The first reference genome assembly of the Chilean sea fig (Carpobrotus chilensis)

Abstract

Carpobrotus chilensis (Chilean sea fig) is a coastal succulent of uncertain origin that has naturalized along the California coast, where it co-occurs and hybridizes with the invasive species, Carpobrotus edulis. Despite their ecological importance and widely supported hybridization, genomic resources for this genus remain scarce. Here, we present a draft genome assembly of C. chilensis generated from PacBio HiFi long reads. The assembled nuclear genome spans 981.7 Mb across 178 contigs. The contig N50 was 73.0 Mb, and BUSCO completeness was 96.3%. K-mer and SNP-based analyses indicate extremely low heterozygosity (3.4 x 10-), reduced genetic diversity in this population. The genome is highly repetitive, with 81.67% of the sequences composed of transposable elements, predominantly long terminal repeat (LTR) retrotransposons. Gene prediction identified 21,744 protein-coding genes, with BUSCO completeness of 95.8%. Comparative analysis with C. edulis identified 8,783 single-copy orthologous gene pairs, with a median synonymous substitution rate (dS) of 0.019, indicating low sequence divergence between the two species. This genome assembly provides a foundational resource for investigating the genomic basis of hybridization and invasion in Carpobrotus.