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Genome-wide identification and expression pattern analysis of the Polygalacturonase gene family in blueberry (Vaccinium spp.)

agricultural-science
bioinformatics
molecular-biology
plant-science

Abstract

Fruit firmness is an important quality attribute of blueberry fruit, mainly regulated by cell wall degradation. Polygalacturonases (PGs) are cell wall-modifying enzymes known to influence fruit firmness. In this study, we identified 135 VcPGs from the blueberry genome that were unevenly distributed across 40 chromosomes and classified them into 7 clades through phylogenetic analysis. Members of the same subfamily had relatively conserved gene structures and motif distributions. A variety of cis-acting regulatory elements were investigated in VcPGs promoter regions, with light-responsive, abscisic acid-responsive, and MYB transcription factor binding site elements being the most abundant. Most VcPGs were under purifying selection during evolution, and whole genome duplication or fragmental duplication were the main reasons for VcPGs' expansion. Analysis of cis-acting elements implied the potential effects of abscisic acid on VcPGs. Motivated by the promoter analysis, we analyzed transcriptome data to study the effects of exogenous abscisic acid treatment on VcPGs expression during fruit maturation. Furthermore, to investigate the potential involvement of VcPGs in fruit firmness regulation, we analyzed the differential expression patterns of VcPGs during the ripening process of firm and soft blueberry fruits, and validated the transcriptomic data accuracy by conducting real-time fluorescent quantitative analysis on five differentially expressed VcPGs. The obtained results provide the basics for further mechanistic research of VcPGs in blueberry fruit firmness regulation and other functions.
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