Identification and Characterization of the APX Gene Family and Its Expression Pattern under Phytohormone Treatment and Abiotic Stress in Populus trichocarpa

Leng, Xue; Wang, Hanzeng; Zhang, Shuang; Qu, Chunpu; Yang, Chuanping; Zhang, Xu; Liu, Guanjun

doi:10.3390/genes12030334

Cited by 25 publications

(9 citation statements)

References 70 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The results of the phylogenetic tree showed that five genes of subfamily I were located in the peroxisome, two genes of subfamily II were located in chloroplasts/mitochondria, one gene of subfamily III was located in cytoplasm and extracell, and one member of subfamily IV was only located in chloroplasts, indicating that the close relatives may have had the same subcellular localization results ( Figure 2 ). CaAPX3 and CaAPX4 of subfamily II were all located in two chloroplast/mitochondrial organelles, as well as in previous studies of PtrAPX1 and PtrAPX5 in Populus trichocarpa ( Leng et al., 2021 ). CaAPX genes located in peroxisome all contain eight different conserved motifs and have eight to ten exon regions.…”

Section: Discussionsupporting

confidence: 83%

Genome-wide characterization of ascorbate peroxidase gene family in pepper (Capsicum annuum L.) in response to multiple abiotic stresses

Pang

Liu

et al. 2023

Front. Plant Sci.

View full text Add to dashboard Cite

Pepper is widely grown all over the world, so it faces many abiotic stresses, such as drought, high temperature, low temperature, salt damage, and so on. Stresses causing the accumulation of reactive oxidative species (ROS) in plants are removed by antioxidant defense systems, and ascorbate peroxidase (APX) is an important antioxidant enzyme. Therefore, the present study performed genome-wide identification of the APX gene family in pepper. We identified nine members of the APX gene family in the pepper genome according to the APX proteins’ conserved domain in Arabidopsis thaliana. The physicochemical property analysis showed that CaAPX3 had the longest protein sequence and the largest molecular weight of all genes, while CaAPX9 had the shortest protein sequence and the smallest MW. The gene structure analysis showed that CaAPXs were composed of seven to 10 introns. The CaAPX genes were divided into four groups. The APX genes of groups I and IV were localized in the peroxisomes and chloroplasts, respectively; the group II genes were localized in the chloroplasts and mitochondria; and the group III genes were located in the cytoplasm and extracell. The conservative motif analysis showed that all APX genes in the pepper had motif 2, motif 3, and motif 5. The APX gene family members were distributed on five chromosomes (Chr. 2, 4, 6, 8, and 9). The cis-acting element analysis showed that most CaAPX genes contain a variety of cis-elements related to plant hormones and abiotic stress. RNA-seq expression analysis showed that the expression patterns of nine APXs were different in vegetative and reproductive organs at different growth and development stages. In addition, the qRT-PCR analysis of the CaAPX genes revealed significant differential expression in response to high temperature, low temperature, and salinity stresses in leaf tissue. In conclusion, our study identified the APX gene family members in the pepper and predicted the functions of this gene family, which would provide resources for further functional characterization of CaAPX genes.

show abstract

Section: Discussionsupporting

confidence: 83%

Genome-wide characterization of ascorbate peroxidase gene family in pepper (Capsicum annuum L.) in response to multiple abiotic stresses

Pang

Liu

et al. 2023

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…As efficient ROS scavengers, APX and CAT proteins work against multiple biotic and abiotic stresses. Previous studies reported that APX and CAT genes play regulatory roles with respect to tolerance against multiple stresses, such as salt, heat, drought, UV radiation and oxidative stress [ 15 , 29 , 75 ]. We screened the upstream region of APX and CAT genes of both species to mark the cis elements.…”

Section: Discussionmentioning

confidence: 99%

Whole-Genome Identification of APX and CAT Gene Families in Cultivated and Wild Soybeans and Their Regulatory Function in Plant Development and Stress Response

