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Article

Analysis of PRX Gene Family and Its Function on Cell Lignification in Pears (Pyrus bretschneideri)

by
Zhihua Xie
1,†,
Weikang Rui
1,†,
Yazhou Yuan
1,
Xiaofei Song
1,
Xing Liu
1,
Xin Gong
1,
Jianping Bao
2,
Shaoling Zhang
1,
Khanizadeh Shahrokh
3 and
Shutian Tao
1,*
1
Pear Engineering Research Centre, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
2
College of Plant Science, Tarim University, Ala’er 843300, China
3
ELM Consulting Inc., St-Lazare, QC J7T 3C2, Canada
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Plants 2021, 10(9), 1874; https://doi.org/10.3390/plants10091874
Submission received: 20 August 2021 / Revised: 4 September 2021 / Accepted: 7 September 2021 / Published: 10 September 2021
Browse Figures
Versions Notes

Abstract

:
Class III peroxidases (PRXs) are plant-specific enzymes that play key roles in the responses to biotic and abiotic stress during plant growth and development. In addition, some peroxidases also play roles in plant lignification. In this study, a total of 114 PRX (designated PbPRXs) genes were identified in the pear (Pyrus bretschneideri Rehd) genome based on systematic analysis. These PRX genes were divided into 12 groups based on their phylogenetic relationships. We performed systematic bioinformatics analysis of the PRX genes, including analysis of gene structures, conserved motifs, phylogenetic relationships, and gene expression patterns during pear fruit growth. The PbPRXs are unevenly distributed on the 17 pear chromosomes and some of them on other scaffolds. Gene duplication event analysis indicated that whole-genome duplication (WGD) and segmental duplication play key roles in PRX gene amplification. Ka/Ks analysis suggested that most duplicated PbPRXs experienced purifying selection, with limited functional divergence during the duplication events. Furthermore, the analysis indicated that those highly expressed genes might play significant roles in the lignification of cells to form stone cells in pear fruit. We examined the expression of those highly expressed genes during fruit growth using quantitative real-time PCR (qRT-PCR), verifying differential expression patterns at different stages of fruit. This study provides useful information for further functional analysis of the PRX gene family in pears.

1. Introduction

Class III peroxidases (PRXs; EC 1.11.1.7) are plant-specific enzymes that can catalyze the reduction of H2O2 by moving electrons to various donor molecules such as phenolic compounds, lignin precursors, or secondary metabolites [1]. Plant PRX proteins are involved in several important physiological and developmental processes, including lignin and suberin formation, the cross-linking of cell wall components, wound healing, the removal of H2O2, the oxidation of toxic reductants, and defense against pathogen or insect attack [1,2,3]. For example, Arabidopsis peroxidase 72 (AtPrx72), which is homologous to ZePrx, plays an important role in lignification [4]. Besides AtPrx72, AtPrx02, AtPrx09, AtPrx17, AtPrx30, and AtPrx37 are involved in Monolignol polymerization, AtPrx53 and AtPrx66 are involved in the lignification of vascular bundles [1]. PRXs include all secretory plant-specific peroxidases [1,5,6], which comprise large multigene families in many plants, such as Arabidopsis thaliana, Oryza sativa, and Populus trichocarpa, with 73, 138, and 93 PRXs, respectively [7,8,9].
Pear is one of the most important commercial fruits and is cultivated in all temperate-zone countries of both hemispheres. Stone cell content is an important factor affecting fruit quality. If the content of stone cells is higher, the rougher the fruit flesh will be. Therefore, a decrease of stone cell content is directly related to the improvement of fruit quality.
Unfortunately, most previous studies focused on cultivation, such as bagging and pruning, but this view in its nature is still lacking. As we all know, lignin is the main component of stone cells [10,11]. Thus, identification of important genes related to lignin formation and accumulation, and understanding their functional mechanism, will help reduce lignin content in pears, thus improve the quality of the pear.
However, peroxidases, which may be involved in lignin accumulation, have little been reported in pears.
Due to the fast development of sequencing techniques, more and more genomes in plants have been sequenced. In the past few years, repeated episodes of small-scale and large-scale gene duplication events have been shown to play important roles during the evolution of gene families. Large-scale gene duplication includes segmental duplications and whole-genome duplications (WGDs) [12]. In pears, evidence has indicated that two WGDs occurred during pear genome evolution, with an ancient WGD event ~140 million years (Myr) [13], and a recent WGD event at 30–45 Myr [14]. Small-scale gene duplication events, such as tandem duplications, also play important roles during gene family expansion [15]. The sum of other small-scale duplications and tandem duplications are estimated to contribute duplicates on a scale comparable to large segmental duplications in rice [16]. The evidence has indicated that tandem and segmental duplications are important during gene family expansion [17,18].
Recently, the pear (Pyrus bretschneideri Rehd) genome was also sequenced and assembled by the strategy of BAC by BAC, combined with whole-genome shotgun data, a total of 194x genome coverage sequencing. The high quality of the assembled sequence and annotation were assessed and confirmed using Sanger-derived BAC sequences along with RNA-seq of different tissues and public protein database alignment [19]. The high quality of the pear genome is suitable for genome-wide identification and analysis of gene families.
The present study is the first to report on the genome-wide identification of class III peroxidase genes in pear, although they have been identified from other ligneous or herbaceous species, together with phylogenetic, structural, and evolutionary analysis. In addition, RNA-seq databases of pear fruit were used to determine the expression pattern for all PRX genes and select key genes affecting lignin formation. This study will help to reveal the roles of these PRX genes in pear stone cell formation as well as provide gene resources for the future genetic improvement of pears. The obtained results will also provide a reference on lignin formation for other related plants.

2. Materials and Methods

2.1. Identification of Class III Peroxidase Genes (PRXs) in Pear

To identify members of the class III peroxidase gene family, multiple database searches were performed. The Arabidopsis class III peroxidase (AtPRXs) gene sequences obtained from the TAIR database were used as queries to perform repetitive blast searches against the Pear Center (http://peargenome.njau.edu.cn/) [19]. Additionally, all protein sequences were then used as queries to perform multiple database searches against proteome and genome files downloaded from these databases. Stand-alone versions of BLASTP and TBLASTN available from the Basic Local Alignment Search Tool were used with the e-value cutoff set to 1 × 10−3. All retrieved nonredundant sequences were collected from the phytozome database v9.1, and subjected to domain analysis by using two different domain analysis programs: the Pfam 27.0 and SMART, with the default cut off parameters [20,21]. Genes without PRX-specific peroxidase domains were rejected.

2.2. Phylogenetic Analysis, Gene Structure and Conserved Motif Analysis

The PRX family protein sequence alignments and the phylogenetic tree were created by using the Muscle program. The phylogenetic trees for pear class III peroxidase genes were constructed using the maximum likelihood (ML) method in MEGA6.0 and assessed by bootstrap analysis with 1000 resampling replicates.
To determine the exon/intron structures of the PbPRX genes, the Gene Structure Display Server (GSDS) (http://gsds.cbi.pku.edu.cn/) [22] was used to align their cDNAs with the corresponding genomic DNA sequences. The conserved motifs were detected using the online MEME (Multiple Expectation Maximization for Motif Elicitation) tool (http://meme.sdsc.edu/meme430/intro.html) [23]. Parameters were set as follows: number of repetitions; optimum motif width set to ≥6 and ≤200; maximum number of motifs set to 20. The conserved motifs were analyzed with the SMART (http://smart.embl-heidelberg.de/) and Pfam (http://pfam.sanger.ac.uk/search) programs.

