Evolutionary and Integrative Analysis of Gibberellin-Dioxygenase Gene Family and Their Expression Profile in Three Rosaceae Genomes (F. vesca, P. mume, and P. avium) Under Phytohormone Stress

Abstract

The gibberellin-dioxygenase (GAox) gene family plays a crucial role in regulating plant growth and development. GAoxs, which are encoded by many gene subfamilies, are extremely critical in regulating bioactive GA levels by catalyzing the subsequent stages in the biosynthesis process. Moreover, GAoxs are important enzymes in the GA synthesis pathway, and the GAox gene family has not yet been identified in Rosaceae species (Prunus avium L., F. vesca, and P. mume), especially in response to gibberellin and PCa (prohexadione calcium; reduce biologically active GAs). In the current investigation, 399 GAox members were identified in sweet cherry, Japanese apricot, and strawberry. Moreover, they were further classified into six (A-F) subgroups based on phylogeny. According to motif analysis and gene structure, the majority of the PavGAox genes have a remarkably well-maintained exon–intron and motif arrangement within the same subgroup, which may lead to functional divergence. In the systematic investigation, PavGAox genes have several duplication events, but segmental duplication occurs frequently. A calculative analysis of orthologous gene pairs in Prunus avium L., F. vesca, and P. mume revealed that GAox genes are subjected to purifying selection during the evolutionary process, resulting in functional divergence. The analysis of cis-regulatory elements in the upstream region of the 140 PavGAox members suggests a possible relationship between genes and specific functions of hormone response-related elements. Moreover, the PavGAox genes display a variety of tissue expression patterns in diverse tissues, with most of the PavGAox genes displaying tissue-specific expression patterns. Furthermore, most of the PavGAox genes express significant expression in buds under phytohormonal stresses. Phytohormones stress analysis demonstrated that some of PavGAox genes are responsible for maintaining the GA level in plant-like Pav co4017001.1 g010.1.br, Pav sc0000024.1 g340.1.br, and Pav sc0000024.1 g270.1.mk. The subcellular localization of PavGAox protein utilizing a tobacco transient transformation system into the tobacco epidermal cells predicted that GFP signals were mostly found in the cytoplasm. These findings will contribute to a better understanding of the GAox gene family’s interaction with prohexadione calcium and GA, as well as provide a strong framework for future functional characterization of GAox genes in sweet cherry.

Distinct hormonal and morphological control of dormancy and germination in Chenopodium album dimorphic seeds

“…Biochemical analyses not only with the Arabidopsis proteins, but also with Cucumis proteins from other subgroups ( Figure 5 ) demonstrated that they have GA-oxidase enzyme activity ( Lange and Lange, 2020 ), suggesting that this is also the case for related diversified Chenopodium subgroup members. Divergence and subgroups without Arabidopsis genes were also observed for the GA-oxidase subfamilies in other species in phylogenetic analyses ( Giacomelli et al., 2013 ; Huang et al., 2015 ; Sabir et al., 2022 ). The situation is similar for NCED ( Arshad et al., 2021 ; Li et al., 2021 ) and CYP707A ( Zheng et al., 2012 ).…”

“…Key enzymes in ABA and GA metabolism include 9- cis -epoxycarotenoid dioxygenases (NCED), ABA 8’-hydroxylases (CYP707A), and GA-oxidases for GA biosynthesis (GA20ox, GA3ox) and inactivation (GA2ox) ( Nambara et al., 2010 ; Urbanova et al., 2011 ; Hedden, 2020 ). They are encoded by multigene families ( Huang et al., 2015 ; Lange and Lange, 2020 ; Arshad et al., 2021 ; Li et al., 2021 ; Sabir et al., 2022 ) and for Arabidopsis thaliana the members expressed during seed dormancy and germination are well known ( Ogawa et al., 2003 ; Kushiro et al., 2004 ; Lefebvre et al., 2006 ; Okamoto et al., 2006 ; Nambara et al., 2010 ). To identify Chenopodium sequences of GA and ABA metabolism genes expressed in seeds we mined the Chenopodium quinoa genome ( Jarvis et al., 2017 ) and conducted BLAST analyses with the A. thaliana and C. quinoa sequences via TAIR and Phytozome ( Goodstein et al., 2012 ) as presented in detail in Supplementary Figure 4 .…”

Reprisal of Schima superba to Mn stress and exploration of its defense mechanism through transcriptomic analysis

“…Our GO analysis indicates that DEGs were involved in metabolic processes, macro and supra molecular complex, transporter activities, stimulus responses which suggest that DEG in this cellular complex would be involved in metal tolerance in plants (Raza et al, 2022). Furthermore, DNA binding transcription factor activity, extracellular region, detoxification process and biological regulation have been reported to exhibit metal tolerance in different plants Sabir et al, 2022). The DEGs involved in metal ion binding process are likely to promote metal tolerance of plants via regulation of downstream target gene's expression.…”

Evolutionary and Integrative Analysis of the Gibberellin 20-oxidase, 3-oxidase, and 2-oxidase Gene Family in Paeonia ostii: Insight into Their Roles in Flower Senescence

“…Gibberellins (GAs), a group of diterpenoid phytohormones, are instrumental across plant development stages and in mitigating stress, significantly influencing plant yield and quality (Toyomasu et al, 2015) [8]. Agricultural practices routinely manipulate GA concentrations for various purposes, including the following: enhancing seedless grapefruit growth; promoting sugarcane stem growth; augmenting fruit set in pome fruits; retarding fruit senescence in citrus; controlling vegetative expansion in canola, apple, and cotton; and terminating bud dormancy in various species (Fuentes et al, 2012;Gao et al, 2023;Sabir et al, 2022) [9][10][11]. GAs are also pivotal in the regulation of key physiological functions, such as seed germination, shoot elongation, leaf development, and fruit and flower senescence (Liao et al, 2019;Wang et al, 2016) [12,13].…”

“…Investigations into GA20ox, GA3ox, and GA2ox sequences have shown their affiliation with the 2-oxoglutarate-dependent dioxygenase (2-ODD) superfamily, sharing significant homology within their functional domains (Kaul et al, 2000;Sabir et al, 2022) [11,24]. The three GAoxs are evidenced by the conserved sequences NXYPXCXXP, three histidine residues, and LPWKET, which may be related to the binding of the common co-substrate 2-oxoglutarate, the Fe 2+ and GA substrates, respectively (Wang et al, 2020) [25].…”