Discovery of 2,586 orphan genes in Rosa chinensis reveals stress adaptation and flower development
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Orphan genes, found only in specific lineages, are key drivers of new functions and phenotypic traits. This discovery lays a foundation for understanding how roses thrive under environmental challenges.
Rosa chinensis, a beloved ornamental plant, is a central figure in the horticultural industry. Despite its global popularity, little was known about the role of orphan genes in its development and stress tolerance. Orphan genes have no homologs in other species, which makes them particularly important in species–specific adaptations and evolutionary innovations.
A study published in Tropical Plants on 23 October 2024, has significant implications for rose breeding and horticulture.
Researchers utilized BLASTP analysis and various genomic databases to identify orphan genes (OGs) in Rosa chinensis. They analyzed 36,377 protein-coding genes from the rose genome and compared them to related species. Through a stepwise screening process across multiple databases, they filtered out non-orphan genes (NOGs), resulting in the identification of 2,586 OGs, representing 7.11% of the genome.
Comparative analysis between OGs and NOGs revealed that OGs were significantly smaller in gene and protein size, had fewer exons, lower GC content, and a higher isoelectric point. Further distribution analysis showed that 2,560 OGs were spread across seven chromosomes, with a higher density near the telomeres, indicating no strong chromosomal preference.
Subcellular localization analysis revealed OGs were primarily positioned in extracellular space, chloroplasts, and the nucleus. Gene duplication analysis showed that about 10.6% of OGs originated from gene duplication, with a majority attributed to dispersed duplication. Expression profiling demonstrated that OGs were predominantly expressed in reproductive tissues, particularly in the stamen and pistil ovary, suggesting their role in reproduction.
Using Weighted Gene Co-Expression Network Analysis (WGCNA), five modules of co-expressed genes were identified, showing involvement in key biological processes such as photosynthesis and hormone signaling. Additionally, 107 OGs were found to respond to both salt and drought stress, highlighting their potential role in environmental adaptation.
According to the study's senior researcher, Dr. Jian Mao, "Our study represents the first systematic identification of orphan genes in Rosa chinensis and provides valuable clues into how these genes contribute to stress resistance and flower development. This data will be crucial for future research on rose breeding and cultivation."
The identification of 2,586 OGs in R. chinensis opens new avenues for research into the unique genetic features that enable roses to adapt and thrive. This study provides a valuable genomic resource for future efforts aimed at improving rose cultivation and resilience.
More information: Dongna Ma et al, Orphan genes are involved in environmental adaptations and flowering process in the rose, Tropical Plants (2024). DOI: 10.48130/tp-0024-0036
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