Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing
Advances in transcriptomics have provided an exceptional opportunity to study functional implications of the genetic variability. Technologies such as RNA-Seq have emerged as state-of-the-art techniques for transcriptome analysis that take advantage of high-throughput next-generation sequencing. How...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-04-01
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| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.00384/full |
| _version_ | 1818187719488045056 |
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| author | Bo Wang Vivek Kumar Andrew Olson Doreen Ware Doreen Ware |
| author_facet | Bo Wang Vivek Kumar Andrew Olson Doreen Ware Doreen Ware |
| author_sort | Bo Wang |
| collection | DOAJ |
| description | Advances in transcriptomics have provided an exceptional opportunity to study functional implications of the genetic variability. Technologies such as RNA-Seq have emerged as state-of-the-art techniques for transcriptome analysis that take advantage of high-throughput next-generation sequencing. However, similar to their predecessors, these approaches continue to impose major challenges on full-length transcript structure identification, primarily due to inherent limitations of read length. With the development of single-molecule sequencing (SMS) from PacBio, a growing number of studies on the transcriptome of different organisms have been reported. SMS has emerged as advantageous for comprehensive genome annotation including identification of novel genes/isoforms, long non-coding RNAs and fusion transcripts. This approach can be used across a broad spectrum of species to better interpret the coding information of the genome, and facilitate the biological function study. We provide an overview of SMS platform and its diverse applications in various biological studies, and our perspective on the challenges associated with the transcriptome studies. |
| first_indexed | 2024-12-11T23:15:30Z |
| format | Article |
| id | doaj.art-9108cd5813504a479688f54d6c3589c9 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-11T23:15:30Z |
| publishDate | 2019-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-9108cd5813504a479688f54d6c3589c92022-12-22T00:46:33ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-04-011010.3389/fgene.2019.00384440207Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome SequencingBo Wang0Vivek Kumar1Andrew Olson2Doreen Ware3Doreen Ware4Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United StatesCold Spring Harbor Laboratory, Cold Spring Harbor, NY, United StatesCold Spring Harbor Laboratory, Cold Spring Harbor, NY, United StatesCold Spring Harbor Laboratory, Cold Spring Harbor, NY, United StatesUSDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United StatesAdvances in transcriptomics have provided an exceptional opportunity to study functional implications of the genetic variability. Technologies such as RNA-Seq have emerged as state-of-the-art techniques for transcriptome analysis that take advantage of high-throughput next-generation sequencing. However, similar to their predecessors, these approaches continue to impose major challenges on full-length transcript structure identification, primarily due to inherent limitations of read length. With the development of single-molecule sequencing (SMS) from PacBio, a growing number of studies on the transcriptome of different organisms have been reported. SMS has emerged as advantageous for comprehensive genome annotation including identification of novel genes/isoforms, long non-coding RNAs and fusion transcripts. This approach can be used across a broad spectrum of species to better interpret the coding information of the genome, and facilitate the biological function study. We provide an overview of SMS platform and its diverse applications in various biological studies, and our perspective on the challenges associated with the transcriptome studies.https://www.frontiersin.org/article/10.3389/fgene.2019.00384/fulltranscriptomicsRNA-SeqIso-Seqsingle-molecule transcriptome sequencingalternative splicingisoforms |
| spellingShingle | Bo Wang Vivek Kumar Andrew Olson Doreen Ware Doreen Ware Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing Frontiers in Genetics transcriptomics RNA-Seq Iso-Seq single-molecule transcriptome sequencing alternative splicing isoforms |
| title | Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing |
| title_full | Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing |
| title_fullStr | Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing |
| title_full_unstemmed | Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing |
| title_short | Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing |
| title_sort | reviving the transcriptome studies an insight into the emergence of single molecule transcriptome sequencing |
| topic | transcriptomics RNA-Seq Iso-Seq single-molecule transcriptome sequencing alternative splicing isoforms |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.00384/full |
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