scholarly journals Genome-Wide Identification and Analysis of Polygalacturonase Genes in Solanum lycopersicum

2018 ◽  
Vol 19 (8) ◽  
pp. 2290 ◽  
Author(s):  
Xubo Ke ◽  
Huasen Wang ◽  
Yang Li ◽  
Biao Zhu ◽  
Yunxiang Zang ◽  
...  
Keyword(s):  
Solanum Lycopersicum ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Amino Acid Sequences ◽  
Evolutionary Analysis ◽  
Environmental Stress Response ◽  
Promoter Regions ◽  
Genome Wide ◽  
Specific Organ ◽  
Organ Tissue

Polygalacturonase (PG), a large hydrolase family in plants, is involved in pectin disassembly of the cell wall in plants. The present study aims to characterize PG genes and investigate their expression patterns in Solanum lycopersicum. We identified 54 PG genes in the tomato genome and compared their amino acid sequences with their Arabidopsis counterpart. Subsequently, we renamed these PG genes according to their Arabidopsis homologs. Phylogenetic and evolutionary analysis revealed that these tomato PG genes could be classified into seven clades, and within each clade the exon/intron structures were conserved. Expression profiles analysis through quantitive real-time polymerase chain reaction (qRT-PCR) revealed that most SlPGs had specific or high expression patterns in at least one organ, and particularly five PG genes (SlPG14, SlPG15, SlPG49, SlPG70, and SlPG71) associated with fruit development. Promoter analysis showed that more than three cis-elements associated with plant hormone response, environmental stress response or specific organ/tissue development exhibited in each SlPG promoter regions. In conclusion, our results may provide new insights for the further study of PG gene function during plant development.

scholarly journals Genome-wide identification and characterization of SPX-domain-containing protein gene family in Solanum lycopersicum

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12689
Author(s):  
Chunwei Li ◽  
Qiuye You ◽  
Panfeng Zhao
Keyword(s):  
Gene Family ◽  
Solanum Lycopersicum ◽  
Protein Gene ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Major Facilitator Superfamily ◽  
Phosphate Ions ◽  
Genome Wide ◽  
New Gene ◽  
Major Facilitator

The SYG1, PHO81, and XPR1 (SPX) domain is named after the suppressor of yeast gpa1 (Syg1), yeast phosphatase (Pho81) and the human Xenotropic and Polytrophic Retrovirus receptor1 (XPR1). SPX-domain-containing proteins play pivotal roles in maintaining phosphate ions (Pi) homeostasis in plant. This study was to genome-wide identification and analysis of Solanum lycopersicum SPX-domain-containing protein gene family. The Solanum lycopersicum genome contains 19 SPX-domain-containing protein genes. These SPX-domain-containing protein genes were located in seven of the 12 chromosomes. According to the different conserved domains, the proteins encoded by those genes could be divided into four SPX-domain-containing protein families, which included SPX Family, SPX-ERD1/XPR1/SYG1(SPX-EXS) Family, SPX-Major Facilitator Superfamily (SPX-MFS) Family and SPX-Really Interesting New Gene (SPX-RING) Family. Phylogenetic analysis of SPX-domain-containing protein genes in Arabidopsis thaliana, Solanum tuberosum, Capsicum annuum and Solanum lycopersicum classified these genes into eight clades. Expression profiles derived from transcriptome (RNA-seq) data analysis showed 19 SPX-domain-containing protein genes displayed various expression patterns. SPX-domain-containing protein may play different roles in phosphate nutrition of Solanum lycopersicum different tissues and development stages. And, this study can provide the selection of candidate genes for functional research and genome editing in Solanum lycopersicum phosphate ions (Pi) nutrition.

