Scientia Agricultura Sinica ›› 2025, Vol. 58 ›› Issue (18): 3728-3743.doi: 10.3864/j.issn.0578-1752.2025.18.011

• HORTICULTURE • Previous Articles     Next Articles

Genome-Wide Identification and Expression Analysis of Peroxiredoxins Gene Family in Asparagus officinalis

YI ZeHui(), WANG Ying, SONG HuiXia, ZHAO Jing, MAO LiPing   

  1. College of Horticulture, Shanxi Agricultural University/Shanxi Key Laboratory of Germplasm Resources Innovation and Utilization of Vegetable and Flower, Taiyuan 030031
  • Received:2025-04-25 Accepted:2025-06-19 Online:2025-09-18 Published:2025-09-18

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Abstract:

【Objective】The peroxiredoxin (Prx) gene family in garden asparagus was systematically identified at the genome-wide level. The tissue-specific expression profiles and responses to abiotic stress, dormancy, and dormancy release were comprehensively investigated, providing a critical foundation for further functional characterization and breeding applications of AoPrxs. 【Method】Using the genomic data of asparagus, the members of the Prx family were identified through bioinformatics methods. The physicochemical properties, subcellular localization, gene structures, and conserved motifs of the AoPrxs were predicted using ProtParam, Cell-PLoc 2.0, SWISS-MODEL, and MEME tools, respectively. The tissue-specific expression patterns of AoPrxs and their responses to diverse stresses, dormancy, and dormancy release were systematically analyzed using RNA-Seq data and real-time fluorescent quantitative PCR (qRT-PCR). 【Result】The AoPrx family contains six members, designated AoPrx1-AoPrx6, all of which contain the conserved PXXXTXXC sequence. Their amino acid sequences ranged from 162 to 268 residues, with molecular weights ranging from 17 397.96 to 29 246.45 Da. A total of 220 (38 types) cis-acting elements were identified in AoPrxs, including those involved in plant growth and development, stress response, hormone signaling, and light response. Collinearity analysis revealed that AoPrx has a higher homology with TaPrx and OsPrx. Phylogenetic analysis classified the AoPrxs into five subfamilies, each exhibiting highly conserved gene structures, amino acid sequences, and protein structures. Notably, AoPrx1 and AoPrx2 lack the ‘resolving’ Cys residue but exhibit greater similarity in both amino acid sequence and protein structure to members of the PrxⅡB subfamily than to those of the 1-Cys subfamily. Consequently, they were classified into the PrxⅠB subfamily. Tissue expression analysis showed that AoPrx2 is ubiquitously expressed across all tissues, in contrast to AoPrx5, which showed stamen-specific upregulation in supermale flowers. The expression profile under adverse stress conditions indicated that salt-alkali stress significantly upregulated AoPrx5 expression in the roots of asparagus seedlings. Additionally, salt, drought, and low-light treatments markedly enhanced AoPrx4 expression levels in the stems and leaves of asparagus seedlings, while infection by Phomopsis asparagi exerted an opposite regulatory effect on AoPrx4 expression. Furthermore, AoPrx2, AoPrx4, and AoPrx5 may also be involved in the regulatory processes of dormancy induction and release in asparagus. 【Conclusion】Six Prx family members were identified in the asparagus genome, distributed across five chromosomes. All members contained the conserved PXXXTXXC motif and were phylogenetically classified into five subfamilies. Expression profiling revealed subfunctionalization among Prx paralogs: AoPrx5 was closely associated with stamen development and root salt tolerance. AoPrx4 played a pivotal role in the responses of stem and leaf tissues to salt, drought, low-light conditions, and phomopsis asparagi stress. Moreover, AoPrx2, AoPrx4, and AoPrx5 were also involved in the regulation of asparagus dormancy induction and release.

Key words: Asparagus officinalis L., Prx gene family, genome-wide identification, bioinformatics, expression analysis

Table 1

Primers used for qRT-PCR"

基因Gene 基因ID Gene ID 正向引物Forward primer (5′-3′) 反向引物Reverse primer (5′-3′)
AoUBI LOC109836288 ACACCATCGGCGATCTCAAG TTGACATCTTTGACAACCTTGTGG
AoPrx1 LOG109848397 GCTCCCCATGCATTCCCTT TAGGTTTTTGCCCATGCCTTC
AoPrx2 LOG109848405 AGCATGTGCCGAGTTTCATC GCGTGAGTGTAGGTTCCAGAT
AoPrx3 LOG109830907 ACGATTGCTTGCGTCTCAGT CGCTCTCGTAAAGTCCCCAT
AoPrx4 LOG109836803 CTTGCTTCAAACCCGAAGGC GCTCAATCCGCTGAAGCTCT
AoPrx5 LOG109842952 ATGACGTGGAGAGCCACAAG CTGACCCTTGTCATCGTGCT
AoPrx6 LOG109822385 ATCCTGCTGATGAGACCCCT CCCCGCTTATTCCTACCACC

