A chromosome‐level Populus qiongdaoensis genome assembly provides insights into tropical adaptation and a cryptic turnover of sex determination

Abstract Populus species have long been used as model organisms to study the adaptability of trees and the evolution of sex chromosomes. As a species belonging to the section Populus and limited to tropical areas, the P. qiongdaoensis genome contains important information for tropical poplar studies and protection. Here, we report a chromosome‐level genome assembly and annotation of a female P. qiongdaoensis . Gene family clustering, positive selection detection and historical reconstruction of population dynamics revealed the tropical adaptation of P. qiongdaoensis , and showed convergent evolution with another tropical poplar, P. ilicifolia , at the molecular level, especially on some functional genes (e.g., PIF3 and PIL1 ). In addition, we also identified a ZW sex determination system on chromosome 19 of P. qiongdaoensis , and inferred that it seems to have a similar sex determination mechanism to other poplars, controlled by a type‐A cytokinin response regulator ( RR ) gene. However, comparison and phylogenetic analysis of the sex determination regions confirmed a cryptic sex turnover event in the section Populus , which may be caused by the translocation and duplication of the RR gene driven by Helitron ‐like transposable elements. Our study provides new insights into the environmental adaptation and sex chromosome evolution of poplars, and emphasizes the importance of using long read sequencing in ecological and evolutionary inferences of plants.