Bioinformatics analysis of the lignin-related protein——PgCAD protein in pomegranate

Abstract: 【Objective】Study on the mechanism of Punica granatuma soft-seed by analyzing its lignin-re⁃lated protein—PgCAD protein.【Methods】In this article，by utilizing the bioinformatics method，we ana⁃lyzed the phylogenetic of 18 CAD protein that is related to growth of Punica granatuma firstly，and thenpredicted and analyzed PgCAD protein，EgCAD protein and AtCAD protein amino acid composition，physical and chemical characteristics，as well as secondary and teriary structures，meanwhile，we still assayedtheir domains and motifs.【Results】These 18 amino acid sequences could be clustered into three groups，the closest relationship with Punica granatuma is Eucalyptus grandis，and the furthest relationship with isArabidopsis thaliana. The research still found that the number of amino acid between these amino acid se⁃quences presented some differences，meanwhile both PgCAD protein and EgCAD protein are hydrophilicprotein，AtCAD protein being opposite of them. In addition，the results of secondary structure predictedthat the main composition of PgCAD protein and EgCAD protein was α- helix and random curl，butAtCAD protein’s is α-helix，random curl and extended strand. Furthermore，The tertiary structure ofPgCAD protein and EgCAD protein were quite similar，which is totally differernt from AtCAD protein. Fur⁃ther，PgCAD protein and EgCAD protein has the same domain-NADB domain，which is differernt fromAtCAD protein’s. The type and distribution of motifs discovered of PgCAD protein is similar to its proxi⁃mal species，which AtCAD protein presented some differences from others.【Conclusion】These resultsdemonstrate that the CAD protein is conserved in the structure of Punica granatuma and Eucalyptus grandis，but differs greatly from that of Arabidopsis thaliana. Interpret PgCAD protein regulation of lignin synthesis how to effect Punica granatuma soft-seed development，to further understand the biological func⁃tion of PgCAD protein in the process of Punica granatuma lignin synthesis and lay the foundation .