Fittonia albivenis, commonly known as the nerve plant, is an ornamental species native to the Peruvian rainforest, valued for its vibrant and diverse leaf coloration. Understanding the genetic mechanisms underlying this coloration is crucial for enhancing its ornamental value and adaptation to environmental stressors. Here, by leveraging advanced sequencing technologies such as PacBio HiFi, Oxford Nanopore, and Hi-C, we achieved a nearly complete haplotype-phased genome assembly for F. albivenis, revealing a 2.08-Gb genome composed of 18 chromosome pairs and containing 66 telomeres. This assembly enabled the identification of subgenome-specific repetitive sequences, elucidating their impact on gene expression and structural variations. Through RNA sequencing, metabolomic profiling, and resequencing, we dissected the regulatory networks influencing chlorophyll and anthocyanin biosynthesis, identifying key genes and transcription factors driving leaf color variation. Our findings highlight the roles of gene duplication and specific transcription factors in pigment synthesis pathways, providing a foundation for future genetic studies and breeding programs aimed at enhancing ornamental and adaptive traits in F. albivenis and related species.
© The Author(s) 2025. Published by Oxford University Press on behalf of Nanjing Agricultural University.