Genome-wide identification and transcriptome-based expression analysis of hybrid sugarcane calmodulin-binding transcription activators under drought

Abstract

As the highly demanding complex genome of the hybrid sugarcane cultivar became publicly available recently (2023), it opened avenues to further study this important crop at molecular level. We are interested in digging the multiple stress responsive transcription factors family, the Calmodulin-Binding Transcription Activator (CAMTA) of sugarcane. This manuscript presents a comprehensive study of ScCAMTA family based on the latest sugarcane genome sequence information. Within the 10 gb genome, through HMM model prepared from sorghum CAMTA common domains, we found 48 genes, 46 out of which carry all the CAMTA-associated domains including CG-1, TIG, IQ and Ank. The phylogenetic analysis clustered then into seven classes. Keeping sorghum as reference, we named them as ScCAMTA1 – ScCAMTA7, while each one representing a class having 5–7 copies such as ScCAMTA1A – ScCAMTA1E, present in each sub-genome (chromosome) within the hybrid sugarcane. In parallel to determining their physico-chemical attributes, miRNA targets, protein interaction network and genome collinearity, we observed evolutionary conservation in gene structures, protein domains, and motif organization across the phylogenetic classes. Promoter analysis revealed the presence of multiple stress-responsive cis-regulatory elements, such as MBS (drought) and MYB (salinity), suggesting their direct involvement in stress adaptation. MicroRNA target analysis predicted 20 unique miRNAs targeting ScCAMTA transcripts, highlighting potential post-transcriptional regulation. Additionally, protein-protein interaction networks indicated functional connections to stress signaling pathways. Finally, their expression patterns under drought stress were determined using RNA-seq data, which revealed that ScCAMTA7 is highly active under drought conditions, underscoring its potential role in drought response. This study furthers the insights into complex sugarcane genome and will assist in developing its drought-tolerant varieties.