Chromosome-scale genome assembly of Sauvagesia rhodoleuca (Ochnaceae) provides insights into its genome evolution and demographic history.

Abstract

Sauvagesia rhodoleuca is an endangered species endemic to southern China. Due to human activities, only 6 fragmented populations remain in Guangdong and Guangxi. Despite considerable conservation efforts, its demographic history and evolution remain poorly understood, particularly from a genomic perspective. To address this, we assembled a chromosome-scale genome of S. rhodoleuca using Nanopore long-read sequencing, DNA short-read sequencing, RNA-seq, and Hi-C data. A total of 290.37 Mb of assembled sequences, accounting for 99.76% of the genome, were successfully anchored to 19 pseudo-chromosomes, achieving a BUSCO completeness of 98.40% and a long terminal repeat assembly index of 17.28. Genome annotation identified 26,758 protein-coding genes and 369 tRNA genes. Demographic analysis revealed a sharp decline in the effective population size of S. rhodoleuca beginning approximately 1 million years ago. Whole-genome duplication (WGD) analysis revealed that S. rhodoleuca experienced a whole-genome triplication (WGT) followed by a more recent WGD after diverging from the Rhizophoraceae. Genes retained from WGT and WGD events played key roles in the development and survival of S. rhodoleuca, as indicated by Gene Ontology analysis. The high-quality genome of S. rhodoleuca provides insights into its genomic characteristics and evolutionary history, offering a valuable resource for conservation and genetic management.