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

Peng-Fei MaYun-Long LiuCen GuoGuihua JinZhen-Hua GuoLing MaoYi-Zhou YangLiang-Zhong NiuYu-Jiao WangLynn G ClarkElizabeth A KelloggZu-Chang XuXia-Ying YeJing-Xia LiuMeng-Yuan ZhouYan LuoYang YangDouglas Edward SoltisJeffrey L BennetzenPamela S SoltisDe-Zhu Li
Published in: Nature genetics (2024)
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.
Keyphrases
  • genome wide
  • copy number
  • gene expression
  • dna methylation
  • rna seq
  • quantum dots