Aleem

Sharif

et al. 2022

Antioxidants

View full text Add to dashboard Cite

Plants coevolved with their antioxidant defense systems, which detoxify and adjust levels of reactive oxygen species (ROS) under multiple plant stresses. We performed whole-genome identification of ascorbate peroxidase (APX) and catalase (CAT) families in cultivated and wild soybeans. In cultivated and wild soybean genomes, we identified 11 and 10 APX genes, respectively, whereas the numbers of identified CAT genes were four in each species. Comparative phylogenetic analysis revealed more homology among cultivated and wild soybeans relative to other legumes. Exon/intron structure, motif and synteny blocks are conserved in cultivated and wild species. According to the Ka/Ks value, purifying selection is a major force for evolution of these gene families in wild soybean; however, the APX gene family was evolved by both positive and purifying selection in cultivated soybean. Segmental duplication was a major factor involved in the expansion of APX and CAT genes. Expression patterns revealed that APX and CAT genes are differentially expressed across fourteen different soybean tissues under water deficit (WD), heat stress (HS) and combined drought plus heat stress (WD + HS). Altogether, the current study provides broad insights into these gene families in soybeans. Our results indicate that APX and CAT gene families modulate multiple stress response in soybeans.

show abstract

“…The Phytozome and PopGenIE ( http://popgenie.org/chromosome-diagram ) databases were mined for chromosomal location data of PtrCOBLs ( Leng et al., 2021 ). Every single gene was mapped on the representing chromosome based on its position report.…”

Section: Methodsmentioning

confidence: 99%

Recent genome resequencing paraded COBRA-Like gene family roles in abiotic stress and wood formation in Poplar

Sajjad,

Ahmad,

Riaz

et al. 2023

Front. Plant Sci.

View full text Add to dashboard Cite

A cell wall determines the mechanical properties of a cell, serves as a barrier against plant stresses, and allows cell division and growth processes. The COBRA-Like (COBL) gene family encodes a putative glycosylphosphatidylinositol (GPI)-anchored protein that controls cellulose deposition and cell progression in plants by contributing to the microfibril orientation of a cell wall. Despite being studied in different plant species, there is a dearth of the comprehensive global analysis of COBL genes in poplar. Poplar is employed as a model woody plant to study abiotic stresses and biomass production in tree research. Improved genome resequencing has enabled the comprehensive exploration of the evolution and functional capacities of PtrCOBLs (Poplar COBRA-Like genes) in poplar. Phylogeny analysis has discerned and classified PtrCOBLs into two groups resembling the Arabidopsis COBL family, and group I genes possess longer proteins but have fewer exons than group II. Analysis of gene structure and motifs revealed PtrCOBLs maintained a rather stable motif and exon–intron pattern across members of the same group. Synteny and collinearity analyses exhibited that the evolution of the COBL gene family was heavily influenced by gene duplication events. PtrCOBL genes have undergone both segmental duplication and tandem duplication, followed by purifying selection. Promotor analysis flaunted various phytohormone-, growth- and stress-related cis-elements (e.g., MYB, ABA, MeJA, SA, AuxR, and ATBP1). Likewise, 29 Ptr-miRNAs of 20 families were found targeting 11 PtrCOBL genes. PtrCOBLs were found localized at the plasma membrane and extracellular matrix, while gene ontology analysis showed their involvement in plant development, plant growth, stress response, cellulose biosynthesis, and cell wall biogenesis. RNA-seq datasets depicted the bulk of PtrCOBL genes expression being found in plant stem tissues and leaves, rendering mechanical strength and rejoinders to environmental cues. PtrCOBL2, 3, 10, and 11 manifested the highest expression in vasculature and abiotic stress, and resemblant expression trends were upheld by qRT-PCR. Co-expression network analysis identified PtrCOBL2 and PtrCOBL3 as hub genes across all abiotic stresses and wood developing tissues. The current study reports regulating roles of PtrCOBLs in xylem differentiating tissues, tension wood formation, and abiotic stress latency that lay the groundwork for future functional studies of the PtrCOBL genes in poplar breeding.

show abstract

Identification and Characterization of the APX Gene Family and Its Expression Pattern under Phytohormone Treatment and Abiotic Stress in Populus trichocarpa

Cited by 25 publications

References 70 publications

Genome-wide characterization of ascorbate peroxidase gene family in pepper (Capsicum annuum L.) in response to multiple abiotic stresses

Genome-wide characterization of ascorbate peroxidase gene family in pepper (Capsicum annuum L.) in response to multiple abiotic stresses

Whole-Genome Identification of APX and CAT Gene Families in Cultivated and Wild Soybeans and Their Regulatory Function in Plant Development and Stress Response

Recent genome resequencing paraded COBRA-Like gene family roles in abiotic stress and wood formation in Poplar

Contact Info

Product

Resources

About