Genome-wide identification and stress response analysis of cyclophilin gene family in apple (Malus × domestica)

Abstract

Background Cyclophilin (CYP) belongs to the immunophilin family and has peptidyl-prolyl cis-trans isomerase (PPIase) activity, which catalyzes the cis-trans isomerization process of proline residues. CYPs widely exist in eukaryotes and prokaryotes, and contain a conserved cyclophilin-like domain (CLD). Plant cyclophilins are widely involved in a range of biological processes including stress response, metabolic regulation, and growth and development. Result In this study, 30 cyclophilin genes on 15 chromosomes were identified from the ‘Golden Delicious’ apple (M. domestica) genome. Phylogenetic analysis showed that the cyclophilin family genes can be divided into three clades in Malus. Collinear analysis showed that ten gene pairs were the result of segmental duplication. Analysis of gene and protein structure further supported the phylogenetic tree and collinearity analysis. The expression of MdCYPs in different organs was higher in leaves, flowers, and fruits. Ten and eight CYPs responded to drought and salt stress, respectively. MdCYP16, a nuclear-localized MD CYP, was screened from the intersection of the two expression profiling datasets and was highly sensitive to drought and salt stress. GUS staining of transgenic Arabidopsis indicated that MdCYP16 may be involved in the regulation of abiotic stress. Conclusion This study systematically analyzed members of the apple cyclophilin family and confirmed the involvement of MdCYP16 as a nuclear-localized MD cyclophilin that acts in response to salt and drought stress in apple. Our work identifies members of the apple cyclophilin gene family, and provides an important theoretical basis for in-depth study of cyclophilin function. Additionally, the analysis provides candidate genes that may be involved in stress response in apple.

Evaluation of Candidate Reference Genes for Gene Expression Analysis in Wild Lamiophlomis rotata

“…Among all the samples from different regions of L. rotata , TFIIS and CYP95 were the most stable reference genes based on the RefFinder method. Plant cyclophilins ( CYPs ) are widely involved in a range of biological processes, including stress response, metabolic regulation, and growth and development [ 54 , 55 ]. CYP belongs to the immunophilin family and has peptidyl-prolyl cis - trans isomerase (PPIase) activity, which catalyzes the cis - trans isomerization process of proline residues.…”

Identification and Functional Characterization of MdNRT1.1 in Nitrogen Utilization and Abiotic Stress Tolerance in Malus domestica

“…This finding suggested that NRT1.1 may regulate NO 3 − -dependent Na + transport. Apples, as an important horticultural product, have significant economic benefits globally [39][40][41][42][43][44]. China has the highest apple production and nitrogen fertilizer application rates in the world.…”

“…China has the highest apple production and nitrogen fertilizer application rates in the world. Excess nitrogen fertilizer is applied to cultivated apple trees to achieve high production, but the absorption efficiency of the plant body is less than 40%, which is a large discrepancy compared to developed countries [40][41][42][43][44] and causes serious environmental problems. Furthermore, the relatively poor local climate of apple orchards in China (mainly in mountainous, rural areas), insufficient rainfall, and reduced groundwater level, as well as soil salinization caused by unreasonable irrigation and single application chemical fertilizer over a long time period, mean that the apple trees are to a large extent vulnerable to drought and salt stress, resulting in a decline in apple yield and quality.…”