PR1 proteins are among the best-characterized defense-related proteins in plants. They belong to the broader pathogenesis-related protein superfamily, which accumulates in plant tissues following attack by pathogens or exposure to stress-inducing signals. Although PR1 gene families have been catalogued in numerous plant species, their composition and behavior in watermelon during CGMMV infection had remained largely unexplored. The new study addresses that gap by combining genome-wide identification with expression profiling under viral challenge, offering a systematic view of how this gene family is organized and regulated in the face of a major viral pathogen.

The researchers began by scanning the reference watermelon genome of cultivar 97103 for PR1 sequences. They identified 19 ClPR1 genes, named according to their position in the genome. Phylogenetic analysis, which compares protein sequences to reconstruct evolutionary relationships, classified these genes into three subgroups spanning Groups II to IV. The genes were unevenly distributed across five chromosomes, a pattern that hints at lineage-specific duplications and losses during the evolution of this gene family in watermelon. Structural analysis showed that each ClPR1 gene contains a CAP or CAP superfamily domain, the signature feature of PR1 proteins, and that 78.95 percent of the genes are intronless, meaning they lack the non-coding interruptions commonly found in plant genes. Intronless genes can often be transcribed rapidly, a property that may be advantageous during the early stages of a pathogen attack.

To understand how these genes might be regulated, the team predicted cis-acting elements in the promoter regions upstream of each ClPR1 gene. Promoters act as molecular switches that determine when and where a gene is transcribed, and the elements they contain reveal which signals can activate them. The analysis found that the main cis-acting elements in ClPR1 promoters respond to hormone signaling, stress responses, and transcription factor binding, with recognition sites for MYB and MYC transcription factors particularly prominent. This suggests that ClPR1 genes are wired to respond to a broad range of endogenous and environmental cues, including those triggered by viral infection.

Expression profiling across different tissues showed that ClPR1 genes are not confined to a single organ but are expressed in various parts of the plant. More importantly, the researchers found that CGMMV infection induces the expression of specific ClPR1 genes in a manner that depends on both the tissue and the genotype of the plant. Four genes in particular, ClPR1-1, ClPR1-2, ClPR1-6, and ClPR1-15, showed tissue- and genotype-specific induction following viral challenge. ClPR1-2 stood out for being strongly induced at the early stage of infection in leaves, suggesting it may serve as an early sentinel in the plant’s defense response.

The study also compared two watermelon genotypes with contrasting responses to CGMMV: a resistant line designated PI and a sensitive line designated ZK. Differentially expressed ClPR1 genes between these two genotypes, specifically ClPR1-1, ClPR1-6, and ClPR1-15, were identified as candidates that may play important roles in the plant’s response to CGMMV infection. The fact that these genes behave differently between resistant and sensitive lines suggests that their regulation, rather than their mere presence, may determine how effectively a watermelon plant can mount a defense against the virus.

Beyond expression profiling, the researchers used transcription factor binding-site prediction to identify potential upstream regulators of the CGMMV-inducible ClPR1 genes. This analysis pointed to the ERF family of transcription factors, which are central components of the ethylene signaling pathway, as likely regulators. To test this experimentally, the team applied exogenous ethylene, or ETH, to watermelon plants and found that the treatment significantly enhanced the expression of specific ClPR1 genes. These findings suggest that ethylene signaling may be involved in the transcriptional regulation of ClPR1 genes during the watermelon response to CGMMV infection, linking a well-known plant hormone pathway to the antiviral defense machinery of this crop.

CGMMV is a member of the genus Tobamovirus and is a serious constraint on watermelon and other cucurbit production worldwide. The virus spreads through contaminated soil, seed, and mechanical contact, and once it establishes in a field it is difficult to eradicate. Understanding the molecular basis of watermelon’s response to this pathogen is therefore of considerable practical importance. By pinpointing the ClPR1 genes that respond to CGMMV and identifying the signaling pathways that regulate them, the study provides a foundation for breeding programs aimed at developing resistant cultivars and for biotechnological approaches that could enhance antiviral defense in this crop.

The authors emphasize that their findings offer comprehensive insights into the ClPR1 gene family and identify candidate genes for further functional investigations into how watermelon responds to CGMMV. The work was published as an open access article in BMC Plant Biology, received no external funding, and is citable with a permanent DOI. As research into plant-virus interactions continues to advance, studies like this one, which systematically catalogue defense gene families and connect them to specific pathogens and signaling pathways, are essential for translating molecular knowledge into agricultural practice.

Subject of Research: Genome-wide characterization and CGMMV-responsive expression profiling of the pathogenesis-related protein 1 gene family in watermelon

Article Title: Genome-wide characterization and CGMMV-responsive expression profiling of the pathogenesis-related protein 1 gene family in watermelon

Article References: Liu, M., Feng, Y., Li, Q., & Li, W. (2026). Genome-wide characterization and CGMMV-responsive expression profiling of the pathogenesis-related protein 1 gene family in watermelon. BMC Plant Biology. https://doi.org/10.1186/s12870-026-10167-8

Image Credits: AI Generated

DOI: 10.1186/s12870-026-10167-8

Keywords: Genome-wide, characterization, CGMMV-responsive, expression, profiling, pathogenesis-related, protein, gene, family, watermelon, scientific research