2.3. Chromosomal Location and Synteny Analysis

The chromosomal location information of the PbPRX genes was obtained from genome annotations. The data were then displayed by using Circos. The analysis of synteny in the pear genomes was conducted locally by using a method similar to that developed for the PGDD (http://chibba.agtec.uga.edu/duplication/) [24]. Duplications of PbPRXs were identified using MCScanX software (http://chibba.pgml.uga.edu/mcscan2/) [25]. First, BLASTP was performed to search for potential paralogy gene pairs (E < 1 × 10−5, top 5 matches) genomes. Then, these paralogy pairs were used as the input for MCScanX to identify syntenic chains [25]. MCScanX was further used to identify WGD, segmental, tandem duplications in the PbPRX gene family.

2.4. Calculating Ka and Ks of the PbPRX Gene Family

The valid gene pairs derived from different gene duplication modes were used to calculate the nonsynonymous (Ka) and synonymous (Ks) substitution rates. KaKs Calculator 2.0 software with default parameters was used to calculate Ka and Ks values, and Ka/Ks ratios based on a model-averaged method [26].
Ka/Ks calculation was applied to estimate the selection pressure of PRX gene pairs. The algorithm was NG.

2.5. Gene Ontology Enrichment Analysis

InterPro domains were annotated by InterProScan [27] Release 36.0 and functional assignments were mapped onto Gene Ontology (GO) [28]. Furthermore, the GO classification and draw GO tree using WEGO [29].

2.6. Genome-Wide Expression Analysis of PRX Gene Family

To investigate the expression of PRX gene family members, pear fruit samples of the ‘Dangshansuli’ cultivar on 22 April (15 days after full bloom, DAFB), 13 May (36 DAFB), 27 June (81 DAFB), 28 July (110 DAFB), and 30 August (145 DAFB) were collected in 2011, which included the key stages of pear fruit development from early fruit setting to mature. RNA sequencing libraries of five fruit developmental stages were constructed using an Illumina standard mRNA-Seq Prep Kit (TruSeq RNA and DNA Sample Preparation Kits version 2). The RNA-seq data was downloaded from our center website (http://peargenome.njau.edu.cn/). Expression values of each gene were logarithm, the cluster analyses were performed using cluster software with the hierarchical cluster method of “complete linkage” and Euclidean distances. Finally, the Treeview program was used to display the results of the cluster.

2.7. RNA Extraction and First-Strand cDNA Synthesis

In our research, four fruit stages were sampled depending on the status of pear development in 2016, 25 April (21 DAFB), 17 May (42 DAFB), 28 June (84 DAFB), and 26 July (112 DAFB) for quantitative real-time PCR (qRT-PCR) analysis. Total genomic RNA was extracted from the pear fruit using the Plant Total RNA Isolation Kit Plus (FOREGENE CO.,LTD, China). A260/A280 ratios of the RNA ranged from 1.9 to 2.1 quantified with a NanoDrop ND1000 spectrophotometer. Finally, about 2 μg of total RNA was used for first-strand cDNA synthesis using REVERTAID 1ST CDNA SYNTH KIT (Fermentas Co.,Ltd, Lithuania) according to the manufacturer’s protocol.

2.8. Quantitative Real-Time PCR Analysis

The primers used for amplifying PRX genes are listed in Supplementary Table S1. In the present study, the LightCycler 480 SYBR GREEN I Master (Roche, Nutley, NJ, USA) was used according to the manufacturer’s protocol. Each reaction mixture contained 10 μL of LightCycler 480 SYBR GREEN I Master, 0.4 μL of each primer, 1 μL of diluted cDNA and 7.4 μL nuclease-free water. The qRT-PCR was performed on the LightCycler 480 (Roche, USA) and all reactions were run as duplicates in 96-well plates. The qRT-PCR reaction conditions were as follows: pre-incubation at 95 °C for 10 min and then 40 cycles of 94 °C for 15 s, 60 °C for 30 s, 72 °C for 30 s, and finally, extension at 72 °C for 3 min, and reading the plate for fluorescence data collection at 60 °C. A melting curve was performed from 60 °C to 95 °C in order to check the specificity of the amplified product. The real-time PCR experiment was carried out three times under identical conditions. Finally, the average threshold cycle (Ct) was calculated per sample, Pyrus Actin was used as the internal control, and the relative expression levels were calculated with the 2−ΔΔCt method described by Livak et al. [30].

2.9. Determination of Stone Cells and Lignin Content

Each fruit was peeled, cored, and diced into cubes. A 100 g sample of pear flesh was stored in the refrigerator at −20 °C for at least 24 h then homogenized with distilled water in a blender for 10 min. The homogenate was then diluted with distilled water. The suspension was incubated at room temperature for 30 min and the supernatant phase was decanted. Finally, the sediment was suspended in 0.5 M HCl for 30 min, decanted, and washed with distilled water. This operation was repeated several times until the stone cells were almost free of extraneous cell debris [31].
The method was carried out as described by Tao et al. [10] with some modifications. Pear flesh was dried in an oven at 65 °C. The dry pear flesh was ground and pestled in 95% ethanol, then the sediment was washed with 95% ethanol and ethanol: hexane (1:2, v/v) three times, respectively, and dried. Dried sediments were digested in 2 mL of 25% (v/v) acetyl bromide in acetic acid and incubated for 30 min at 70 °C. The reaction was terminated by adding 0.9 mL of 2 M NaOH with an extra 5 mL of acetic acid and 0.1 mL of 7.5 M hydroxylamine hydrochloride. The volume was corrected to 10 mL with acetic acid and the absorbance at A280 was measured. The amount of lignin was calculated from a linear calibration curve with commercial alkali lignin (Sigma–Aldrich, St. Louis, MO, USA).

