Resequencing of 284 genomes reveals evolutionary history and hotspot of genetic diversity of the giant bamboos

The Dendrocalamus giganteus complex comprises D. giganteus , D. calostachyus and D. sinicus , being the largest known, iconic bamboo species and is economically, ecologically and culturally significant in Southeast Asia, serving as a pillar of daily life of indigenous people. However, lack of understanding of its genetic diversity pattern and population history has hindered effective germplasm conservation and development as sustainable non-timber forest resources. Here, we present a population genomic study of the giant bamboos with whole-genome resequencing of 284 accessions of three closely related species across their potentially native geographical ranges in Myanmar and Yunnan Province, China. We identified seven highly supported phylogenetic clades for the populations of the D. giganteus complex, and all populations exhibit low levels of genetic diversity while a high degree of genetic differentiation among them. One of them in the remote northern and northwestern Myanmar was found as the hotspot of genetic diversity of the giant bamboos. Tajima’s D value and demographic history inference suggested the occurrence of population bottleneck, leading to a sharp decline in Ne during the last glacial period. Strikingly, D. sinicus displayed the lowest genetic diversity in the complex likely due to predominance of selfing or inbreeding. Overall, our study provides valuable insights into the evolutionary history and population genetics of the D. giganteus complex, serving as an important foundation for developing effective conservation strategies for the giant bamboos in Southeast Asia. • We identified seven phylogenetic groups of the Dendrocalamus giganteus complex and northern and northwestern Myanmar as the hotspot of genetic diversity and possible center of origin. • Our results indicate low genetic diversity coupled with high genetic differentiation among populations. • The Dendrocalamus giganteus complex has experienced historical population bottlenecks and currently faces reduced population size related to human activities. • We advocate for intensified effort in ex situ conservation with appropriate conservation strategies.