The unique evolutionary pattern of the Hydroxyproline-rich glycoproteins superfamily in Chinese white pear (Pyrus bretschneideri)

Abstract

Background: The hydroxyproline-rich glycoprotein (HRGP) superfamily, comprising three families (arabinogalactan-proteins, AGPs; extensins, EXTs; proline-rich proteins, PRPs), is a class of proline-rich proteins that exhibit high diversity and are involved in many aspects of plant biology.

Results: In this study, 838 HRGPs were identified from Chinese white pear (Pyrus bretschneideri) by searching for biased amino acid composition and conserved motifs. 405 HRGPs were derived from whole genome duplication (WGD) events which is suggested to be the major force of driving HRGPs expansion and the recent WGD event shared by apple and pear generated most duplicated HRGPs in pear. This duplication event drived the structural variation of the HRGPs encoding hydroxyproline (Hyp)-rich motifs. The rate of HRGPs evolution mainly impacted the Hyp-rich motifs even in chimeric HRGPs. During the evolution of 53 PRPs that are also typified by 7-deoxyloganetin glucosyltransferase-like genes, the duplication from PRP to non-PRP was indirectly modified by positive selection. These results suggested that the rate of HRGP evolution mainly influenced the Hyp-rich motifs even in chimeric HRGPs. The expression divergence of HRGPs was higher than that of other commonly duplicated genes. In pear pistil, 601 HRGPs exhibited expression, while in pear pollen, 285 HRGPs were expressed. The qPCR results revealed that Pbr036330.1 and Pbr010506.1 showed different expression profile in self-incompatibility of pear pistil.

Conclusions: The researches indicated that WGD events was the main duplication type during the evolution of HRGPs, and the highly variable Hyp-motifs might be accountable for the expansion, evolution and expression divergence of HRGPs and that this divergence may be responsible for the gain of new functions in plants.

Keywords: Evolutionary pattern; Expression divergence; Gene duplication; HRGPs; Hyp-rich motif; Positive selection.

Fig. 1

Phylogenetic tree of the AGP family. Green columns indicate the percentage of P, A, S and T in each AGP; pink columns indicate the total number of P, A, S and T in each AGP

Fig. 2

Gene duplication analysis of HRGPs in pear. a. Gene pairs within HRGPs are joined by red lines; gene pairs in which only one duplicated gene is an HRGP are joined by black lines. Average GC content is indicated by coloured columns outside the chromosomes. Regions with high GC content are indicated by red columns, and low GC regions are indicated by green columns. b. The alignments of two collinear gene pairs between EXT-AGPs and lysine-rich AGPs. The mutant amino acid sequences are indicated by black boxes

Fig. 3

The relative duplication time of HRGPs as indicated by Ks values. a-c. The relative duplication time of the AGP (A), EXT (B) and PRP (C) families. The yellow region ranging from 0.15 to 0.3 indicates the recent WGD events shared by pear and apple

Fig. 4

Comparison of evolutionary rates between chimeric EXTs and corresponding homology genes without proline-rich motifs. a Comparison of evolutionary rates between LRR family and LRR-HRGP family. b Comparison of evolutionary rates between Pkinase-Tyr family and Pkinase-Tyr-HRGP family. c Comparison of evolutionary rates between RRM family and RRM-HRGP family. d Comparison of evolutionary rates between LTP family and LTP-HRGP family. Abbreviations: LRR: leucine-rich domain; Pkinase-Tyr: protein tyrosine kinase; RRM: RNA recognition motif; LTP: liquid transfer domain

Fig. 5

The variation of Hyp-rich motifs in PRPs is affected by selective pressure. a. The phylogenetic tree and corresponding motifs of PRPs and non-PRPs. Red taxa refer to PRPs and black taxa refer to non-PRPs. b. Amino acid compositions of 53 PRPs and non-PRPs. c. Comparison of omega among all sites within the motif

Fig. 6

The evolution pattern of PRPs in the 7-deoxyloganetin glucosyltransferase family. a. The selective pressure acting on total amino acid sites. The significant positively selected sites are marked by red circles. b. The positively selected site S₁₂₀ mutated to K₁₂₀ among PRPs and non-PRPs. Red taxa refer to PRPs and black taxa refer to non-PRPs. c. The divergence time of 7-deoxyloganetin glucosyltransferase family. The red line refers to 0.4871, indicating the divergence time of PRPs and non-PRPs in the blue clade

Fig. 7

Selective pressure promotes the structure variation of chimeric HRGPs. a. The selective pressure acting on total amino acid sites. The statistically significant positively selected sites are marked by red circles. b. A phylogenetic tree constructed from 42 sequences containing the Pollen Ole e I domain among all chimeric HRGPs. Violet refers to the recent WGD event and Orange H indicates the positively selected amino acid site

Fig. 8

Comparison of the expression divergence among HRGP gene pairs, randomly paired HRGP genes and total gene pairs. The gene pairs of totally expressed genes were acquired by MCScanX. The expression profile employed in this analysis was the RPKM value of pollinated pistils