Genome-wide identification and expression analysis of PG gene family in wax apple [Syzygium samarangense (Bl.) Merr. et Perry]

Abstract:【Objective】Polygalacturonase (PGs) is a large gene family, which is expressed in different stages and tissues of plant development and plays different functions. In this study, we identified and an-alyzed the PGs gene family from the genome data of wax apple [Syzygium samarangense (Bl.) Merr. et Perry] with bioinformatics technology. It can provide reference for revealing its function and help to study its regulation mechanism for fruit cracking of wax apple.【Methods】The SsPGs were identified and analyzed by bioinformatics. The Arabidopsis PGs (AtPGs) protein sequences that were downloaded from NCBI gene database(https://www.ncbi.nlm.nih.gov) according to the gene ID were used as que-ries to search against wax apple genome data. The putative genes were identified based on a local BLASTP search of TBtool software at the score of e-20.0 value. The online website Pfam database and NCBI were further used to verify the conservative domain of the candidate protein by the Hidden Mar  kov Model (HMM) profiles of the PG gene family, which was Glyco_hydro_28 (PF00295). It was made further efforts to eliminate the genes that were too short and seriously missing the conservative do-main of the PG protein. In the end, 25 PG genes were identified in the whole genome of wax apple. TB-tool software was used to obtain the 2 kb upstream sequence of the translation initiation site of SsPGs gene from the genome of wax apple. The cis- acting elements in promoter region were predicted by plantcare, which is an online cis-element analysis website, and the predicted results were visualized by TBtools. The results showed that most of the SsPGs contained ABA response element. It is significant to study the function of gene by verifying the expression pattern of SsPGs. In order to study the re-sponse of wax apple to ABA, the fruit of wax apple was sprayed with 100 µmol·L^-1 ABA and distilled water as the control. After the treatment of 1 h, 4 d, 7 d and 10 d, the peel was collected. The peel was frozen in liquid nitrogen immediately, some of which was sent to the transcriptome and the other was used to test for the PG enzyme activity. Based on the transcriptome data, the expression of SsPGs in peel was analyzed and verified by qRT-PCR.【Results】25 members of SsPGs were identified in the whole genome of wax apple. They were randomly distributed on chromosomes 2 to 41 and were named as SsPG1- SsPG25 according to their positions on chromosomes from top to bottom. Among them, SsPG3 and SsPG4 on chromosome 2 and SsPG12 and SsPG13 on chromosome 18 were tandem re-peats. The protein length of the SsPGs ranged from 262 to 781 aa. Their isoelectric points were between 5.16 and 9.67, their protein molecular weights were between 28.27 and 84 ku, and their instability coef-ficients ranged from 27.48 to 59.88. Phylogenetic analysis showed that the PG proteins of wax apple, Arabidopsis, tomato, apple, grape, and jujube could be divided into seven groups (Group A-G). Except for SsPG1 of Group G, all the other SsPGs had highly conserved domains of PG family, and all the Ka/Ks values were less than 1, which indicated that the PG gene family was the mainly affected by purifica-tion selection in the process of evolution. The analysis of gene structure showed that the protein motifs of SsPGs family genes had obvious block identity, sequence homology and conservation. All the SsPGs contained introns and most of them had four conserved motifs (except SsPG1 of Group G), which indi-cated that they might play different functions in the evolution process. Expression pattern analysis showed that the expression of SsPGs was tissue-specific. It can be predicted that they might be related to nutritional and reproductive growth and participate in different signal transduction pathways. Gene expression analysis showed that SsPG2, SsPG4, SsPG18 and SsPG19 were expressed in the flower and ovary and SsPG22 was expressed in flesh, which indicated that they might be related to fruit develop- ment. The specifical expression of SsPG12, SsPG13 and SsPG24 in roots and the high expression of SsPG2, SsPG3 and SsPG5 in stems and leaves suggested that they might be related to vegetative growth. After exogenous ABA treatment, PG activity increased significantly and decreased after reach- ing the maximum value. The fruit cracking rate of the treatment group was higher than that of the con-trol group after 10 d; qRT-PCR data analysis showed that compared with the control group, the expres-sion of SsPG2 and SsPG4 in peel was all up-regulated, and the expression of SsPG4 was the highest in the SsPGs family.【Conclusion】A total of 25 SsPGs were identified from the genome data of wax apple, all of which contained introns and distributed into 6 groups, which were named Group A-E and G. SsPG2, SsPG4, SsPG18 and SsPG22 might play an important role in the change of PG activity and fruit cracking. SsPGs might have different functions and participate in different signal transduction pathways in the process of vegetative and reproductive growth.