Discovery of 2,586 orphan genes in Rosa chinensis reveals stress adaptation and floral development

Orphan genes, found only in specific lineages, are important drivers of new functions and phenotypic traits. This discovery lays the foundation for understanding how roses grow under environmental challenges.

Rosa chinensis, a beloved ornamental plant, is a mainstay in the horticultural world. Despite their worldwide popularity, little was known about the role of orphan genes in their development and stress tolerance. Orphan genes have no homologues in other species and are therefore particularly important for species-specific adaptations and evolutionary innovations.

The study, published October 23, 2024 in Tropical Plants, has significant implications for rose breeding and horticulture.

Researchers identified orphan genes (OGs) in Rosa chinensis using BLASTP analysis and various genomic databases. They analyzed 36,377 protein-coding genes from the rose genome and compared them with closely related species. Through a stepwise screening process across multiple databases, non-orphan genes (NOGs) were excluded, resulting in the identification of 2,586 OGs, representing 7.11% of the genome.

Comparative analysis of OG and NOG revealed that OG has significantly smaller gene and protein sizes, fewer exons, lower GC content, and higher isoelectric point. Further distribution analysis showed that the 2,560 OGs were distributed across seven chromosomes, with higher density near telomeres and no strong chromosomal preference.

Subcellular localization analysis revealed that OG was mainly located in the extracellular space, chloroplasts, and nucleus. Gene duplication analysis showed that approximately 10.6% of OGs were derived from gene duplications, with the majority coming from dispersed duplications. Expression profiling demonstrated that OG is mainly expressed in reproductive tissues, especially in the stamen and pistil ovary, suggesting a role for OG in reproduction.

Using Weighted Gene Co-Expression Network Analysis (WGCNA), five coexpressed modules were identified, indicating their involvement in important biological processes such as photosynthesis and hormone signaling. Additionally, 107 OGs were found to be responsive to both salinity and drought stress, highlighting their potential role in environmental adaptation.

According to Dr. Jian Mao, the study’s senior researcher, “Our study provides the first systematic identification of orphan genes in Rosa chinensis and sheds light on how these genes contribute to stress tolerance and floral development.” This data will be of great importance for future research on rose breeding and cultivation. ”

The identification of 2,586 OGs in R. chinensis opens new avenues for studying the unique genetic characteristics that enable roses to adapt and thrive. This study provides valuable genomic resources for future efforts aimed at improving rose cultivation and resilience.