In silico cloning and characterization of chitinase gene from sugarcane using bioinformatics tools

A novel chitinase gene SCCHI1 from sugarcane (Saccharum officinarum) was cloned in silico based on the corresponding sugarcane EST sequences in NCBI database.Some characters of amino acids encoded by SCCHI1 gene,including the composition of amino acid sequence,physical and chemical properties,transmembrane domain,hydrophobicity/hydrophilicity,subcellular localization,secondary and tertiary structure of protein plus the functional domain,were analyzed by bioinformatics tools.Bioinformatic analysis showed that the full-length SCCHI1 gene from sugarcane was 1 236 bp and it contained a complete ORF which encoded 329 amino acids.Furthermore,SCCHI1 belonged to glycoside hydrolase family 19 and contained a N-terminal signal peptide,a hinge region and a catalytic domain,which was highly conservative among chitinases from several different plant species.The results above provided some references for experimental cloning of SCCHI1 gene from sugarcane,identification and its application.