A Telomere-to-Telomere Genome Assembly and Demographic History Inference of Ostrya rehderiana

Ostrya rehderiana is a critically endangered plant species with an extremely small population size. However, the absence of high-quality genome assembly has impeded the understanding of the causes and genetic consequences of its endangered status, especially how theses genetic consequences result in the failure of its population regeneration. In this study, we integrated PacBio HiFi, Oxford Nanopore (ONT) long-read sequencing, Hi-C, Illumina resequencing, and RNA-seq data to generate a telomere-to-telomere (T2T) genome assembly and annotation for this species. The assembled genome has a total size of 349.04 Mb and was successfully anchored to eight pseudochromosomes. A total of 28,698 protein-coding genes were predicted, of which 27,476 were functionally annotated. The BUSCO completeness score reached 98.9%, indicating a high level of assembly completeness and accuracy. Based on this T2T genome assembly, we reconstructed historical changes in effective population size using the PSMC model. The results revealed pronounced long-term fluctuations in population size, followed by a recent continuous decline. This study provides an important genomic resource for exploring the mechanisms underlying the endangered status of O. rehderiana offering a foundation for conservation genetics research on plant species with extremely small populations.