Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns
- University of Minnesota, United States
- North Carolina State University, United States
- Dartmouth College, United States
- Donald Danforth Plant Science Center, United States
Abstract
An important challenge of crop improvement strategies is assigning function to paralogs in polyploid crops. Here, we describe the circadian transcriptome in the polyploid crop Brassica rapa. Strikingly, almost three quarters of expressed genes exhibited circadian rhythmicity. Genetic redundancy resulting from whole genome duplication is thought to facilitate evolutionary change through sub- and neo-functionalization among paralogous gene pairs. We observed genome-wide expansion of circadian expression phase among retained paralogous pairs. Using gene regulatory network models, we compared transcription factor targets between B. rapa and Arabidopsis circadian networks to reveal evidence for divergence between B. rapa paralogs that may be driven in part by variation in conserved non-coding sequences (CNS). Additionally, differential drought response among retained paralogous pairs suggests further functional diversification. These findings support the rapid expansion and divergence of the transcriptional network in a polyploid crop and offer a new approach for assessing paralog activity at the transcript level.
Data availability
Sequencing data have been deposited in GEO under accession codes GSE123654
Article and author information
Author details
C Robertson McClung
Funding
National Science Foundation (IOS-1202779)
- Kathleen Greenham
National Science Foundation (IOS-1711662)
- Ryan C Sartor
National Science Foundation (IOS-1547796)
- C Robertson McClung
Rural Development Administration (Next Generation BioGreen 21,grant number SSAC PJ01327306)
- C Robertson McClung
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Christian S Hardtke, University of Lausanne, Switzerland
Version history
- Received: May 15, 2020
- Accepted: September 29, 2020
- Accepted Manuscript published: September 30, 2020 (version 1)
- Version of Record published: November 10, 2020 (version 2)
Copyright
© 2020, Greenham et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns
eLife 9:e58993.
https://doi.org/10.7554/eLife.58993
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