3. Results

3.1. Identification and Construction of Phylogenetic Tree of Class III Peroxidase Gene Family (PRXs) in Pear

In the present study, a total of 114 open reading frames (ORFs) encoding putative PRX proteins were identified in the pear (Pyrus bretschneideri)(cultivar: ‘Dangshansuli’) genome using the HMMER profile and BLASTp search for further analysis.
Originally, a total of 126 candidate PRX genes were identified in pears. Among these, 12 nontargeted or overlapping protein sequences were manually removed. The results show that all 114 putative pear PRX genes contain a conserved PRX domain; this number is greater than that in Arabidopsis (73) [9]. Finally, on the basis of previous research in Arabidopsis, we assigned names to these PRX genes (PbPRX1–114) according to their chromosomal positions for convenience. The length of the 114 newly identified PRX proteins varies from 84 to 1315 aa, with an average of 336 aa. Other information about the clone number, chromosomal location, molecular weight (Mw), isoelectric point (PI), and exon number of each PbPRX gene/protein is listed in Table 1.
To gain insight into the structure of the PRX genes, the exon and intron boundaries, which are known to play crucial roles in the evolution of multiple gene families, were analyzed. Results showed that exon numbers of 114 PRX genes ranged from one to eighteen (Figure 1C). Different subfamilies contained different exon numbers, the fact that the PbPRX64 gene has 18 exons, and PbPRX18, PbPRX53, PbPRX83, PbPRX112, and PbPRX113 have only one exon, indicates that both exon gain or loss has occurred during the evolution of the PRX gene family, which might lead to the functional diversity of closely related PRX genes. However, it was found that within each subfamily, genes usually have a similar number of exons.
Phylogenetic analysis of the 114 identified nucleotide sequences of PbPRXs could be classified into 12 subfamilies (Figure 2). Group I contains 30 members and group I is the biggest subfamily. Group III, IV, VII, and IX are the smallest subfamilies only containing two members. Across the Maximum Likelihood (ML) tree, most bootstrap values were 80 or higher, and 12 nodes of each subfamily clade had a good bootstrap value.

3.2. Analysis of Conserved Motifs and Domain

A total of 20 conserved motifs were identified in the pear PRX proteins. Detailed information about the conserved amino acid sequences and lengths of the 20 motifs is shown in Table 2. The conserved motifs obtained from MEME analysis were annotated using the Pfam and SMART programs. Most of the closely related members have the same motif compositions, suggesting that there are functional similarities between PRX proteins within the same subfamily. Figure 2 depicts the structure diagrams of motif 5, which shows that the structure may be the core structure of the function of the PRX gene family in pears. Furthermore, some subfamily-specific motifs with unknown functions were also detected, indicating that these motifs are likely required for subfamily-specific functions. However, some motifs are distributed in nearly every subfamily, although their functions remain unknown (motif 4, 5, 10, 11); these motifs might be important for the functions of PbPRX proteins.
All conserved domains of the PbPRX gene family are shown in Figure 1B. All PRX proteins contain one or more PRX domain, and this is one of the main bases of the gene family screening.

3.3. Chromosomal Locations, Gene Duplication, and Collinearity Analyzes

To determine the genome organization and distribution of PbPRXs on different chromosomes in pears, a chromosome map was constructed. The results show that the 99 PbPRX genes are distributed on 17 chromosomes with a nonrandom distribution, and 15 PbPRX genes are mapped onto the other 10 scaffolds, as shown in Table 1. Chromosome 3 contains the most PbPRX genes (13), followed by chromosome 7 (11) and chromosome 8 (11). By contrast, only one PbPRX gene is present on chromosomes 1 and 14. In addition, some chromosomes exhibit a relatively high density of PbPRX genes, such as the bottoms of chromosomes 3 and 7 and the top of chromosome 10. Gene duplication, including segmental or whole-genome duplication (WGD) and tandem duplication, is considered to be one of the primary driving forces in the evolution of genomes [32,33]. During the evolution of a gene family, tandem duplication and WGD/segmental duplication play important roles in generating new members. Therefore, in order to clarify the potential mechanism of evolution of the PRX gene family, both tandem duplication and segmental duplication events were investigated in this study. In this study, 26 related duplicated gene pairs were identified (Table 3), which cover most of the 30 sister pairs. Among the 114 PbPRX genes identified, a total of 26 gene pairs (46 genes) were localized to WGD/segmentally duplicated regions, while there is no gene in tandem repeats. These results indicate that WGD/segmental duplications were the main contributors to the expansion of the pear PRX family. To explore the selection pressures among PbPRX duplicated genes, we calculated the Ka, Ks, and Ka/Ks values for all the PRX gene pairs. The results were not shown except for 26 gene pairs (Table 3). In general, Ka/Ks > 1 indicates positive selection, Ka/Ks = 1 indicates neutral selection, and Ka/Ks < 1 indicates negative or purifying selection. The Ka/Ks ratios of most PbPRX gene pairs were <1, suggesting that these gene pairs evolved under purifying selection in pears. The results of this Ka/Ks analysis suggest that negative or purifying selection was vital to the functional divergence of PbPRX genes.

3.4. Functional Annotation with Gene Ontology

In this study, a total of 109 differentially expressed genes that could be categorized into 25 functional groups were found (Figure 3). The major subcategories were as follows: one for cellular component (‘extracellular region’); three for molecular function (‘catalytic activity’, ‘binding’, and ‘antioxidant activity’); and three for biological process (‘metabolic process’, ‘single-organism process’, and ‘response to stimulus’). These results indicate that PbPRX genes are mainly functioning in ‘catalytic activity’, ‘binding’, ‘metabolic process’.

3.5. Expression of the PRX Gene Family in Pears

To investigate the transcript pattern of PRX family genes during fruit development, the expression patterns over six developmental stages of the pear fruit, from the early to mature stage, were analyzed using the RNA-seq database available from our previous research [19]. According to publicly available genome-wide transcript profiling data from pear tissues, of the 114 PbPRX genes, only 64 PbPRXs are expressed in fruit. Finally, a hierarchical cluster with the logarithm of average values for the 64 PRX family members was generated. As shown in Figure 4, PRX family genes can be divided into four major groups based on their expression profiles. Group A contained seven PRX genes, all of them exhibited preferential expression in the first two stages, indicating that those genes may play important roles in lignin formation during early fruit development. In addition, 23 PRX genes belong to group B, which showed high expression in the first three stages, among them, PbPRX55 and PbPRX111 had the highest expression levels in the first stage of fruit development. Group C included 13 PRX genes, which showed high expression in the S3 stages, but were almost all lower than the expression of group A and B. Group D consisted of 21 PRX genes that displayed higher expression in the last three stages, and with low expression during the foregoing stage of fruit development.

3.6. Stone Cells and Lignin Content of Pear Fruit during Pear Fruit Development

To investigate the formation of stone cells, we determined the content of stone cells from early fruit set to maturity. We found that the content of stone cells reached a maximum at 49 DAFB, and after that, the stone cells number was reduced. The content of stone cells was at a minimum when the fruit was mature (Figure 5).
To investigate the formation of lignin during pear fruit development, we determined the content of lignin in the pulp powder of pear. We found that the content of lignin reached its maximum at 35 DAFB (Figure 6).

3.7. Verification of Gene Expression by qRT-PCR

On the basis of the RNA-seq database which combines the content of stone cells and lignin, we found that the expression levels of nine PRX (PbPRX2, PbPRX3, PbPRX6, PbPRX17, PbPRX25, PbPRX27, PbPRX53, PbPRX55, and PbPRX110) genes were closely related to lignin formation during pear fruit development, and may play a more important role than other genes. In order to verify whether these genes were associated with lignin content during pear fruit development, the expression levels of these eleven genes were analyzed by qRT-PCR. We chose the first four stages of pear fruit development which lignin is mostly formed in. Finally, the results of the qRT-PCR analysis indicated that the expression levels of all these nine PRX genes are closely tied with the content change of lignin during pear fruit development (Figure 7), none of them were different from RNA-seq data, supporting the reliability of our RNA-seq data.

