Chromosome-level genome assembly and demographic history of Euryodendron excelsum, in monotypic genus endemic to China

Abstract

Euryodendron excelsum is in a monotypic genus Euryodendron, endemic to China. It has intermediate morphisms in the Pentaphylacaceae or Theaceae families, which make it distinct. Due to anthropogenic disturbance, E. excelsum is currently only found in very restricted and fragmented areas with extremely small populations. Although much research and effort has been applied toward its conservation, its long-term survival mechanisms and evolutionary history remain elusive, especially from a genomic aspect. Therefore, using a combination of long/short whole genome sequencing, RNA sequencing reads, and Hi-C data, we assembled and annotated a high-quality genome for E. excelsum. The genome assembly of E. excelsum comprised 1,059,895,887 bp with 99.66% anchored into 23 pseudo-chromosomes, and a 99.0% BUSCO completeness. Comparative genomic analysis revealed the expansion of terpenoid and flavonoid secondary metabolite genes, and displayed a tandem and/or proximal duplication framework of these genes. E. excelsum also displayed genes associated with growth, development, and defence adaptation from whole genome duplication. Demographic analysis indicated that its fluctuations in population size and its recent population decline was related to cold climate changes. The E. excelsum genome assembly provides a highly valuable resource for evolutionary and ecological research in the future, aiding its conservation, management, and restoration.