Genome-Wide Identification and In-silico Expression Analysis of CCO Gene Family in Sunflower (Helianthus annnus)

Abstract

Abstract Carotenoid cleavage oxygenases (CCOs) enzymes play an important role in plant growth and development by producing a wide array of apocarotenoids and their derivatives. These compounds are vital for colouring flowers and fruits and synthesizing plant hormones such as abscisic acid and strigolactones. Despite their importance, the gene family responsible for CCOs in sunflowers has not been studied. In this study, we identify the CCO genes of the sunflower plant to fill this knowledge gap. Phylogenetic and synteny analysis indicated that the Helianthus annnus CCO (HaCCO) proteins are conserved in different plant species and they can be divided into three subgroups based on their conserved domains. MEME analysis and multiple sequence alignment showed that conserved motifs exist in the sequence of HaCCO genes. Cis-regulatory elements (CREs) analysis of the HaCCO genes revealed the presence of multiple plant hormones and abiotic and biotic responsive elements in their promoters, suggesting that these genes might be responsive to plant hormones, developmental and drought stress, which could be utilized to develop more resilient crops. Genes belonging to the 9-cis-epoxy carotenoid dioxygenases (NCED) subgroups predominantly exhibit chloroplast localization, whereas the genes found in other groups are primarily localized in the cytoplasm. These 21 identified HaCCOs were regulated by 60 miRNAs indicating the crucial role of microRNAs in gene regulation in sunflowers. Gene expression analysis under drought stress revealed significant up-regulation of HaNCED16 and HaNCED19 genes that provide pivotal role in ABA hormone biosynthesis. While during organ-specific gene expression analysis HaCCD12 and HaCCD20 genes exhibit higher activity in leaves, indicating a potential role in leaf pigmentation. These studies provide a foundation for future research on the regulation and functions of this gene family. It could potentially be utilized to develop molecular markers that could be used in breeding programs to develop new sunflower lines.