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

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.

Oryza genome evolution through a tetraploid lens

“…The most abundant group of class-I TEs was the Ty3- Gypsy LTR-retroelement (with an average of 24.3% across the (sub)genomes), and the most abundant group of class-II DNA transposons was CACTA (with an average of 6.3% across the (sub)genomes) (Supplementary Table 3; Supplementary Figure 2). As shown in other plant systems 33 , (sub)genome size highly correlates with TE content in the Oryza genus (Pearson’s correlation coefficient: 0.9987) (Supplementary Table 4; Figure 2a). The diploid species with the largest genomes, i.e.…”

Culm Morphological Analysis in Moso Bamboo Reveals the Negative Regulation of Internode Diameter and Thickness by Monthly Precipitation

“…Moso bamboo is widely distributed and extensively utilized in the bamboo industry [ 52 ], but its adaptability varies across different regions of China [ 47 , 53 ]. Therefore, investigating culm morphological variations among different Moso bamboo populations provides valuable genetic insights and identifies adaptations to diverse environmental conditions [ 46 ].…”