Subgenomic Stability of Progenitor Genomes During Repeated Allotetraploid Origins of the Same Grass Brachypodium hybridum

Wenjie Mu, Kexin Li, Yongzhi Yang, Adina Breiman, Jiao Yang, Ying Wu, Mingjia Zhu, Shuai Wang, Pilar Catalan*, Eviatar Nevo*, Jianquan Liu*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Both homeologous exchanges and homeologous expression bias are generally found in most allopolyploid species. Whether homeologous exchanges and homeologous expression bias differ between repeated allopolyploid speciation events from the same progenitor species remains unknown. Here, we detected a third independent and recent allotetraploid origin for the model grass Brachypodium hybridum. Our homeologous exchange with replacement analyses indicated the absence of significant homeologous exchanges in any of the three types of wild allotetraploids, supporting the integrity of their progenitor subgenomes and the immediate creation of the amphidiploids. Further homeologous expression bias tests did not uncover significant subgenomic dominance in different tissues and conditions of the allotetraploids. This suggests a balanced expression of homeologs under similar or dissimilar ecological conditions in their natural habitats. We observed that the density of transposons around genes was not associated with the initial establishment of subgenome dominance; rather, this feature is inherited from the progenitor genome. We found that drought response genes were highly induced in the two subgenomes, likely contributing to the local adaptation of this species to arid habitats in the third allotetraploid event. These findings provide evidence for the consistency of subgenomic stability of parental genomes across multiple allopolyploidization events that led to the same species at different periods. Our study emphasizes the importance of selecting closely related progenitor species genomes to accurately assess homeologous exchange with replacement in allopolyploids, thereby avoiding the detection of false homeologous exchanges when using less related progenitor species genomes.

Original languageEnglish
Article numbermsad259
JournalMolecular Biology and Evolution
Issue number12
StatePublished - 1 Dec 2023


FundersFunder number
Spanish Aragon GovernmentLMP82_21
Spanish Aragon Government-European Social Fund BiofloraA01-23R
Lanzhou University
Chinese Academy of SciencesXDB31010300
Ministerio de Ciencia e InnovaciónPID2019-108195GB-I00


    • allopolyploids
    • comparative genomics
    • drought response
    • ecological adaptation
    • homeologous exchanges
    • homeologous expression bias
    • recurrent origins
    • subgenome dominance


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