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

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...

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Bibliographic Details
Published in:eLife 2020-09, Vol.9
Main Authors: Greenham, Kathleen, Sartor, Ryan C, Zorich, Stevan, Lou, Ping, Mockler, Todd C, McClung, C Robertson
Format: Article
Language:English
Subjects:
Analysis
Arabidopsis thaliana
Brassica rapa - genetics
Brassica rapa - metabolism
circadian clock
Circadian Rhythm - genetics
Climate change
diversification
Gene Expression Profiling
Gene Expression Regulation, Plant - genetics
Gene Expression Regulation, Plant - physiology
gene regulatory network
Gene Regulatory Networks - genetics
Genes
Genetics and Genomics
Genome, Plant - genetics
Genome, Plant - physiology
Genomes
Genomics
Plant genetics
polyploidy
Stress, Physiological
Transcription (Genetics)
transcriptome
Transcriptome - genetics
Transcriptome - physiology
Weather
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Summary: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.
ISSN:2050-084X
2050-084X
DOI:10.7554/eLife.58993