Wang, B., Tseng, E., Regulski, M., Clark, T. A., Hon, T., Jiao, Y., Lu, Z., Olson, A., Stein, J. C., Ware, D. (June 2016) Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. Nat Commun, 7. p. 11708. ISSN 2041-1723 (Electronic)2041-1723 (Linking)
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Abstract
Zea mays is an important genetic model for elucidating transcriptional networks. Uncertainties about the complete structure of mRNA transcripts limit the progress of research in this system. Here, using single-molecule sequencing technology, we produce 111,151 transcripts from 6 tissues capturing approximately 70% of the genes annotated in maize RefGen_v3 genome. A large proportion of transcripts (57%) represent novel, sometimes tissue-specific, isoforms of known genes and 3% correspond to novel gene loci. In other cases, the identified transcripts have improved existing gene models. Averaging across all six tissues, 90% of the splice junctions are supported by short reads from matched tissues. In addition, we identified a large number of novel long non-coding RNAs and fusion transcripts and found that DNA methylation plays an important role in generating various isoforms. Our results show that characterization of the maize B73 transcriptome is far from complete, and that maize gene expression is more complex than previously thought.
| Item Type: | Paper |
|---|---|
| Subjects: | organism description > plant > maize Investigative techniques and equipment > assays > next generation sequencing Investigative techniques and equipment > assays > whole genome sequencing |
| CSHL Authors: | |
| Communities: | CSHL labs > Ware lab |
| Depositing User: | Matt Covey |
| Date: | 24 June 2016 |
| Date Deposited: | 29 Jun 2016 19:50 |
| Last Modified: | 10 Sep 2019 18:06 |
| PMCID: | PMC4931018 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/32922 |
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