Maternal dominance contributes to subgenome differentiation in allopolyploid fishes

Min-Rui-Xuan Xu, Zhen-Yang Liao, Jordan R. Brock, Kang Du, Guo-Yin Li, Zhi-Qiang Chen, Ying-Hao Wang, Zhong-Nan Gao, Gaurav Agarwal, Kevin H-C Wei, Feng Shao, Shuai Pang, Adrian E. Platts, Jozefien Velde, Hong-Min Lin, Scott J. Teresi, Kevin Bird, Chad E. Niederhuth, Jin-Gen Xu, Guo-Hua Yu, Jian-Yuan Yang, Si-Fa Dai, Andrew Nelson, Ingo Braasch, Xiao-Gu Zhang (), Manfred Schartl (), Patrick P. Edger (), Min-Jin Han () and Hua-Hao Zhang ()
Additional contact information
Min-Rui-Xuan Xu: Jiujiang University
Zhen-Yang Liao: Chinese Academy of Agricultural Sciences
Jordan R. Brock: Michigan State University
Kang Du: Texas State University
Guo-Yin Li: Zhoukou Normal University
Zhi-Qiang Chen: Glbizzia Biosciences
Ying-Hao Wang: Chinese Academy of Agricultural Sciences
Zhong-Nan Gao: Jiujiang University
Gaurav Agarwal: Michigan State University
Kevin H-C Wei: University of California Berkeley
Feng Shao: Southwest University, School of Life Sciences
Shuai Pang: Glbizzia Biosciences
Adrian E. Platts: Michigan State University
Jozefien Velde: Max Planck Institute for Plant Breeding Research
Hong-Min Lin: Jiujiang University
Scott J. Teresi: Michigan State University
Kevin Bird: Michigan State University
Chad E. Niederhuth: Michigan State University
Jin-Gen Xu: Jiujiang Academy of Agricultural Sciences
Guo-Hua Yu: Jiujiang University
Jian-Yuan Yang: Jiujiang University
Si-Fa Dai: Jiujiang University
Andrew Nelson: Boyce Thompson Institute
Ingo Braasch: Michigan State University
Xiao-Gu Zhang: Jiujiang University
Manfred Schartl: Texas State University
Patrick P. Edger: Michigan State University
Min-Jin Han: Southwest University
Hua-Hao Zhang: Jiujiang University

Nature Communications, 2023, vol. 14, issue 1, 1-19

Abstract: Abstract Teleost fishes, which are the largest and most diverse group of living vertebrates, have a rich history of ancient and recent polyploidy. Previous studies of allotetraploid common carp and goldfish (cyprinids) reported a dominant subgenome, which is more expressed and exhibits biased gene retention. However, the underlying mechanisms contributing to observed ‘subgenome dominance’ remains poorly understood. Here we report high-quality genomes of twenty-one cyprinids to investigate the origin and subsequent subgenome evolution patterns following three independent allopolyploidy events. We identify the closest extant relatives of the diploid progenitor species, investigate genetic and epigenetic differences among subgenomes, and conclude that observed subgenome dominance patterns are likely due to a combination of maternal dominance and transposable element densities in each polyploid. These findings provide an important foundation to understanding subgenome dominance patterns observed in teleost fishes, and ultimately the role of polyploidy in contributing to evolutionary innovations.

Date: 2023
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DOI: 10.1038/s41467-023-43740-y

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