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

Author:

Ma Peng-FeiORCID,Liu Yun-LongORCID,Guo Cen,Jin Guihua,Guo Zhen-Hua,Mao Ling,Yang Yi-ZhouORCID,Niu Liang-Zhong,Wang Yu-Jiao,Clark Lynn G.,Kellogg Elizabeth A.ORCID,Xu Zu-ChangORCID,Ye Xia-Ying,Liu Jing-Xia,Zhou Meng-YuanORCID,Luo YanORCID,Yang Yang,Soltis Douglas E.ORCID,Bennetzen Jeffrey L.ORCID,Soltis Pamela S.ORCID,Li De-ZhuORCID

Abstract

AbstractPolyploidy (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.

Funder

National Natural Science Foundation of China

China Postdoctoral Science Foundation

Publisher

Springer Science and Business Media LLC

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