Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance

Peng Fei Ma, Yun Long Liu, Cen Guo, Guihua Jin, Zhen Hua Guo, Ling Mao, Yi Zhou Yang, Liang Zhong Niu, Yu Jiao Wang, Lynn G. Clark, Elizabeth A. Kellogg, Zu Chang Xu, Xia Ying Ye, Jing Xia Liu, Meng Yuan Zhou, Yan Luo, Yang Yang, Douglas E. Soltis, Jeffrey L. Bennetzen, Pamela S. SoltisDe Zhu Li

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes in a polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of a bamboo system (Poaceae: Bambusoideae) comprising a series of lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies and 476 transcriptome samples. We find that woody bamboo subgenomes exhibit stunning karyotype stability, with parallel subgenome dominance in the two tetraploid clades and a gradual shift of dominance in the hexaploid clade. Allopolyploidization and subgenome dominance have shaped the evolution of tree-like lignified culms, rapid growth and synchronous flowering characteristic of woody bamboos as large grasses. Our work provides insights into genome dominance in a remarkable polyploid system, including its dependence on genomic context and its ability to switch which subgenomes are dominant over evolutionary time.

Original languageEnglish
Pages (from-to)710-720
Number of pages11
JournalNature Genetics
Volume56
Issue number4
DOIs
StatePublished - Apr 2024

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