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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #343892

Research Project: Enhancing Plant Genome Function Maps Through Genomic, Genetic, Computational and Collaborative Research

Location: Plant, Soil and Nutrition Research

Title: A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing

Author
item WANG, BO - Cold Spring Harbor Laboratory
item REGULSKI, MICHAEL - Cold Spring Harbor Laboratory
item TSENG, ELIZABETH - Pacific Biosciences Inc
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item GOODWIN, SARA - Cold Spring Harbor Laboratory
item MCCOMBIE, RICHARD - Cold Spring Harbor Laboratory
item Ware, Doreen

Submitted to: Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/12/2018
Publication Date: 4/30/2018
Citation: Wang, B., Regulski, M., Tseng, E., Olson, A., Goodwin, S., Mccombie, R., Ware, D. 2018. A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing. Genome Research. doi:10.1101/gr.227462.117.
DOI: https://doi.org/10.1101/gr.227462.117

Interpretive Summary: This study is the first comparative transcriptome study in maize and sorghum using large-scale single-molecule sequencing. The high quality intact isoforms used in this study enable the findings in this study are very convincing, which will provide great value for plant scientists to better understand the architecture divergence between evolutionarily closely related species at the transcriptional level.

Technical Abstract: Maize and sorghum are both important crops with similar overall plant architectures, but they have key differences, especially in regard to their inflorescences. To better understand these two organisms at the molecular level, we compared the expression profiles of both protein- coding and non-coding transcripts in 11 matched tissues using single-molecule long-read and deep RNA sequencing. This comparative analysis revealed a large number of novel isoforms in both maize and sorghum. Evolutionarily young genes were likely to be generated in reproductive tissues, and usually had fewer isoforms than old genes. We also found both similarities and differences in alternative splicing patterns and activities among tissues, as well as between species. The maize sub-genomes exhibited no bias in isoform generation; however, genes in the B genome were more highly expressed in pollen tissue, whereas genes in the A genome were more highly expressed in endosperm. We also identified a number of splicing events that are conserved between maize and sorghum. In addition, we generated comprehensive and high-resolution maps of polyA sites, revealing similarities and differences in mRNA cleavage between the two species. Overall, our results reveal considerable splicing and expression diversity between sorghum and maize, well beyond what was reported in previous studies, likely reflecting the differences in architecture between these two species.