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

Wang, B., Regulski, M., Tseng, E., Olson, A., Goodwin, S., McCombie, W. R., Ware, D. (2018) A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing. Genome Res, 28 (6). pp. 921-932. ISSN 1088-9051

URL: https://www.ncbi.nlm.nih.gov/pubmed/29712755
DOI: 10.1101/gr.227462.117

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 expression profiles of both protein-coding and noncoding transcripts in 11 matched tissues using single-molecule, long-read, deep RNA sequencing. This comparative analysis revealed large numbers of novel isoforms in both species. Evolutionarily young genes were likely to be generated in reproductive tissues and usually had fewer isoforms than old genes. We also observed similarities and differences in alternative splicing patterns and activities, both among tissues and between species. The maize subgenomes 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 conserved between maize and sorghum. In addition, we generated comprehensive and high-resolution maps of poly(A) 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.

Item Type: Paper
Subjects: organism description > plant > maize
Investigative techniques and equipment > assays > RNA-seq
CSHL Authors:
Communities: CSHL labs > McCombie lab
CSHL labs > Ware lab
Depositing User: Matt Covey
Date Deposited: 22 May 2018 20:02
Last Modified: 20 Jun 2018 20:13
PMCID: PMC5991521
Related URLs:
URI: http://repository.cshl.edu/id/eprint/36566

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