Dissecting the complex molecular evolution and expression of polygalacturonase gene family in Brassica rapa ssp. chinensis

Abstract

Polygalacturonases (PGs) participate in pectin disassembly of cell wall and belong to one of the largest hydrolase families in plants. In this study, we identified 99 PG genes in Brassica rapa. Comprehensive analysis of phylogeny, gene structures, physico-chemical properties and coding sequence evolution demonstrated that plant PGs should be classified into seven divergent clades and each clade's members had specific sequence and structure characteristics, and/or were under specific selection pressures. Genomic distribution and retention rate analysis implied duplication events and biased retention contributed to PG family's expansion. Promoter divergence analysis using "shared motif method" revealed a significant correlation between regulatory and coding sequence evolution of PGs, and proved Clades A and E were of ancient origin. Quantitative real-time PCR analysis showed that expression patterns of PGs displayed group specificities in B. rapa. Particularly, nearly half of PG family members, especially those of Clades C, D and F, closely relates to reproductive development. Most duplicates showed similar expression profiles, suggesting dosage constraints accounted for preservation after duplication. Promoter-GUS assay further indicated PGs' extensive roles and possible redundancy during reproductive development. This work can provide a scientific classification of plant PGs, dissect the internal relationships between their evolution and expressions, and promote functional researches.

Genome-Wide Identification and Analysis of Polygalacturonase Genes in Solanum lycopersicum

“…In accordance with previous research, we found that more than half SlPGs of Group I belonged to Clade E and were also defined as being expressed ubiquitously (Figure 4, Table S3) which further proved the previous theory that the Clade E members of PG family are possibly ancient proteins and are fundamental and indispensable in almost all plant organs of different species [7,10]. The PG genes of Clades C, D, and F may be associated with flower development, and the main expression pattern of PGs in clades C and F may be different between the grasses and dicots [7,9,10,12]. Coincidentally, most PGs of Clades C and D can also be observed to show flower-specific expressions in tomato.…”

“…Phylogenetic analysis of the PG gene family has been carried out in many studies, from the initial classification of three Clades (A, B, and C) to the adjustment and expansion of the six and seven Clades (A to F and A to G) [2,5,10,12]. In this study, the tomato PG gene family was classified by the A to G classification according to the analysis of their phylogenetic tree as in the previous research about the PG gene family of C. sativus and B. rapa [8,12]. The analysis of the structure of introns and exons and the conserved motif and domain of tomato PG genes revealed that Clades A, B, and F contained relatively more introns.…”

“…The SlPG genes could be clustered into six groups according to the expression patterns in different tomato tissues based on the hierarchical clustering results. In B. rapa and C. sativus , most BrPG and CsPG genes in Clade E were found to be ubiquitously expressed in different tissues [8,12]. Expression patterns of PG genes in the other two dicots ( Glycine max and Medicago truncatula ) and two grasses ( Zea mays and O. sativa ) also showed that most of the clade E members could be detected at high overall expression levels in all tissues [7].…”

“…On the basis of the amino acid sequence of the 68 Arabidopsis PG genes identified and systematically nominated in a previous research [12], TBLASTN searches were conducted in tomato genome database. In detail, TBLASTN search of Arabidopsis PG protein sequences were carried out in the tomato genome database v2.5 (available online: ) with default algorithm parameters.…”

“…Up to now, the expression patterns of 75, 53, 46, 68, 99, and 85 PG genes in Populus , Cucumis sativus , Oryza sativa , Arabidopsis thaliana , Brassica rapa and Malus × domestica have been respectively investigated [8,9,10,11,12]. Additionally, a total of 577 PGs have been identified from five grasses and five dicots.…”