Fig. 1

Multiple sequence alignment of Prx protein in garden asparagus"

Table 2

Analysis of physicochemical properties of Prx genes in garden asparagus"

基因
Gene		 基因ID
GeneID		 CDS长度
CDS length (bp)		 氨基酸数
Amino acid number		 分子量
Molecular weight (Da)		 等电点
pI		 不稳定系数
Instability index		 亲水性GRAVY 亚细胞定位
Subcellular localization
AoPrx1 LOC109848397 489 162 17397.96 4.99 30.46 0.017 细胞质、细胞核Cytoplasm, nucleus
AoPrx2 LOC109848405 489 162 17455.09 5.54 36.71 0.015 细胞质Cytoplasm
AoPrx3 LOC109830907 534 177 18906.72 5.27 33.81 0.001 细胞核Nucleus
AoPrx4 LOC109836803 807 268 29246.45 6.18 39.63 -0.051 叶绿体、细胞质Chloroplast, cytoplasm
AoPrx5 LOC109842952 657 218 24097.49 5.28 34.82 -0.375 细胞核Nucleus
AoPrx6 LOC109822385 645 214 23642.20 9.53 51.42 -0.416 叶绿体、细胞核Chloroplast, nucleus

Fig. 2

Classification of the plant Prx protein family and the conservation of each subfamily"

Fig. 3

Phylogenetic tree of PrxⅡB protein sequences genes in garden asparagus, Arabidopsis, Upland cotton, rice and wheat Ao: Asparagus officinalis; At: Arabidopsis thaliana; Gh: Gossypium hirsutum; Os: Oryza sativa; Ta: Triticum aestivum"

Fig. 4

Phylogenetic tree of Prx protein of garden asparagus, Arabidopsis, Upland cotton, rice and wheat A: Amino acid sequence; B: Putative three-dimensional structure"

Fig. 5

Phylogenetic tree and gene structure of Prx gene family in garden asparagus A: Phylogentic tree of AoPrx protein; B: AoPrx conserved motif; C: AoPrx gene structure; D: Domain location; E: Sequence logos of some conserved motifs"

Fig. 6

Characteristics of secondary structure of Prx proteins in garden asparagus"

Fig. 7

Predicted tertiary structures of Prx proteins in garden asparagus"

Fig. 8

Putative Cis-acting existed in the 2 000 bp upstream region of AoPrx gene family"

Fig. 9

Chromosome location of AoPrx gene family"

Fig. 10

Colinear analysis of Prx gene family in garden asparagus, Arabidopsis, Upland cotton, wheat and rice"

Fig. 11

Tissue expression analysis of Prx gene family in garden asparagus"

Fig. 12

The response of Prx gene family in garden asparagus to stresses (A), dormancy and releasing dormancy (B) S1: Salt stress Ⅰ, S-0h, S-6h, and S-48h indicates the salt stress time was 0, 6, and 48 hours, respectively; S2: Salt stress Ⅱ, FD and GJ refer to the varieties Fengdao and Champion, while S and PI denote salt stress and inoculation with Piriformospora indica; S3: Salt stress Ⅲ, P0, P1, and P2 indicates the NaCl concentrations was 0, 171 and 342 mmol·L-1, respectively; D1: Drought stress, J and P represent the varieties Jinglv No. 3 and Pacific Early, with DS signifying drought stress; L1: Weak-light stress, Light-25. Light-45, Light-65, and Light-100% refers to light intensity was 25%, 45%, 65%, and 100% of normal light, respectively; PI1: Phomopsis asparagi stress, PI-0h. PI-24h and PI-48h denotes the sampling time was 0, 24 and 48 hours post-inoculation, respectively; A1 and A2 refer to the dormancy and dormancy release. F20 and S20 represent the fall and spring of 2020, GM and UC stand for the varieties Guelph Millennium and UC157, A-C indicate the 1st to 3rd sampling, and Rz, Bu, and BL refer to rhizome, dormant bud, and growing bud, respectively. The same as below"

Fig. 13

The qRT-PCR analysis of AoPrx in different tissues (A) and under salt stress conditions (B) M: Male; F: Female"

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