Fagaceae species have a long evolutionary history and serve as a primary component of woody plant in temperate and subtropical forests of the Northern Hemisphere. Within Fagaceae, Quercus is one of the largest genera, consisting of approximately 500 species that are distributed across Asia, Europe, Africa and North America (Plomion et al., 2016; Zhou et al., 2022). Quercus species fulfill crucial ecological functions such as maintaining biodiversity, conserving water and soil, and sequestering carbon (Han et al., 2022). Due to their ecological dominance, remarkable diversity and the availability of phylogenetic, genomic, and ecological data, Quercus species are regarded as important clades for ecological and evolutionary studies (Petit et al., 2013; Gugger et al., 2021). This genus has been classified into eight sections: Cyclobalanopsis, Cerris, Ilex, Quercus, Lobatae, Virentes, Protobalanus and Ponticae. Recently, genome sequences of some Quercus species, including Quercus acutissima (Fu et al., 2022), Quercus lobata (Sork et al., 2022), Quercus mongolica (Ai et al., 2022), Quercus robur (Plomion et al., 2018), Quercus suber (Ramos et al., 2018), Quercus gilva (Zhou, X. et al., 2022), Quercus variabilis (Han et al., 2022) and Quercus dentata (Wang et al., 2023), have been reported and significantly contributed to resolving phylogenetic relationships within Quercus section Quercus and Cerris. However, there are still limited genome resources for species in the Quercus section Cyclobalanopsis, which is an important oak lineage found in East Asian evergreen broad-leaved forests (Deng et al., 2018). Additionally, the fruit of Cyclobalanopsis species is abundant in starch and the wood possesses desirable features such as robust texture, corrosion resistance, and wear resistance, which makes Cyclobalanopsis a valuable economic resource that warrants widespread promotion, cultivation, and offers significant potential for exploitation and utilization. But how these closely related species with timber evolved and the genetic mechanisms underlying the accumulation of starch synthesize remain unclear.

To investigate the adaptive evolution of Cyclobalanopsis and understand its key economic characteristics, such as high starch content in fruits and quality wood, we reported the high-quality chromosome-scale genome assemblies of two Quercus species in Cyclobalanopsis section, namely Quercus sichourensis and Quercus rex, and performed comparative genomic studies of Quercus species. Besides, protecting plant resources and rescuing rare and endangered plants have become focal points of international attention. Whole-genome resequencing offers profound insights into critical issues in conservation biology. Quercus sichourensis belongs to the category of plant species with extremely small populations (PSESP) (Wade et al., 2016). To explore the genomic signatures of Q. sichourensis with extremely small populations and Q. rex, we performed population genome analyses by re-sequencing an additional 20 and 14 individuals from each species, respectively. Our results not only provide the whole genome information for this species but also has important significance for the field investigation, search and protection in the future.