Identification and bioinformatics analysis of thaumatin-like protein gene in Chinese jujube

Abstract：【Objective】Thaumatin like proteins (TLPs) include thaumatin, osmotin, zeamatin, and related proteins, which belong to the pathogenesis-related family (PR5) of plant defense proteins and are encoded by a multiple gene family. TLPs play an vital role in the enhancement of plant resistance to biotic and abiotic stresses due to involvement in defense system. Like other PRs, TLPs belong to a general plant stress response pathway rather than being specific to distinct stresses. TLPs possess antifungal, glucanase, allergens activities. Fruit diseases and storage would affect yield and fruit quality of Chinese jujube (Ziziphus jujuba Mill.). A genome-wide identification was performed to investigate the TLP gene number, evolution and gene expression ability in Chinese jujube, through comparison with those of Arabidopsis thaliana, Oryza sativa and Populus trichocarpa.【Methods】TLP family member were identified based on the genome database of Chinese jujube. TLP sequences of A. thaliana were used as queries to obtain the member of the TLP family through searching the database of Chinese jujube protein on NCBI website. The sequences were then confirmed as encoding TLP for the presence of a thaumatin domain signature by SMART database searches. Chromosomal locations were determined using the annotation information of TLP genes genome data. The physiological and biochemical characteristics of protein were predicted using Prot Param at Ex PASy server. The schematic diagrams of the gene structure were drawn using Gene Structure Display Server. Multiple sequence alignments of full-length proteinsequences were accomplished using Clustal W. And the neighbor-joining (NJ) method in MEGA 5 software was used to carry out phylogenetic tree analyses of the Chinese jujube TLPs with the default evolutionary model, and bootstraps with 1 000 replicates were used to test the convergence of phylogenetic trees. The cis-acting elements distribution of the gene promoter was analyzed by Plant CARE database. Codon usage parameters were analysed using Codon W software. Relative synonymous codon usage were calculated using Cusp at the EMBOSS explorer server. The optimal codon was defined with the abundance values relative synonymous codon usage (RSCU) >1 in the high expression genes group [the first 10% genes of low effective number of codons (ENC) value] and the abundance values RSCU<1 in the low expression genes group (the last 10% genes of high ENC value) .【Results】Thirtyfour genes of the TLP family were identified in Chinese jujube. They were located on nine chromosomes. Four types of gene structures were found. The numbers of genes containing 1, 2, 3 and 4 exons were 10, 11, 11, and 2, respectively. Gene structure analysis indicated that TLP family gene structures were relatively simple in Chinese jujube, implying that the gene structures were relatively stable, and alternative splicing was rare during replication. Phylogenetic analysis indicated that Chinese jujube TLP gene family was classified into nine clusters, and the cluster five and six had the largest number of TLPs, suggesting that partial TLP members were involved in the tandem and segmental duplication events. The disequilibrium of the distribution of TLP family members in each cluster might be related to gene functions. Multiple cis-acting elements related to strengthen expression, hormone and stress response were found on the promoter region of TLP genes, indicating that these genes would play a role in plant defense against stresses. Codon analysis showed that the mean value of CAI was 0.235. ENC values were higher than 45.00 and the distribution of GC3 s value was dispersed. Eleven optimal codons were found, and the number of ending with A, T, G and C were 3, 3, 2 and 3, respectively. Codon analysis indicated that the gene codon usage was weak, and the gene evolution was mainly affected by gene mutation. Purifying selection might play an important role in function maintenance of this family.【Conclusion】This was the first comprehensive experimental survey of the TLP gene family in Chinese jujube. TLP family genes would be conservative in evolutionary process, being involved in plant development and stress response regulation. The evolution of Chinese jujube TLP family genes might be mainly influenced by base mutation pressure, and few genes might be affected by natural selection pressure.These investigations would provide theoretical support for functional analysis and genetic breeding application of this gene family in Chinese jujube.