Genome-Wide identification, phylogenetic analysis, and expression of CONSTANS-Like genes in Rosa chinensis in response to Tetranychus urticae infestation

Abstract

CONSTANS-Like genes play critical roles in plant responses to both biotic and abiotic stresses, but their functions in Rosa chinensis remain poorly understood. In this study, we conducted a genome-wide investigation of COL genes in R. chinensis, identifying 18 genes, designated from RcCOL_1 to RcCOL_18. Phylogenetic analysis revealed that these genes were unevenly distributed across three subfamilies (RcCOL_I to RcCOL_III), with RcCOL_III containing the most members. Interspecies evolutionary analysis of 14 Rosaceae species showed that COL genes presented across all these species, though the number of genes varied. Cis-acting element analysis indicated that the RcCOL genes mainly contained elements related to biotic and abiotic stress, light response, as well as growth and development, with RcCOL_4/_13/_14/_15, RcCOL_8/_17/_18, and RcCOL_5/_6/_16 showing highly consistent element distributions. Expression pattern analysis under red spider (Tetranychus urticae) attack revealed that subfamilies I and II of the COL gene family play a primary role in the regulation of plant response. Quantitative real-time polymerase chain reaction (qRT-PCR) verification showed that nearly all RcCOL genes were highly expressed following red spider infestation; however, these over-expressed genes were suppressed after introducing predatory mite (Neoseiulus californicus). This indicates that the RcCOL genes may play significant roles in the biotic stress response in R. chinensis. Correlation analysis of RcCOL genes with secondary metabolites demonstrated strong associations. For instance, RcCOL_1 and RcCOL_2 were highly correlated with geranylacetone, periplogenin, and syringetin, while RcCOL_3 and RcCOL_12 showed strong correlations with N-acetyltryptamine, uridine 5′-monophosphate, and isorhamnetin. Additionally, RcCOL_7 was highly correlated with L‑serine and 3-methylxanthine, and RcCOL_10 with byakangelicin, hippuric acid, and nicotineamide. RcCOL_14 and RcCOL_15 were strongly correlated with metabolites such as pidotimod, vinorelbine tartrate, and okadaic acid. These findings suggest that RcCOL genes modulate secondary metabolite production and play critical roles in the biotic stress response of plants.