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09 30, 2020;9

Expansion of the circadian transcriptome in and genome-wide diversification of paralog expression patterns.

Kathleen Greenham, Ryan C Sartor, Stevan Zorich, Ping Lou, Todd C Mockler, C Robertson McClung
Author Information
  1. Kathleen Greenham: Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, United States. ORCID
  2. Ryan C Sartor: Crop and Soil Sciences, North Carolina State University, Raleigh, United States. ORCID
  3. Stevan Zorich: Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, United States. ORCID
  4. Ping Lou: Department of Biological Sciences, Dartmouth College, Hanover, United States. ORCID
  5. Todd C Mockler: Donald Danforth Plant Science Center, St. Louis, United States. ORCID
  6. C Robertson McClung: Department of Biological Sciences, Dartmouth College, Hanover, United States. ORCID
PMID: 32996462 DOI: 10.7554/eLife.58993

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 . Strikingly, almost three-quarters of the 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 the circadian expression phase among retained paralogous pairs. Using gene regulatory network models, we compared transcription factor targets between and Arabidopsis circadian networks to reveal evidence for divergence between 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.

Keywords

circadian clock diversification gene regulatory network genetics genomics polyploidy transcriptome

Associated Data

GEO | GSE123654; GSE90841

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Grants

  1. IOS-1202779/National Science Foundation
  2. IOS-1711662/National Science Foundation
  3. IOS-1547796/National Science Foundation
  4. Next Generation BioGreen 21,grant number SSAC PJ01327306/Rural Development Administration
  5. Next Generation BioGreen 21 grant number SSAC PJ01327306/Rural Development Administration

MeSH Term

Brassica rapa
Circadian Rhythm
Gene Expression Profiling
Gene Expression Regulation, Plant
Gene Regulatory Networks
Genome, Plant
Stress, Physiological
Transcriptome
Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.
Article has an altmetric score of 78

Word Cloud

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