4. Discussion

Class III peroxidases are plant-specific enzymes that play key roles in the responses to biotic and abiotic stress during plant growth and development, as well as being involved in plant lignification. While systematic and comprehensive whole-genome analyses of PRX gene families in Arabidopsis thaliana, Oryza sativa, and Populus trichocarpa have been reported [7,8,9], a systematic whole-genome study of this family has not previously been reported in pears. The full pear genome sequence serves as a useful tool for analyzing the pear PRX gene family to predict its evolutionary history and function [19]. In this study, we performed a comprehensive analysis of the PRX family genes in pears, including analysis of their phylogeny, gene structures, conserved motifs, chromosomal locations, gene duplication, and expression profiles. The number of PRX genes in pear (114) is higher than that in Arabidopsis (73) and Poplar (93) but slightly lower than that in rice (138), similar to that in maize(119), which indicates that the PRX genes in pear have expanded compared to those in Arabidopsis and poplar. Gene duplications are one of the primary driving forces in the evolution of genomes and genetic systems [33]. An increasing number of studies have shown that segmental duplication was largely responsible for the expansion of pear gene families. In this study, the number of PbPRX genes involved in segmental duplication is much more than that involved in tandem duplication, suggesting that segmental duplications are the main contributors to the expansion of the pear PRX family. By contrast, tandem duplication has contributed significantly to the expansion of this gene family in poplar [8]. According to the above analysis, we speculate that the expansion of the PRX gene family differed between monocotyledons and eudicotyledons. The Ka/Ks ratios of the 26 duplicated pairs show that purifying selection may be largely responsible for maintaining the functions of pear PRX proteins.
Phylogenetic analysis of the PbPRX gene family revealed that the exon/intron structures and motif compositions of these genes are relatively conserved. The 114 PbPRX genes contain different numbers of introns/exons, with most PRX genes containing more than two introns, indicating that there is some diversity in the pear PRX gene family. It is well known that the structural diversity of genes drives the evolution of multigene families. Furthermore, the differences in these characteristics detected between different subfamilies suggest that pear PRX members are functionally diversified.
Many studies have shown that introns were specifically inserted into plants and were retained in the genome during the course of evolution [34]. Therefore, we speculate that introns were gained or lost from the PRX coding region in a subfamily-specific manner.
Furthermore, MEME analysis revealed that different conserved motifs are present in each of the pear PRX proteins. However, some motifs with unknown functions are present in nearly every subgroup, these motifs might play important roles in the PbPRX family.
PRXs can catalyze the reduction of H2O2 by moving electrons to it and receiving electrons from various donor molecules. and are involved in several important physiological and developmental processes, including lignin and suberin formation, the cross-linking of cell wall components, wound healing, the removal of H2O2, the oxidation of toxic reductants, and defense against pathogen or insect attack. The result of Gene Ontology (GO) analysis indicates that ‘catalytic activity’, ‘antioxidant activity’, and ‘response to stimulus’ are the main functions of the PbPRX gene family, which corresponds to the acknowledged function of the peroxidase enzyme.
Gene expression patterns can provide important clues about gene function. We used publicly available genome-wide transcript profiling data from pear tissues as a resource to investigate the expression patterns of PbPRXs [19]. Of the 114 PbPRX genes, only 64 PbPRXs are expressed in fruit. According to the hierarchical cluster, 64 PbPRXs can be divided into ABCD four groups. We speculate that there are functional divergences in the four groups. PRX genes in Group A and B are smainly expressed at the first three stages of fruit development, which are major stages of lignification. So we speculate these genes are more important in lignification.
The content of stone cells in our study reached a peak at 49 DAFB, which agrees with the study carried out by Tao etc. [10]. The content of lignin increased at the earlier stage, the peak value was 35 DAFB, which is ten days earlier than that of stone cells. As is known to all, Stone cells mainly consist of lignin and cellulose. Lignin was accumulating in the cell wall, the secondary cell wall was then thickened constantly and eventually turned into stone cells, so that the content of stone cells reached a maximum after ten days. According to the RNA-seq database and qPCR, we found that PbPRX2, PbPRX3, PbPRX6, PbPRX17, PbPRX25, PbPRX27, and PbPRX55 are likely to be involved in the lignification of pear stone cells.

5. Conclusions

In summary, the PRX family contains a large group of genes with essential functions in various developmental processes in plants. This study provides a foundation for further studying the functions of PbPRX genes, particularly for members with potentially important functions in lignification. However, further experiments should be conducted to directly examine the functions of PbPRX genes and their potential regulatory factors, including external cultivation and internal genetic factors.

Supplementary Materials

The following are available online at https://www.mdpi.com/article/10.3390/plants10091874/s1, Table S1 List of PbPRX and internal control genes primers used for qPCR gene expression.

Author Contributions

S.T. contributed to the experimental design and management, data analysis, and paper review. Z.X. and W.R. contributed to the performance of laboratory work and manuscript preparation. Y.Y., X.S. prepared the plant materials and performed tissue collection. X.L., X.G. and J.B. contributed to the data analysis and laboratory materials preparation during the experiments. S.Z. and K.S. provided suggestions and reviewed and modified this paper. All authors read and approved the published version of the manuscript.

Funding

This work was supported by the National Key Research and Development Program of China (2020YFD100020), the National Natural Science Foundation of China (31672105, 31372044 and 31000888, the Major Science and Technology Project of Crops (2017DB006).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

