scholarly journals Comparative analysis of the P-type ATPase gene family in seven Rosaceae species and an expression analysis in pear (Pyrus bretschneideri Rehd.)

Genomics ◽  
2020 ◽  
Vol 112 (3) ◽  
pp. 2550-2563 ◽  
Author(s):  
Yuxin Zhang ◽  
Qionghou Li ◽  
Linlin Xu ◽  
Xin Qiao ◽  
Chunxin Liu ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Gene Family ◽  
Expression Analysis ◽  
Rosaceae Species ◽  
Atpase Gene ◽  
P Type

scholarly journals Genome-Wide Identification of the Vacuolar H+-ATPase Gene Family in Five Rosaceae Species and Expression Analysis in Pear (Pyrus bretschneideri)

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1661
Author(s):  
Hongsheng Zhou ◽  
Wen Huang ◽  
Shufen Luo ◽  
Huali Hu ◽  
Yingtong Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Prunus Persica ◽  
Proton Pumps ◽  
Event Analysis ◽  
Specific Expression ◽  
Rosaceae Species ◽  
Genome Wide ◽  
A Genome ◽  
Atpase Gene

Vacuolar H+-ATPases (V-ATPase) are multi-subunit complexes that function as ATP hydrolysis-driven proton pumps. They play pivotal roles in physiological processes, such as development, metabolism, stress, and growth. However, there have been very few studies on the characterisation of V-ATPase (VHA) genes in Rosaceae species. Therefore, in the present study, we performed a genome-wide analysis and identified VHA gene family members in five Rosaceae species (Pyrus bretschneideri, Malus domestica, Prunus persica, Fragaria vesca, and Prunus mume). A total of 159 VHA genes were identified, and were classified into 13 subfamilies according to the phylogenetic analysis. The structure of VHA proteins revealed high similarity among different VHA genes within the same subgroup. Gene duplication event analysis revealed that whole-genome duplications represented the major pathway for expansion of the Pyrus bretschneideri VHA genes (PbrVHA genes). The tissue-specific expression analysis of the pear showed that 36 PbrVHA genes were expressed in major tissues. Seven PbrVHA genes were significantly downregulated when the pollen tube growth stopped. Moreover, many PbrVHA genes were differentially expressed during fruit development and storage, suggesting that VHA genes play specific roles in development and senescence. The present study provides fundamental information for further elucidating the potential roles of VHA genes during development and senescence.

scholarly journals Genome-wide identification and comparative analysis of the ADH gene family in Chinese white pear (Pyrus bretschneideri) and other Rosaceae species

Genomics ◽  
2020 ◽  
Vol 112 (5) ◽  
pp. 3484-3496
Author(s):  
Weiwei Zeng ◽  
Xin Qiao ◽  
Qionghou Li ◽  
Chunxin Liu ◽  
Jun Wu ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Gene Family ◽  
Rosaceae Species ◽  
Chinese White ◽  
Genome Wide ◽  
Adh Gene

Gene structure, evolution and expression analysis of the P-ATPase gene family in Chinese pear (Pyrus bretschneideri)

2020 ◽  
Vol 88 ◽  
pp. 107346
Author(s):  
Muhammad Aamir Manzoor ◽  
Xi Cheng ◽  
Guohui Li ◽  
Xueqiang Su ◽  
Muhammad Abdullah ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Gene Structure ◽  
Structure Evolution ◽  
Atpase Gene

Isolation and expression analysis of four members of the plasma membrane H+-ATPase gene family in Hevea brasiliensis

Trees ◽  
2015 ◽  
Vol 29 (5) ◽  
pp. 1355-1363 ◽  
Author(s):  
Jiahong Zhu ◽  
Jing Xu ◽  
Wenjun Chang ◽  
Zhili Zhang
Keyword(s):  
Plasma Membrane ◽  
Gene Family ◽  
Expression Analysis ◽  
Hevea Brasiliensis ◽  
Atpase Gene

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

2021 ◽  
Vol 22 (22) ◽  
pp. 12492
Author(s):  
Muhammad Aamir Manzoor ◽  
Irfan Ali Sabir ◽  
Iftikhar Hussain Shah ◽  
Han Wang ◽  
Zhao Yu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Comparative Analysis ◽  
Gene Family ◽  
Prunus Persica ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Composition Analysis ◽  
Rosaceae Species ◽  
Gata Transcription Factors ◽  
Gata Gene

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.

scholarly journals Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear (Pyrus bretschneideri)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6628
Author(s):  
Xueqiang Su ◽  
Tiankai Meng ◽  
Yu Zhao ◽  
Guohui Li ◽  
Xi Cheng ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Gene Family ◽  
Expression Analysis ◽  
Prunus Avium ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Prunus Mume ◽  
Rosaceae Species ◽  
Chinese White

