Hybridization footprint and the mechanism of leaf color differences in Philodendron cultivars

Abstract

The genus Philodendron exhibits exceptional diversity and ornamental value, but the genetic and evolutionary mechanisms driving its speciation and trait variation remain largely unknown. In this study, we constructed a haplotype-resolved, near-complete genome of Philodendron tatei to investigate its evolutionary origins, resolve its phylogenomic placement within Araceae, reconstruct karyotype evolution, and explore genetic clusters and hybridization patterns within Philodendron cultivars. Additionally, the genetic and regulatory mechanisms underlying leaf color variation, a key horticultural trait, were explored. Phylogenomic analysis placed Philodendron within the Araceae family and provided insights into its karyotype evolution. Comparative genomic analyses identified five major genetic clusters across the genus, highlighting extensive hybridization and allele-specific expression as key contributors to Philodendron ’s diversity. To investigate leaf color variation, variant mining and transcriptome profiling were conducted on samples with diverse pigmentation. Func- tional validation identified PtSGR1 as a critical regulator of pigmentation formation, with differences in promoter activity driving variation in leaf coloration. Overall, this study provides a comprehensive genomic framework for understanding Philodendron evolution and diversity, tracing the significant role of hybridization in shaping its speciation and identify- ing key genetic mechanisms underlying ornamental traits. These insights advance our understanding of plant evolution, contribute to horticultural innovation, and enhance the genetic resources available for studying this ecologically and economically important genus.

Acknowledgements

This study was supported by The Key Science and Technology Project for Social Development in Dongguan (20231800940412), Science and Technology Projects in Guangzhou (2023B03J1355), the National Natural Science Foundation of China (32472129), and The major science and technology research projects of Guangdong Laboratory for Lingnan Modern Agriculture (NT2021001). We thank Huacai Zhuang (Agricultural Science Research Center of Dongguan) for providing Philodendron materials in this work.

Author contributions

S.B., X.F., and F.L. designed and coordinated the project. J.C. completed most experiments with help from J.L., Z.H., Z.H., Z.P., Y.M., X.Y., X.F., and C.X. performed the collection of samples. F.L., J.C., and S.B. performed the analyses and drafted this manuscript. S.W., H.H., and Z.W. provided suggestions about experimental design and manuscript. All authors read and approved the final manuscript.

Data availability

The raw genome and transcriptome sequencing data generated and analyzed in this study have been deposited in the NCBI Sequence Read Archive (SRA) under BioProject accession number PRJNA1294177 and NGDC Genome Sequence Archive (GSA) under BioProject accession number PRJCA052160. The Phylogenetic tree files have been uploaded to the TreeBASE under accession ID 32444. The assembled genome sequences, as well as corresponding genome annotation files, have been made publicly available on Figshare at the following link: https:// figshare.com/articles/dataset/Philodendron_genome_assembly _and_annotation/29625863 (10.6084/m9.figshare.29625863). All other relevant data supporting the findings of this study are available from the corresponding author upon reasonable request.

Conflicts of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Supplementary material

Supplementary material is available at Horticulture Research online.

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