All data, tables, figures, and results in this paper are our own and original.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Cosio, C.; Dunand, C. Specific functions of individual class III peroxidase genes. J. Exp. Bot. 2009, 60, 391–408. [Google Scholar] [CrossRef]
  2. Bindschedler, L.V.; Dewdney, J.; Blee, K.A.; Stone, J.M.; Asai, T.; Plotnikov, J.; Denoux, C.; Hayes, T.; Gerrish, C.; Davies, D.R.; et al. Peroxidase-dependent apoplastic oxidative burst in Arabidopsis required for pathogen resistance. Plant J. 2006, 47, 851–863. [Google Scholar] [CrossRef] [Green Version]
  3. Daudi, A.Z.; Cheng, J.A.; Brien, O.; Mammarella, N.; Khan, S.; Ausubel, F.M.; Bolwell, G.P. The apoplastic oxidative burst peroxidase in Arabidopsis is a major component of pattern-triggered immunity. Plant Cell 2012, 24, 275–287. [Google Scholar] [CrossRef] [Green Version]
  4. Herrero, J.; Fernández-Pérez, F.; Yebra, T.; Novo-Uzal, E.; Pomar, F.; Pedreo, M.; Cuello, J.; Guéra, A.; Esteban-Carrasco, A.; Zapata, J.M. Bioinformatic and functional characterization of the basic peroxidase 72 from Arabidopsis thaliana involved in lignin biosynthesis. Planta 2013, 237, 1599–1612. [Google Scholar] [CrossRef] [PubMed]
  5. Welinder, K.G. Plant peroxidases: Structure–function relationships. In Plant Peroxidases; University of Geneva: Geneva, The Switzerland, 1992; pp. 1–24. [Google Scholar]
  6. Welinder, K.G. Superfamily of plant, fungal and bacterial peroxidases. Curr. Opin. Struct. Biol. 1992, 2, 388–393. [Google Scholar] [CrossRef]
  7. Passardi, F.; Longet, D.; Penel, C.; Dunand, C. The class III peroxidase multigenic family in rice and its evolution in land plants. Phytochemistry 2004, 65, 1879–1893. [Google Scholar] [CrossRef] [PubMed]
  8. Ren, L.; Liu, Y.; Qian, T.; Qi, L.; Wang, X.; Zeng, Q. Subcellular relocalization and positive selection play key roles in the retention of duplicate genes of populus class III peroxidase family. Plant Cell 2014, 26, 2404–2419. [Google Scholar] [CrossRef] [Green Version]
  9. Tognolli, M.; Penel, C.; Greppin, H.; Simon, P. Analysis and expression of the class III peroxidase large gene family in Arabidopsis thaliana. Gene 2002, 288, 129–138. [Google Scholar] [CrossRef]
  10. Tao, S.T. Characterization of Sclereid Structure and Composition and Cloning of Sclereid Related Enzyme Genes in Pear (Pyrus) Fruit. Ph.D. Thesis, Nanjing Agricultural University, Nanjing, China, 2009. [Google Scholar]
  11. Tao, S.T.; Khanizadeh, S.; Zhang, H.; Zhang, S.L. Anatomy, ultrastructure and lignin distribution of stone cells in two Pyrus species. Plant Sci. 2009, 176, 413–419. [Google Scholar] [CrossRef]
  12. Van de Peer, Y.; Meyer, A. Large-scale gene and ancient genome duplications. Evol. Genome 2005, 9, 329–368. [Google Scholar]
  13. Fawcett, J.A.; Maereand, S.; Van de Peer, Y. Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc. Natl. Acad. Sci. USA 2009, 106, 5737–5742. [Google Scholar] [CrossRef] [Green Version]
  14. Velasco, R.; Zharkikh, A.; Affourtit, J.; Dhingra, A. The genome of the domesticated apple (Malus × domestica Borkh). Nat. Genet. 2010, 42, 833–839. [Google Scholar] [CrossRef]
  15. Taylor, J.S.; Raes, J. Duplication and divergence: The evolution of new genes and old ideas. Annu. Rev. Genet. 2004, 38, 615–643. [Google Scholar] [CrossRef] [Green Version]
  16. Yu, J.; Wang, J.; Lin, W.; Song, G.; Li, H.; Zhou, J.; Ni, P.; Dong, W. The Genomes of Oryza sativa: A History of Duplications. PLoS Biol. 2005, 3, 266–281. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  17. Sharoni, A.M.; Nuruzzaman, M.; Satoh, K.; Shimizu, T.; Kondoh, H.; Sasaya, T.; Choi, I.; Omura, T.; Kikuchi, S. Gene Structures, Classification and Expression Models of the AP2/EREBP Transcription Factor Family in Rice. Plant Cell Physiol. 2011, 2, 344–360. [Google Scholar] [CrossRef] [PubMed]
  18. Zhao, Y.X.; Cai, M.J.; Zhang, X.B.; Li, Y.R.; Zhang, J.H.; Zhao, H.L.; Kong, F.; Zheng, Y.L.; Qiu, F.Z. Genome-Wide Identification, Evolution and Expression Analysis of mTERFGene Family in Maize. PLoS ONE 2014, 9, 1–18. [Google Scholar]
  19. Wu, J.; Wang, Z.W.; Shi, Z.B.; Zhang, S.; Ming, R.; Zhu, S.L.; Khan, M.A.; Tao, S.T.; Korban, S.S.; Wang, H.; et al. The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res. 2013, 23, 396–408. [Google Scholar] [CrossRef] [Green Version]
  20. Finn, R.D.; Bateman, A.; Clements, J.; Coggill, P.; Eberhardt, R.Y.; Eddy, S.R.; Heger, A.; Hetherington, K.; Holm, L.; Mistry, J.; et al. Pfam: The protein families database. Nucleic Acids Res. 2014, 42, 222–230. [Google Scholar] [CrossRef] [Green Version]
  21. Letunic, I.; Doerks, T.; Bork, P. SMART 7: Recent updates to the protein domain annotation resource. Nucleic Acids Res. 2012, 40, 302–305. [Google Scholar] [CrossRef] [PubMed]
  22. Hu, B.; Jin, J.; Guo, A.; Zhang, H.; Luo, J.; Gao, G. GSDS 2.0: An upgraded gene feature visualization server. Bioinformatics 2015, 8, 1296–1297. [Google Scholar] [CrossRef] [Green Version]
  23. Bailey, T.L.; Elkan, C. Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization. Mach. Learn. 1995, 21, 51–80. [Google Scholar] [CrossRef] [Green Version]
  24. Lee, T.H.; Tang, H.; Wang, X.; Paterson, A.H. PGDD: A database of gene andgenome duplication in plants. Nucleic Acids Res. 2013, 41, 1152–1158. [Google Scholar] [CrossRef]
  25. Wang, Y.; Tang, H.; DeBarry, J.D.; Tan, X.; Li, J.; Wang, X.; Lee Th Jin, H.; Marler, B.; Guo, H. MCScanX: A toolkit for detection and evolutionary analysis of genesynteny and collinearity. Nucleic Acids Res. 2012, 40, 49. [Google Scholar] [CrossRef] [Green Version]
  26. Wang, D.; Zhang, Y.; Zhang, Z.; Zhu, J.; Yu, J. KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies. Genom. Proteom. Bioinform. 2010, 1, 77–80. [Google Scholar] [CrossRef] [Green Version]
