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Plant J., Nov 23 2023, | https://doi.org/10.1111/tpj.16553 Investigation of regulatory divergence between homoeologs in the recently formed allopolyploids, Tragopogon mirus and T. miscellus (Asteraceae)

Mi-Jeong Yoo^1,*,†, Jin Koh^2,†, J. Lucas Boatwright³, Douglas E. Soltis^4,5,6,7, Pamela S. Soltis^5,6,7, W. Brad Barbazuk^4,5 and Sixue Chen^8,*

¹Department of Biology, Clarkson University, Potsdam, New York 13699, USA,

²Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida 32610, USA,

³Plant and Environmental Science Department, Clemson University, Clemson, South Carolina 29634, USA,

⁴Department of Biology, University of Florida, Gainesville, Florida 32611, USA,

⁵Genetics Institute, University of Florida, Gainesville, Florida 32610, USA,

⁶Biodiversity Institute, University of Florida, Gainesville, Florida 32611, USA,

⁷Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA, and

⁸Department of Biology, University of Mississippi, Oxford, Mississippi 38677, USA

^*For correspondence: Mi-Jeong Yoo, Sixue Chen

^†Equal contribution

Abstract

Polyploidy is an important evolutionary process throughout eukaryotes, particularly in flowering plants. Duplicated gene pairs (homoeologs) in allopolyploids provide additional genetic resources for changes in molecular, biochemical, and physiological mechanisms that result in evolutionary novelty. Therefore, understanding how divergent genomes and their regulatory networks reconcile is vital for unraveling the role of polyploidy in plant evolution. Here, we compared the leaf transcriptomes of recently formed natural allotetraploids (Tragopogon mirus and T. miscellus) and their diploid parents (T. porrifolius X T. dubius and T. pratensis X T. dubius, respectively). Analysis of 35 400 expressed loci showed a significantly higher level of transcriptomic additivity compared to old polyploids; only 22% were non-additively expressed in the polyploids, with 5.9% exhibiting transgressive expression (lower or higher expression in the polyploids than in the diploid parents). Among approximately 7400 common orthologous regions (COREs), most loci in both allopolyploids exhibited expression patterns that were vertically inherited from their diploid parents. However, 18% and 20.3% of the loci showed novel expression bias patterns in T. mirus and T. miscellus, respectively. The expression changes of 1500 COREs were explained by cis-regulatory divergence (the condition in which the two parental subgenomes do not interact) between the diploid parents, whereas only about 423 and 461 of the gene expression changes represent trans-effects (the two parental subgenomes interact) in T. mirus and T. miscellus, respectively. The low degree of both non-additivity and trans-effects on gene expression may present the ongoing evolutionary processes of the newly formed Tragopogon polyploids (~80-90 years).

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형식Research article
게재일2023년 11월 (BRIC 등록일 2023-12-01)
연구진국외 연구진
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