This comprehensive study unveils the first annotated, haplotype-resolved, chromosome-scale reference genome of Lantana camara, alongside insights into candidate genes for unreduced female gamete production through ovary transcriptome sequencing. L. camara, a native of the Caribbean, plays a dual role as a valued ornamental plant and a challenging invasive species. The absence of a high-quality genomic resource has previously limited the exploration of its ornamental and invasive characteristics. This work closes this gap by delivering a critical genomic resource for L. camara, essential for ornamental breeding programs and invasive species management. The genome of a diploid L. camara breeding line UF-T48 was assembled de novo, utilizing HiFi and Hi-C reads, achieving phased genome assemblies with a BUSCO score of 97.7% and LAI score of 19.37, indicating high quality. This assembly resolved all 22 chromosomes into pseudochromosomes, with an average length of 117 Mb, and annotated 83,775 protein-coding genes, laying a foundational step for Verbenaceae family genomic research. Simultaneously, this research delves into the plant’s reproductive biology, specifically targeting the mechanism of unreduced female gamete production, a trait that has played an important role in the evolution and spread of lantana, contributed to the plant’s invasiveness, and and complicated the development of sterile triploids. By aligning RNA-seq data to the reference genome, we identified differentially expressed genes associated with cell division and meiosis, crucial for understanding the genetic underpinnings of unreduced gamete production. These findings not only enhance the genetic comprehension of L. camara but also provide invaluable genomic resources for future genetic studies, conservation efforts, and breeding strategies aimed at producing non-invasive sterile cultivars. This pioneering genomic and transcriptomic analysis marks a significant leap forward in researchers’ ability to manipulate L. camara for both horticultural innovation and environmental management.
