Insilco identification and characterization of superoxide dismutase gene family in Brassica rapa

Abstract

Superoxide Dismutase SODs are defense associated proteins that detoxify ROS and primarily serve as scavengers. They have been described in numerous plant species, but their in-depth characterization in Brassica rapa has not been reported. Therefore, the present investigation on genome wide study of SOD gene family was conducted to identify BrSOD genes, their domain-based organization, gene structure analysis, phylogenetic analysis, intron-exon structure of genes and expression analysis. The sequence characterization of Super oxide dismutase gene family in Brassica rapa, their syntenic associateship of conserved motifs and phylogenetic correlationship, prediction of cis-elements and determing the expression analysis in distinct tissues namely plant callus, root, stem, leaf, flower, and silique under abiotic conditions have been analysed using different software's. The study on SOD gene family identified 17 BrSOD genes which were grouped into eight BrCu-ZnSODs and nine BrFe-MnSODs domain-based organization. Furthermore, the conserved character of BrSODs were confirmed by intron-exon organisation, motif arrangements and domain architectural investigations. Expression analysis using RNA Sequence data of different developmental stages proclaimed that genes were manifested in all six tissues with an exception of BrCu-ZnSOD3, which was not manifested in roots; however, whose transcript was detected in all other tested tissues. The study has genome wide insight into the occurrence and functional specifications of BrSOD gene family in Brassica rapa that can be potentially utilized in breeding program for resilience to climate change and abiotic stresses tolerance Brassica variety.

Keywords: Brassica rapa; Gene family; Genome-wide analysis; In-silico analysis; Reactive oxygen species; Superoxide dismutase.

Fig. 1

Chromosomal locations of seventeen BrCu-ZnSOD & BrFe-MnSOD genes are specified on crown of the chromosomes and chromosome duplication occurred between chromosomes, same colour of stars present on the chromosome represent duplication of chromosomes in Brassica rapa.

Fig. 2

Intron/exon configurations of SODgenes in Brassica rapa.

Fig. 3

(a) Block diagram of ten conserved protein motifs representing motif arrangements and motif sequences in SODs of Brassica rapa. (b) Motif Sequences. Red coloured stars indicate copper metal bind sites in motif 1, 2, 4, 6 &10 and blue coloured stars in motif 1 and 10.

Fig. 4

Phylogenetic relationship of SODs among three species Brassica rapa, Brassica napus, Brassica oleraceae, Arabidopsis thaliana, Triticum sativum, and Oryza sativa. Genes of BrCu-ZnSODs and BrFe-MnSODs of Brassica rapa are marked with different colors.

Fig. 5

a&b: Predicted 3D model structure and binding sites of BrCu-ZnSOD and BrFe-MnSODin Brassica rapa.

Fig. 5

a&b: Predicted 3D model structure and binding sites of BrCu-ZnSOD and BrFe-MnSODin Brassica rapa.

Fig. 6

Interaction analysis of SOD proteins in B. rapa.

Fig. 7

Relative expression profiles BrSODs at various developmental stages of Brassica rapa. The heat map's tint system is based on a log 2 intensity value.