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Nat Commun. 2016 Jun 24;7:11708. doi: 10.1038/ncomms11708.

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

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Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York 11724, USA.
Pacific Biosciences, 1380 Willow Road, Menlo Park, California 94025, USA.
USDA ARS NEA Robert W. Holley Center for Agriculture and Health Cornell University, Ithaca, New York 14853, USA.


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 ∼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.

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