  27. Zdobnov, E.M.; Apweiler, R. InterProScan—An integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17, 847–848. [Google Scholar] [CrossRef] [Green Version]
  28. Harris, M.; Clark, J.; Ireland, A.; Lomax, J.; Ashburner, M.; Foulger, R.; Eilbeck, K.; Lewis, S.; Marshall, B.; Mungall, C.; et al. The gene ontology (GO) database and informatics resource. Annu. Rev. Genet. 2004, 32, 258. [Google Scholar]
  29. Ye, J.; Fang, L.; Zheng, H.; Zhang, Y.; Chen, J.; Zhang, Z.; Wang, J.; Li, S.; Li, R.; Bolund, L.; et al. WEGO: A web tool for plotting GO annotations. Nucleic Acids Res. 2006, 34, 293–297. [Google Scholar] [CrossRef]
  30. Livak, K.J.; Schmittgen, T.D. Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2-DDCT Method. Methods 2001, 4, 402–408. [Google Scholar] [CrossRef] [PubMed]
  31. Syros, T.; Yupsanis, T.; Zafiriadis, H.; Economou, A. Activity and isoforms of peroxidases, lignin and anatomy, during adventitious rooting in cuttings of Ebenus cretica L. J. Plant Physiol. 2004, 161, 69–77. [Google Scholar] [CrossRef] [PubMed]
  32. Cannon, C.P.; Braunwald, E.; McCabe, C.H.; Rader, D.J.; Rouleau, J.L.; Belder, R.; Joyal, S.V.; Hill, K.A.; Pfeffer, M.A.; Skene, A.M. Intensive versus Moderate Lipid Lowering with Statins after Acute Coronary Syndromes. N. Engl. J. Med. 2004, 350, 1495–1504. [Google Scholar] [CrossRef] [PubMed]
  33. Moore, R.C.; Purugganan, M.D. The early stages of duplicate gene evolution. Proc. Natl. Acad. Sci. USA 2003, 100, 15682–15687. [Google Scholar] [CrossRef] [Green Version]
  34. Rogozin, I.B.; Wolf, Y.I.; Sorokin, A.V.; Mirkin, B.G.; Koonin, E.V. Remarkable Interkingdom Conservation of Intron Positions and Massive, Lineage-Specific Intron Loss and Gain in Eukaryotic Evolution. Curr. Biol. 2003, 17, 1512–1517. [Google Scholar] [CrossRef] [Green Version]
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Figure 1. Phylogenetic relation, domain, and gene structure of PbPRX gene family. (A) Phylogenetic tree of the PbPRX gene family. (B) Domain information of members of PbPRX gene family; (C) Exon–intron structure of pear PRX genes. Yellow boxes indicate exons; lines indicate introns; blue boxes indicate the upstream or downstream.
Figure 1. Phylogenetic relation, domain, and gene structure of PbPRX gene family. (A) Phylogenetic tree of the PbPRX gene family. (B) Domain information of members of PbPRX gene family; (C) Exon–intron structure of pear PRX genes. Yellow boxes indicate exons; lines indicate introns; blue boxes indicate the upstream or downstream.
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Plants 10 01874 g002 550
Figure 2. The most motif structure of PbPRX gene family.
Figure 2. The most motif structure of PbPRX gene family.
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Plants 10 01874 g003 550
Figure 3. GO categories of the genes identified. Y-axis (left) represents percentages of genes identified in this study, Y-axis (right) represents the actual gene number. The genes were annotated in three main categories: biological process, cellular component, and molecular function (X-axis).
Figure 3. GO categories of the genes identified. Y-axis (left) represents percentages of genes identified in this study, Y-axis (right) represents the actual gene number. The genes were annotated in three main categories: biological process, cellular component, and molecular function (X-axis).
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Plants 10 01874 g004 550
Figure 4. Heat map representation of PbPRX genes the five stages of pear fruit development. S1 22 Apr, 15 days after full bloom (DAFB); S2 13 May, 36DAFB; S3 27 June, 81DAFB; S4 28 July 110DAFB; S5 30 Aug, 145DAFB. A B C D on the right means different branches.
Figure 4. Heat map representation of PbPRX genes the five stages of pear fruit development. S1 22 Apr, 15 days after full bloom (DAFB); S2 13 May, 36DAFB; S3 27 June, 81DAFB; S4 28 July 110DAFB; S5 30 Aug, 145DAFB. A B C D on the right means different branches.
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Plants 10 01874 g005 550
Figure 5. Content of stone cells during pear development. Different big letters indicate significant difference at 0.01 level.
Figure 5. Content of stone cells during pear development. Different big letters indicate significant difference at 0.01 level.
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Figure 6. Lignin content in the pulp powder. Different small letters indicate significant difference at 0.05 level.
Figure 6. Lignin content in the pulp powder. Different small letters indicate significant difference at 0.05 level.
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Plants 10 01874 g007 550
Figure 7. Expression levels of some particular PbPRX gene of “Dangshansu” pear fruit S1:15 days after full bloom (DAFB); S2:36DAFB; S3:79DAFB; S4:107DAFB.
Figure 7. Expression levels of some particular PbPRX gene of “Dangshansu” pear fruit S1:15 days after full bloom (DAFB); S2:36DAFB; S3:79DAFB; S4:107DAFB.
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Table
Table 1. Structural and biochemical information of members of PbPRX gene family in pear.
Table 1. Structural and biochemical information of members of PbPRX gene family in pear.
Gene NameGene IDChr(Mbp) zStra-Nd yStartEndCDS Length(bp)Genomic Sequence Length(Bp)Protein Length(aa)Molecular Weight(da)Pi xExon Number
PbPRX1Pbr032785.1Chr1(10.7)−81711078172424906131830232,907.38.133
PbPRX2Pbr040489.1Chr2(22.1)+1557037215572304996193333236,405.69.334
PbPRX3Pbr035186.1Chr2(22.1)−1248677412488911978213832635,266.28.824
PbPRX4Pbr023311.1Chr2(22.1)+1600751916009267855174928531,612.29.049
