Bioinformatic Characterization and Phylogenetic Analysis of Cold-Regulated Genes Across the Genus Eucalyptus

Abstract

Cold or frost stress is one of the severest abiotic stresses which hinders the distribution, productivity and yield of Eucalyptus worldwide. Almost all aspects of cellular functions are affected under the exposure of cold stress. Being an economically important species, development of cold tolerance in Eucalyptus is very important. Different signalling cascades are known to be activated under cold stress. ICE1-CBF pathway is found to play master regulatory role in cold stress sensing pathways in majority of woody forest plants. In this study, across the genus Eucalyptus, 24 cold-regulated genes (CORs) are identified, divided in 3 gene families namely ICE, CBF and DHN, characterized by the presence of signature motifs and conserved domains in the sequences. Exhaustive location on chromosomes and sequences for these genes are acquired from several databases. These sequences are further analysed with several bioinformatic tools to establish evolutionary relationships among them. Predicted protein sequences from BLASTX are subjected to multiple sequence analysis and percentage similarity matrices are constructed with BLOSUM62. Phylogenetic trees for every gene family are developed using MEGA X using the Maximum Likelihood (ML) method and statistically validated through bootstrapping method. The analysis of these ICE, CBF and DHN genes directed towards cross-talk of different stress response pathways. Cluster of CBF genes are found in Eucalyptus resembling high similarity suggesting a major duplication event during the evolutionary track of this genus. The results of this study will prove to be beneficial in understanding the cold acclimation process and developing genetically improved cold tolerant Eucalyptus.