen, Xuejing figshare https://doi.org/10.6084/m9.figshare.13578861	dataset	January 2021
Additional file 5 of PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response Liu, Xiaojie; Li, Xiaoshuang; Wen, Xuejing figshare https://doi.org/10.6084/m9.figshare.13578864.v1	dataset	January 2021
Additional file 6 of PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response Liu, Xiaojie; Li, Xiaoshuang; Wen, Xuejing figshare https://doi.org/10.6084/m9.figshare.13578867.v1	image	January 2021
Additional file 7 of PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response Liu, Xiaojie; Li, Xiaoshuang; Wen, Xuejing figshare https://doi.org/10.6084/m9.figshare.13578870	image	January 2021
Additional file 8 of PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response Liu, Xiaojie; Li, Xiaoshuang; Wen, Xuejing figshare https://doi.org/10.6084/m9.figshare.13578873	dataset	January 2021
Additional file 9 of PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response Liu, Xiaojie; Li, Xiaoshuang; Wen, Xuejing figshare https://doi.org/10.6084/m9.figshare.13578876	dataset	January 2021
Additional file 1 of Anthocyanin regulatory networks in Solanum tuberosum L. leaves elucidated via integrated metabolomics, transcriptomics, and StAN1 overexpression Bao, Yanru; Nie, Tengkun; Wang, Dongdong figshare https://doi.org/10.6084/m9.figshare.19711292.v1	dataset	January 2022
Additional file 2 of Anthocyanin regulatory networks in Solanum tuberosum L. leaves elucidated via integrated metabolomics, transcriptomics, and StAN1 overexpression Bao, Yanru; Nie, Tengkun; Wang, Dongdong figshare https://doi.org/10.6084/m9.figshare.19711295	dataset	January 2022
Additional file 3 of Anthocyanin regulatory networks in Solanum tuberosum L. leaves elucidated via integrated metabolomics, transcriptomics, and StAN1 overexpression Bao, Yanru; Nie, Tengkun; Wang, Dongdong figshare https://doi.org/10.6084/m9.figshare.19711298.v1	dataset	January 2022
Additional file 4 of Anthocyanin regulatory networks in Solanum tuberosum L. leaves elucidated via integrated metabolomics, transcriptomics, and StAN1 overexpression Bao, Yanru; Nie, Tengkun; Wang, Dongdong figshare https://doi.org/10.6084/m9.figshare.19711301	dataset	January 2022
Additional file 5 of Anthocyanin regulatory networks in Solanum tuberosum L. leaves elucidated via integrated metabolomics, transcriptomics, and StAN1 overexpression Bao, Yanru; Nie, Tengkun; Wang, Dongdong figshare https://doi.org/10.6084/m9.figshare.19711304.v1	image	January 2022
Additional file 7 of Anthocyanin regulatory networks in Solanum tuberosum L. leaves elucidated via integrated metabolomics, transcriptomics, and StAN1 overexpression Bao, Yanru; Nie, Tengkun; Wang, Dongdong figshare https://doi.org/10.6084/m9.figshare.19711310.v1	dataset	January 2022
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Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris Ojeda, Dario I.; Mattila, Tiina M.; Ruttink, Tom G3: Genes\|Genomes\|Genetics, Vol. 9, Issue 10 https://doi.org/10.1534/g3.119.400357	journal	August 2019
Large Scale Profiling of Protein Isoforms Using Label-Free Quantitative Proteomics Revealed the Regulation of Nonsense-Mediated Decay in Moso Bamboo (Phyllostachys edulis) Yu, Xiaolan; Wang, Yongsheng; Kohnen, Markus V. Cells, Vol. 8, Issue 7 https://doi.org/10.3390/cells8070744	journal	July 2019

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59 BASIC BIOLOGICAL SCIENCES
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