TY  - JA
AU  - Liangzhen Zhao
AU  - Hangxiao Zhang
AU  - Kohnen,M.V.
AU  - Prasad,K.V.S.V.
AU  - Lianfeng Gu
AU  - Reddy,A.S.N.
TI  - Analysis of transcriptome and epitranscriptome in plants using PacBio Iso-Seq and nanopore-based direct RNA sequencing
SN  - 1664-8021
PY  - 2019///
CY  - Switzerland
PB  - Frontiers
KW  - RNA
KW  - AGROVOC
KW  - Transcriptome
KW  - Plant Genetics
N1  - Peer review; Open Access
N2  - 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
UR  - https://doi.org/10.3389/fgene.2019.00253
T2  - Frontiers in Genetics
DO  - https://doi.org/10.3389/fgene.2019.00253
ER  -