Comprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear (Pyrus bretschneideri) Fruit

Abstract

The GATA gene family is one of the most important transcription factors (TFs). It extensively exists in plants, contributes to diverse biological processes such as the development process, and responds to environmental stress. Although the GATA gene family has been comprehensively and systematically studied in many species, less is known about GATA genes in Chinese pears (Pyrus bretschneideri). In the current study, the GATA gene family in the four Rosaceae genomes was identified, its structural characteristics identified, and a comparative analysis of its properties was carried out. Ninety-two encoded GATA proteins were authenticated in the four Rosaceae genomes (Pyrus bretschneideri, Prunus avium, Prunus mume, and Prunus persica) and categorized into four subfamilies (Ⅰ–Ⅳ) according to phylogeny. The majority of GATA genes contained one to two introns and conserved motif composition analysis revealed their functional divergence. Whole-genome duplications (WGDs) and dispersed duplication (DSD) played a key role in the expansion of the GATA gene family. The microarray indicated that, among P. bretschneideri, P. avium, P. mume and P. persica, GATA duplicated regions were more conserved between Pyrus bretschneideri and Prunus persica with 32 orthologous genes pairs. The physicochemical parameters, duplication patterns, non-synonymous (ka), and synonymous mutation rate (ks) and GO annotation ontology were performed using different bioinformatics tools. cis-elements respond to various phytohormones, abiotic/biotic stress, and light-responsive were found in the promoter regions of GATA genes which were induced via stimuli. Furthermore, subcellular localization of the PbGATA22 gene product was investigated, showing that it was present in the nucleus of tobacco (Nicotiana tabacum) epidermal cells. Finally, in silico analysis was performed on various organs (bud, leaf, stem, ovary, petal, and sepal) and different developmental stages of fruit. Subsequently, the expression profiles of PbGATA genes were extensively expressed under exogenous hormonal treatments of SA (salicylic acid), MeJA (methyl jasmonate), and ABA (abscisic acid) indicating that play important role in hormone signaling pathways. A comprehensive analysis of GATA transcription factors was performed through systematic biological approaches and comparative genomics to establish a theoretical base for further structural and functional investigations in Rosaceae species.

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

“…All GAox gene chromosomal positions were retrieved from a genome database (see text footnote 1), and Mapinspect software 11 was used for the visualization of these positions ( Manzoor et al, 2021b , c ). Moreover, the Conserved Domain Architecture Retrieval Tool (CDART), HMMER program 12 , and protein family database (Pfam) 13 were utilized for obtaining the conserved domain of GAox protein of P. avium , Fragaria vesca , and P. mume ( Johnson et al, 2010 ; Mistry et al, 2021 ).…”

Identification and Comprehensive Genome-Wide Analysis of Glutathione S-Transferase Gene Family in Sweet Cherry (Prunus avium) and Their Expression Profiling Reveals a Likely Role in Anthocyanin Accumulation

“…The GSDS 2.0 (Gene Structure and Display Server) 8 was used to emphasize the important features, such as exon-intron arrangement and composition, conserved elements, and binding sites ( Hu et al, 2015 ; Abdullah et al, 2018a ; Manzoor et al, 2021c , d ). The MEME software (Motif Elicitation) 9 ( Bailey et al, 2015 ; Sabir et al, 2022 ) was used to illustrate the conserved motifs.…”

“…All GST gene positions were determined through the Rosaceae Genome Database (see text footnote 1) and then visualized using Mapinspect web tool 10 ( Sneddon et al, 2012 ; Chen et al, 2018 ; Manzoor et al, 2021d ). Furthermore, the Pfam database, 11 HMMER software, 12 and Conserved Domain Architecture Retrieval Tool (CDART) were used to identify the conserved domains of PavGST proteins ( Geer et al, 2002 ; Cheng et al, 2019 ).…”

“…The promoter regions were discovered through the initiation codon along with 1.5 kb upstream sequences for all PavGST members and PlantCARE database 13 was utilized to estimate and display all cis-elements ( Lescot, 2002 ; Manzoor et al, 2021d ).…”

“…All GST gene positions were determined through the Rosaceae Genome Database (see text footnote 1) and then visualized using Mapinspect web tool 10 (Sneddon et al, 2012;Chen et al, 2018; 2 http://www.ebi.ac.uk/interpro/ 3 https://www.genscript.com/tools/pcr-primers-designer 4 http://gsds.gao-lab.org/ 5 https://meme-suite.org/meme/tools/meme 6 https://mapinspect.software.informer.com/ 7 https://bioinformatics.psb.ugent.be/webtools/plantcare/html/ 8 https://popgenie.org/node/42 9 http://services.cbu.uib.no/tools/kaks 10 http://gsds.cbi.pku.edu.cn/ Manzoor et al, 2021d). Furthermore, the Pfam database, 11 HMMER software, 12 and Conserved Domain Architecture Retrieval Tool (CDART) were used to identify the conserved domains of PavGST proteins (Geer et al, 2002;Cheng et al, 2019).…”