Bioinformatics analysis and expression characteristics analysis of UGDH gene family in hybrid Broussonetia kazinoki×Broussonetia papyifera

Cloning, bioinformatics and expression analysis of UGDH gene family members in Broussonetia kazinoki×Broussonetia papyifera.

The UGDH gene sequences were obtained by using the transcriptome data of B. kazinoki×B. papyifera., named BpUGDH1, BpUGDH2 and BpUGDH4, respectively. The primers were designed to clone the UGDH gene family members of the hybrid B. papyrifera (BpUGDH3 has been cloned in the previous study). Bioinformatics analysis was performed using ExPASy, MHMMServerv2.0, Swiss-ModelL, SOPMA, MEGA11.0 and other software. The gene expression differences of different organs and tissues were analyzed by qRT-PCR.

The full-length sequences of BpUGDH1, BpUGDH2, BpUGDH3 and BpUGDH4 were 1 895, 927, 1 658 and 481 bp, respectively, encoding 480, 249, 480 and 131 amino acids. BpUGDH2 was a hydrophobic protein, and the rest was a hydrophilic protein. BpUGDH gene did not contain signal peptide. There is no transmembrane domain, and the proteins all had a conserved domain of the PLNO2353 superfamily. Multiple sequence alignment showed that the similarity between BpUGDH1, BpUGDH2, BpUGDH3 and BpUGDH4 protein sequences was 68.39%. The phylogenetic tree BpUGDH1 was clustered with soybean UGDH2. BpUGDH2 was closely related to soybean UGDH4, and BpUGDH2 and BpUGDH4 were clustered together. BpUGDH4 was closely related to rice UGDH1, rice UGDH2 and maize UGDH2. BpUGDH3 had a close relationship with Arabidopsis. Protein secondary structure analysis showed that BpUGDH1, BpUGDH2 and BpUGD4 were dominated by alpha helix and random coil, while BpUGDH3 was dominated by random coil, accounting for 39.79%. The results of qRT-PCR showed that the expression of BpUGDH1 was the highest in leaves. The expression of BpUGDH2 was the highest in root. The expression level of BpUGDH3 was the highest in the stem, and the expression level of BpUGDH4 was the highest in the stem.

In this study, the UGDH1, UGDH2 and UGDH4 genes of hybrid B. papyrifera were cloned and analyzed by bioinformatics with the UGDH3 gene of hybrid B. papyrifera. It laid a theoretical foundation for the study of the regulation of hemicellulose and pectin content and the interaction between them.