PbPRX5Pbr003171.1Chr2(22.1)+220189272201938831246210411,184.87.852
PbPRX6Pbr000691.1Chr3(27.4)+19118330191202641053193535137,093.44.484
PbPRX7Pbr013075.1Chr3(27.4)+2273330822735595984228832835,036.79.294
PbPRX8Pbr000689.1Chr3(27.4)+19105701191080291053232935137,452.84.294
PbPRX9Pbr000686.1Chr3(27.4)+1906152719064600999307433335,773.78.364
PbPRX10Pbr013078.1Chr3(27.4)+2270829822709659960136232034,387.96.234
PbPRX11Pbr000687.1Chr3(27.4)+1907128919073019975173132534,720.24.484
PbPRX12Pbr013077.1Chr3(27.4)−2271145222712846993139533135,887.76.593
PbPRX13Pbr003832.1Chr3(27.4)−2645499826456517999152033335,669.66.883
PbPRX14Pbr022808.1Chr3(27.4)+16267621627999945123831534,167.45.613
PbPRX15Pbr013214.1Chr3(27.4)−21696976216986051026163034237,353.74.814
PbPRX16Pbr021747.1Chr3(27.4)−121963991219817810651780355undefinedundefined4
PbPRX17Pbr033934.1Chr3(27.4)−24516702245225081059580735338,476.85.6212
PbPRX18Pbr022809.1Chr3(27.4)+163913016394172882889610,491.17.781
PbPRX19Pbr032800.1Chr4(13.4)−11190141111928271026268734238,505.18.934
PbPRX20Pbr006566.1Chr4(13.4)+816311817595462128515416,924.59.473
PbPRX21Pbr002542.1Chr5(28.4)+22011532220126781041114734738,598.69.052
PbPRX22Pbr041097.1Chr5(28.4)+20588048205906141218256740644,469.36.034
PbPRX23Pbr002505.1Chr5(28.4)−21659712216614411059173035339,178.25.913
PbPRX24Pbr000438.1Chr5(28.4)+25395691253976891176199939242,972.19.225
PbPRX25Pbr000146.1Chr5(28.4)−27528334275302971026196434238,740.28.304
PbPRX26Pbr013845.1Chr6(23.1)+19145761191527322607697286998,120.66.3311
PbPRX27Pbr014180.2Chr6(23.1)+87406208743196648257721623,389.35.118
PbPRX28Pbr002948.1Chr7(15.3)−12585545125893151416377147251,545.78.996
PbPRX29Pbr010975.1Chr7(15.3)+1189574111897397990165733035,665.49.654
PbPRX30Pbr002950.1Chr7(15.3)+1260352912604962957143431934,580.59.313
PbPRX31Pbr002956.1Chr7(15.3)+1264480212646457990165633035,812.79.734
PbPRX32Pbr010973.1Chr7(15.3)−1188007011881667957159831934,607.69.433
PbPRX33Pbr040033.1Chr7(15.3)−1472019414721588987139532935,549.39.024
PbPRX34Pbr013905.1Chr7(15.3)−12981008129825021011149533737,239.58.723
PbPRX35Pbr010977.1Chr7(15.3)+119007301190166348693416218,183.79.113
PbPRX36Pbr002947.1Chr7(15.3)−1258267912583729330105111012,014.75.342
PbPRX37Pbr002957.1Chr7(15.3)+1265038812650724252337849,017.36.542
PbPRX38Pbr010976.1Chr7(15.3)+1189779211898914429112314316,177.78.442
PbPRX39Pbr026505.1Chr8(17.1)−44264664427581996111633235,928.08.792
PbPRX40Pbr026503.1Chr8(17.1)+44403334442618996228633236,048.08.622
PbPRX41Pbr026502.1Chr8(17.1)+44441004445303984120432835,583.58.572
PbPRX42Pbr026504.1Chr8(17.1)−44340984435213996111633236,043.28.892
PbPRX43Pbr036549.1Chr8(17.1)−16020359160220201014166233836,117.85.444
PbPRX44Pbr006119.1Chr8(17.1)−1527443915276078966164032234,724.78.414
PbPRX45Pbr036474.1Chr8(17.1)+1646763616469367972173232434,752.35.325
PbPRX46Pbr006117.1Chr8(17.1)−1526933315270972966164032234,697.68.114
PbPRX47Pbr004299.1Chr8(17.1)+60818666083665933180031133,396.94.824
PbPRX48Pbr020588.1Chr8(17.1)−94213579424517972316132434,409.45.8810
PbPRX49Pbr020590.1Chr8(17.1)+95115179514687972317132434,409.45.8810
PbPRX50Pbr005400.1Chr9(22.4)+54665055468645957214131934,371.08.713
PbPRX51Pbr018082.1Chr9(22.4)+1662648416628070984158732835,481.69.084
PbPRX52Pbr018080.1Chr9(22.4)+1663320516634674981147032735,595.79.014
PbPRX53Pbr026235.1Chr9(22.4)+2055930420560595984129232835,943.98.581
PbPRX54Pbr019188.1Chr9(22.4)+10558578105654362637685987997,910.35.8516
PbPRX55Pbr027164.1Chr10(26.2)+24310314243137431053343035138,056.85.203
PbPRX56Pbr010270.1Chr10(26.2)−115317111544461041127634738,616.79.262
PbPRX57Pbr010258.1Chr10(26.2)+104382610482561497443149956,140.48.203
PbPRX58Pbr010213.1Chr10(26.2)−6124846142101071172735739,612.65.444
PbPRX59Pbr031894.1Chr10(26.2)−531740553199831011257933738,342.98.304
PbPRX60Pbr020725.1Chr10(26.2)−1751762817522171789454426328,676.36.518
PbPRX61Pbr020734.1Chr10(26.2)+1737704217381585789454426328,676.36.518
PbPRX62Pbr003308.1Chr11(30.3)−2228034722282143999179733335,706.47.534
PbPRX63Pbr011562.1Chr11(30.3)+2537257125375151945258131533,541.99.354
PbPRX64Pbr011557.1Chr11(30.3)+2533861325347124394585121315143,415.65.7818
PbPRX65Pbr003309.1Chr11(30.3)−22273464222751469751683325347,76.34.574
PbPRX66Pbr011560.1Chr11(30.3)+2536247525363817969134332335,081.39.473
PbPRX67Pbr022326.1Chr11(30.3)−60783386082106906376930232,772.37.544
PbPRX68Pbr011559.1Chr11(30.3)+2535655625357860963130532134,899.88.973
PbPRX69Pbr003310.1Chr11(30.3)−2226680422267913744111024826,540.94.383
PbPRX70Pbr035815.1Chr12(22.8)+16715336167187141017337933935,696.55.104
PbPRX71Pbr014607.1Chr12(22.8)−47103434713291927294930932,685.08.914
PbPRX72Pbr026058.1Chr12(22.8)+37597513760860936111031233,748.38.092
PbPRX73Pbr014605.1Chr12(22.8)−47325914733625750103525026,220.38.943
PbPRX74Pbr008291.1Chr12(22.8)−93914769394142753266725127,632.25.309
PbPRX75Pbr008320.1Chr12(22.8)+91065029107578471107715717,355.45.822
PbPRX76Pbr035513.1Chr12(22.8)+226063332260721448388216117,774.68.752
PbPRX77Pbr034800.1Chr13(15.1)+1434417514345739957156531934,329.09.374
PbPRX78Pbr034821.1Chr13(15.1)+14483716144879561722424157463,176.36.9617
PbPRX79Pbr015016.1Chr13(15.1)−871626487176181002135533435,742.24.424
PbPRX80Pbr030045.1Chr13(15.1)−402484640265041017165933936,936.24.814
PbPRX81Pbr014793.1Chr13(15.1)−1187694711878622996167633236,098.27.034
PbPRX82Pbr015032.1Chr13(15.1)−88339698835416975144832535,052.15.493
PbPRX83Pbr039193.1Chr13(15.1)−3561750356243668768722925,105.68.931
PbPRX84Pbr016853.1Chr14(20.3)−36260453627070834102627829,540.26.413
PbPRX85Pbr005912.1Chr15(43.6)+297837329856962595732486593,865.27.8716
PbPRX86Pbr007872.1Chr15(43.6)−20261904202666431020474034037,262.15.365
PbPRX87Pbr002672.1Chr15(43.6)−12141041216253984215032836,549.09.524