The INDETERMINATE DOMAIN (IDD) gene family encodes hybrid transcription factors with distinct zinc finger motifs and appears to be found in all higher plant genomes. IDD genes have been identified throughout the genomes of the model plants Arabidopsis thaliana and Oryza sativa, and the functions of many members of this gene family have been studied. However, few studies have investigated the IDD gene family in Rosaceae species (among these species, a genome-wide identification of the IDD gene family has only been completed in Malus domestica). This study focuses on a comparative genomic analysis of the IDD gene family in five Rosaceae species (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Rubus occidentalis and Prunus avium). We identified a total of 68 IDD genes: 16 genes in Chinese white pear, 14 genes in F. vesca, 13 genes in Prunus mume, 14 genes in R. occidentalis and 11 genes in Prunus avium. The evolution of the IDD genes in these five Rosaceae species was revealed by constructing a phylogenetic tree, tracking gene duplication events, and performing a sliding window analysis and a conserved microsynteny analysis. The expression analysis of different organs showed that most of the pear IDD genes are found at a very high transcription level in fruits, flowers and buds. Based on our results with those obtained in previous research, we speculated that PbIDD2 and PbIDD8 might participate in flowering induction in pear. A temporal expression analysis showed that the expression patterns of PbIDD3 and PbIDD5 were completely opposite to the accumulation pattern of fruit lignin and the stone cell content. The results of the composite phylogenetic tree and expression pattern analysis indicated that PbIDD3 and PbIDD5 might be involved in the metabolism of lignin and secondary cell wall (SCW) formation. In summary, we provide basic information about the IDD genes in five Rosaceae species and thereby provide a theoretical basis for studying the function of these IDD genes.

scholarly journals Genome-Wide In Silico Analysis and Expression Profiling of Phosphoenolpyruvate Carboxylase Genes in Loquat, Apple, Peach, Strawberry and Pear

Agronomy ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 25
Author(s):  
Cao Zhi ◽  
Muhammad Moaaz Ali ◽  
Shariq Mahmood Alam ◽  
Shaista Gull ◽  
Sajid Ali ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Phosphoenolpyruvate Carboxylase ◽  
Expression Profiling ◽  
In Silico Analysis ◽  
Plant Metabolism ◽  
Motif Analysis ◽  
Rosaceae Species ◽  
Genome Wide ◽  
Syntenic Analysis

Phosphoenolpyruvate carboxylase (PEPC) genes have multiple potential roles in plant metabolism such as regulation and accumulation of organic acids in fruits, movement of guard cells and stress tolerance, etc. However, the systematic identification and characterization of PEPC genes in Rosaceae species i.e., loquat, apple, peach, strawberry, and pear are yet to be performed. In present study, 27 putative PEPC genes (loquat 4, apple 6, peach 3, strawberry 9, and pear 5) were identified. To further investigate the role of those PEPC genes, comprehensive bioinformatics and expression analysis were performed. In bioinformatic analysis, the physiochemical properties, conserved domains, gene structure, conserved motif, phylogenetic and syntenic analysis of PEPC genes were performed. The result revealed that the PEPcase superfamily domain was conserved in all examined PEPC proteins. Most of the PEPC proteins were predicted to be localized in cytonuclear. Genomic structural and motif analysis showed that the exon and motif number of each PEPC gene ranged dramatically, from 8 to 20, and 7 to 10, respectively. Syntenic analysis indicated that the segmental or whole-genome duplication played a vital role in extension of PEPC gene family in Rosacea species. The Ka and Ks values of duplicated genes depicted that PEPC genes have undergone a strong purifying selection. Furthermore, the expression analysis of PEPC genes in root, mature leaf, stem, full-bloom flower, and ripened fruit of loquat, apple, peach, strawberry, and pear was performed. Some genes were differentially expressed in aforementioned plant tissues, signifying their role in plant metabolism. This study provides the first genome-wide identification, characterization, and expression profiling of PEPC gene family in Rosaceae species, and provides the foundation for further functional analysis.

scholarly journals Genome-Wide Identification and Analysis of P-Type Plasma Membrane H+-ATPase Sub-Gene Family in Sunflower and the Role of HHA4 and HHA11 in the Development of Salt Stress Resistance

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 361 ◽  
Author(s):  
Zongchang Xu ◽  
Prince Marowa ◽  
Han Liu ◽  
Haina Du ◽  
Chengsheng Zhang ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Salt Stress ◽  
Gene Family ◽  
Abiotic Factors ◽  
Pcr Analysis ◽  
Future Research ◽  
Genome Database ◽  
Genome Wide ◽  
Atpase Gene ◽  
P Type

The P-type plasma membrane (PM) H+-ATPase plays a major role during the growth and development of a plant. It is also involved in plant resistance to a variety of biotic and abiotic factors, including salt stress. The PM H+-ATPase gene family has been well characterized in Arabidopsis and other crop plants such as rice, cucumber, and potato; however, the same cannot be said in sunflower (Helianthus annuus). In this study, a total of thirteen PM H+-ATPase genes were screened from the recently released sunflower genome database with a comprehensive genome-wide analysis. According to a systematic phylogenetic classification with a previously reported species, the sunflower PM H+-ATPase genes (HHAs) were divided into four sub-clusters (I, II, IV, and V). In addition, systematic bioinformatics analyses such as gene structure analysis, chromosome location analysis, subcellular localization predication, conserved motifs, and Cis-acting elements of promoter identification were also done. Semi-quantitative PCR analysis data of HHAs in different sunflower tissues revealed the specificity of gene spatiotemporal expression and sub-cluster grouping. Those belonging to sub-cluster I and II exhibited wide expression in almost all of the tissues studied while sub-cluster IV and V seldom showed expression. In addition, the expression of HHA4, HHA11, and HHA13 was shown to be induced by salt stress. The transgenic plants overexpressing HHA4 and HHA11 showed higher salinity tolerance compared with wild-type plants. Further analysis showed that the Na+ content of transgenic Arabidopsis plants decreased under salt stress, which indicates that PM H+ ATPase participates in the physiological process of Na+ efflux, resulting in salt resistance of the plants. This study is the first to identify and analyze the sunflower PM H+ ATPase gene family. It does not only lay foundation for future research but also demonstrates the role played by HHAs in salt stress tolerance.

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