Cloning and bioinformatics analysis of β-1,4-xylosyltransferase IRX9 gene from Dendrobium huoshanense / 中草药

ABSTRACT

Objective To clone IRX9 gene from Dendrobium huoshanense and perform the bioinformatics and codon bias analysis. Methods The full-length cDNA sequence was cloned from the IRX9 gene based on transcriptome sequencing data of D. huoshanense generated in our previous study by using RT-PCR and further analyzed by bioinformatic methods. Results The cloned IRX9 gene was 1 533 bp, containing a 1 047 bp open reading frame (ORF) which encoded 348 amino acids. The theoretical molecular weight was 39 350 and its isoelectric point was 7.26. IRX9 protein was a hydrophilic protein and had no signal peptide, which had multiple phosphorylation sites and glycosylation sites and might be located in the plasma membrane. Phylogenetic analysis indicated that sequence of amino acids had the highest homology with D. candidum and the conserved region “DXD” of the GT-A superfamily. Codon bias analysis showed that IRX9 gene prefered to use A/T ending codon, with 27 skewed codons. Nicotiana is the most suitable host for exogenous expression of IRX9 gene. Conclusion The IRX9 gene was cloned from Dendrobium huoshanense successfully and it provided a theoretical basis for regulating the growth and development of D. huoshanense and improving the yield and quality of D. huoshanense.