PbPRX88Pbr009308.1Chr15(43.6)−36772753679424984215032836,549.09.524
PbPRX89Pbr010632.1Chr15(43.6)+1293176112933817963205732134,691.77.534
PbPRX90Pbr027845.1Chr15(43.6)−99819979985179993318333135,362.05.4010
PbPRX91Pbr042913.1Chr15(43.6)−36603917366073711035345534537,741.86.2611
PbPRX92Pbr006005.1Chr16(20.6)−1023690310238012936111031233,748.38.092
PbPRX93Pbr036153.1Chr16(20.6)+62244640191011177633736,758.48.032
PbPRX94Pbr036152.1Chr16(20.6)+59021605711023155134137,562.18.282
PbPRX95Pbr011189.1Chr16(20.6)−670330067069081341360944749,287.09.105
PbPRX96Pbr034488.2Chr17(25.3)−2253704822538599978155232635,455.48.784
PbPRX97Pbr034480.1Chr17(25.3)−2258370022585282981158332735,426.49.014
PbPRX98Pbr026772.1Chr17(25.3)−78145917816038975144832535,052.15.493
PbPRX99Pbr034479.1Chr17(25.3)−2258798722589313600132720021,632.49.415
PbPRX100Pbr006343.1scaffold132.0.1(0.8)−817092818160876106929232,297.85.063
PbPRX101Pbr015968.1scaffold235.0(0.6)−4997835020851035230334537,911.45.254
PbPRX102Pbr015965.1scaffold235.0(0.6)+472592481134876854329231,040.97.554
PbPRX103Pbr015969.1scaffold235.0(0.6)−51320851365533044811011,818.55.102
PbPRX104Pbr027136.1scaffold440.0(0.4)−95386981571308277243647,426.77.7011
PbPRX105Pbr027137.1scaffold440.0(0.4)+1942841970551245277241545,080.07.7111
PbPRX106Pbr037664.1scaffold770.0(0.2)−4424146306888206629631,950.37.534
PbPRX107Pbr037665.1scaffold770.0(0.2)+152615154680888206629631,950.37.534
PbPRX108Pbr037526.1scaffold766.0(0.2)−2791961990168333036,383.75.913
PbPRX109Pbr041827.1scaffold955.0(0.1)−120167121688981152232735,732.68.824
PbPRX110Pbr000988.3scaffold1008.0(0.1)+122239124533768229525627,802.65.829
PbPRX111Pbr007903.1scaffold1455.0(0.04)+21962254411053348035138,098.95.203
PbPRX112Pbr007909.1scaffold1459.0(0.04)+4474545197897832636,027.28.331
PbPRX113Pbr007908.1scaffold1459.0(0.04)+15603254978169532635,817.96.001
PbPRX114Pbr008699.1scaffold1534.0(0.03)−10892136121353272145149,351.15.6310
z On which chromosome every gene is located and the length of the chromosome. y Forward or reverse of gene on chromosome. x Isoelectric point of every protein.
Table
Table 2. Major MEME motif sequences in pear PRX proteins.
Table 2. Major MEME motif sequences in pear PRX proteins.
MotifWidthSeqs zE-ValueConserved Amino Acid Sequences
121789.8 × 10−1252LLRMHFHDCFVQGCDASVLLD
221961.0 × 10−895HTIGQARCTTFRARIYNETNI
315952.0 × 10−883CPGVVSCADILAIAA
4151018.0 × 10−729TGGPTWKVPTGRRDG
5151031.7 × 10−648FFQQFAKSMVKMGNI
632911.4 × 10−1208FDNSYFKNLIQKKGLLHSDQQLFNGGSTDSIV
721815.5 × 10−730PNNNSLRGFEVVDKIKSQVEK
815915.5 × 10−632TGSNGEIRKNCRVVN
921797.7 × 10−611GFYSRTCPTAESIVKQTVQTH
10151001.9 × 10−581SHGLSQTDMVALSGA
11211011.4 × 10−382ANETINLPAPTFNVSQLIQSF
1215884.7 × 10−251NKTYATQLQQMCPKN
135782.1 × 10−180KTKTGGPFGTMRCPAEQAHGANNGLDIAVRLLEPIKQQFPILSYA
DFYQLAGVVAVE
1429126.5 × 10−132RRDLRALIYSKNCAPIMLRIAWHDAGTYD
1511591.9 × 10−132DTPNFTGEKTA
1615348.6 × 10−109GGDNNLSPLDVTSPT
172193.0 × 10−93HTLGRCHKERSGFEGPWTPNP
1829128.3 × 10−117EGLLKLPTDKALLDDPEFRLYVELYAKDE
192192.5 × 10−51PDNLSLAGDGFDTVIKAKAAV
206811.5 × 10−49RDSVVL
z Total number of proteins which have the special motif of PRXs gene family.
Table
Table 3. Duplicated gene pairs, Ka, Ks value, and duplicate type of PbPRX gene family.
Table 3. Duplicated gene pairs, Ka, Ks value, and duplicate type of PbPRX gene family.
Paralogous PairsKaKsKa/KsPurifying SelectionDuplicate Type
PbPRX1-PbPRX340.066070.208240.31728YesSegmental (WGD)
PbPRX2-PbPRX850.360462.112120.17067YesSegmental(WGD)
PbPRX4-PbPRX780.127600.364800.34977YesSegmental(WGD)
PbPRX5-PbPRX890.293460.666140.44053YesSegmental(WGD)
PbPRX7-PbPRX290.216051.826320.11830YesSegmental(WGD)
PbPRX9-PbPRX620.062510.140920.44361YesSegmental(WGD)
PbPRX11-PbPRX690.037890.139690.27123YesSegmental(WGD)
PbPRX12-PbPRX680.216501.215690.17809YesSegmental(WGD)
PbPRX14-PbPRX500.183710.669160.27454YesSegmental(WGD)
PbPRX15-PbPRX800.047320.157920.29963YesSegmental(WGD)
PbPRX17-PbPRX270.039440.270590.14576YesSegmental(WGD)
PbPRX17-PbPRX740.111301.332850.08350YesSegmental(WGD)
PbPRX21-PbPRX560.037890.289080.13109YesSegmental(WGD)
PbPRX21-PbPRX580.343052.242660.15297YesSegmental(WGD)
PbPRX23-PbPRX580.045490.097610.46601YesSegmental(WGD)
PbPRX25-PbPRX590.009460.134150.07055YesSegmental(WGD)
PbPRX28-PbPRX310.006000.010780.55631YesSegmental(WGD)
PbPRX28-PbPRX380.126090.184680.68272YesSegmental(WGD)
PbPRX30-PbPRX320.004140.008820.46968YesSegmental(WGD)
PbPRX36-PbPRX370.203810.216730.94039YesSegmental(WGD)
PbPRX51-PbPRX970.459864.063840.11316YesSegmental(WGD)
PbPRX53-PbPRX830.383680.758050.50614YesSegmental(WGD)
PbPRX56-PbPRX570.010070.025640.39263YesSegmental(WGD)
PbPRX69-PbPRX700.267183.831750.06973YesSegmental(WGD)
PbPRX71-PbPRX1020.157720.353490.44617YesSegmental(WGD)
PbPRX81-PbPRX950.071740.160840.44603YesSegmental(WGD)
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MDPI and ACS Style

Xie, Z.; Rui, W.; Yuan, Y.; Song, X.; Liu, X.; Gong, X.; Bao, J.; Zhang, S.; Shahrokh, K.; Tao, S. Analysis of PRX Gene Family and Its Function on Cell Lignification in Pears (Pyrus bretschneideri). Plants 2021, 10, 1874. https://doi.org/10.3390/plants10091874

AMA Style

Xie Z, Rui W, Yuan Y, Song X, Liu X, Gong X, Bao J, Zhang S, Shahrokh K, Tao S. Analysis of PRX Gene Family and Its Function on Cell Lignification in Pears (Pyrus bretschneideri). Plants. 2021; 10(9):1874. https://doi.org/10.3390/plants10091874

Chicago/Turabian Style

Xie, Zhihua, Weikang Rui, Yazhou Yuan, Xiaofei Song, Xing Liu, Xin Gong, Jianping Bao, Shaoling Zhang, Khanizadeh Shahrokh, and Shutian Tao. 2021. "Analysis of PRX Gene Family and Its Function on Cell Lignification in Pears (Pyrus bretschneideri)" Plants 10, no. 9: 1874. https://doi.org/10.3390/plants10091874

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