Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

Wang, B., Tseng, E., Regulski, M., Clark, T. A., Hon, T., Jiao, Y., Lu, Z., Olson, A., Stein, J. C., Ware, D. (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)

URL: http://www.ncbi.nlm.nih.gov/pubmed/27339440
DOI: 10.1038/ncomms11708

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 Deposited: 29 Jun 2016 19:50
Last Modified: 28 Jul 2016 18:56
PMCID: PMC4931018
Related URLs:
URI: http://repository.cshl.edu/id/eprint/32922

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