Genome analyses provide insights into Engelhardia’s adaptation to East Asia summer monsoon

Genetic information has been instrumental in elucidating the relationship between the East Asian Summer Monsoon (EASM) and subtropical evergreen broad-leaved forests (EBLFs). However, how the genomic insights of EBLFs' species correspond to environmental shifts induced by the EASM remains limited. In this study, we investigated the adaptive mechanisms of evergreen <i>Engelhardia</i> species in response to the EASM through genome sequencing and comparative genomic analyses from the <i>de novo</i> genome assemblies of five closely related <i>Engelhardia</i> taxa and one <i>Rhoiptelea</i> species. Our findings revealed that the divergence of evergreen trees from their sister deciduous species is closely associated with the onset and intensification of the EASM. This genomic transition may have coincided with a significant expansion of the terpene synthase (TPS) gene family in <i>E. fenzelii</i>, driven by four distinct modes of gene duplication. This expansion enhances the biosynthesis of terpene volatiles, providing a defensive mechanism against potential herbivory in EASM affected environments. We also identified a shared whole-genome duplication (WGD) event across <i>Engelhardia</i>, along with substantial differences in transposable element (TE) composition and activity, which contributed to genome size variation between <i>E. fenzelii</i> and <i>E. roxburghiana</i>. In addition, demographic analyses revealed a continuous population decline over the past 10 million years, further exacerbated by recent human disturbance, underscoring the conservation urgency for these species. These results not only provide preliminary insights into the complex evolutionary dynamics within the <i>Engelhardia</i> genus from genomic insights (e.g., the intricate relationships between genomic variations, environmental changes, and adaptive responses driven by significant climatic events such as the EASM), but also provides valuable insights into the conservation significance of EBLFs.