Genome-wide investigation of the AP2/ERF superfamily and their expression under salt stress in Chinese willow (Salix matsudana)

2020 ◽  
Author(s):  
Yanhong Chen ◽  
Yuna Jiang ◽  
Guoyuan Liu ◽  
Chunmei Yu ◽  
Bolin Lian ◽  
...  
Keyword(s):  
Salt Stress ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Evolutionary Analysis ◽  
Sequencing Data ◽  
Genome Wide ◽  
Salix Matsudana

Abstract Background: AP2/ERF transcription factors (TFs) play indispensable roles in plant growth, development, and especially in various abiotic stresses responses. The AP2/ERF TF family has been discovered and classified in more than 50 species, including model plants, horticulture plants, crops, and trees. Many AP2/ERF TFs from various species have been functionally characterized. However, little is known about the AP2/ERF gene family of Chinese willow (Salix matsudana), which is a tetraploid ornamental tree species that is widely planted and is also considered a species that can improve the soil salinity of coastal beaches. The recently produced whole genome sequencing data of Salix matsudana allowed us to conduct an evolutionary analysis on the AP2/ERF genes during polyploidization and study the genome-wide expression profiles of AP2/ERF genes in Salix matsudana under salt stress. Results: In this study, 364 AP2/ERF genes of Salix matsudana (SmAP2/ERF) were identified and renamed according to the chromosomal location of the SmAP2/ERF genes. After phylogenetic analysis with known categories of genes from other species, the AP2/ERF genes were divided into three subfamilies: AP2 (55 members), ERF (301 members), and RAV (six members). Two Soloist genes were also identified. Gene structure and conserved motifs were analyzed in AP2/ERF genes, and introns were not found in most genes of the ERF subfamily, although some unique motifs were found to be important for the function of AP2/ERF genes. Syntenic relationships between the SmAP2/ERF genes and AP2/ERF genes from other species were also investigated to elucidate their evolutionary relationships during polyploidization. Moreover, analyses on the expression profiles under salt stress were also conducted.Conclusion: The progenitors of Salix matsudana underwent whole genome duplication not more than 10 Mya. Synteny analysis with other species showed macrosynteny between willow and poplar AP2/ERF genes and that Salix matsudana is genetically more closely related to Populus trichocarpa than to Salix purpurea. Further investigation of the AP2/ERF TFs demonstrated that differential expression patterns during salt stress and this information can help reveal the mechanism of salt tolerance regulation in Salix matsudana.

scholarly journals Mungbean DIRIGENT Gene Subfamilies and Their Expression Profiles Under Salt and Drought Stresses

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenying Xu ◽  
Tong Liu ◽  
Huiying Zhang ◽  
Hong Zhu
Keyword(s):  
Stress Responses ◽  
Expression Profiles ◽  
Pfam Domain ◽  
Vascular Plant ◽  
Expression Patterns ◽  
Promoter Regions ◽  
Genome Wide ◽  
A Genome ◽  
Salt And Drought Stress ◽  
Gene Structures

DIRIGENT (DIR) genes are key players in environmental stress responses that have been identified in many vascular plant species. However, few studies have examined the VrDIR genes in mungbean. In this study, we characterized 37 VrDIR genes in mungbean using a genome-wide identification method. VrDIRs were distributed on seven of the 11 mungbean chromosomes, and chromosome three contained the most VrDIR genes, with seven members. Thirty-two of the 37 VrDIRs contained a typical DIR gene structure, with one exon; the conserved DIR domain (i.e., Pfam domain) occupied most of the protein in 33 of the 37 VrDIRs. The gene structures of VrDIR genes were analyzed, and a total of 19 distinct motifs were detected. VrDIR genes were classified into five groups based on their phylogenetic relationships, and 13 duplicated gene pairs were identified. In addition, a total of 92 cis-acting elements were detected in all 37 VrDIR promoter regions, and VrDIR genes contained different numbers and types of cis-acting elements. As a result, VrDIR genes showed distinct expression patterns in different tissues and in response to salt and drought stress.

scholarly journals Genome-Wide Analysis of Myeloblastosis-Related Genes in Brassica napus L. and Positive Modulation of Osmotic Tolerance by BnMRD107

2021 ◽  
Vol 12 ◽  
Author(s):  
Jian Li ◽  
Keyun Lin ◽  
Shuai Zhang ◽  
Jian Wu ◽  
Yujie Fang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Brassica Napus ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Functional Study ◽  
Evolutionary Analysis ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Myeloblastosis (MYB)-related transcription factors comprise a large subfamily of the MYB family. They play significant roles in plant development and in stress responses. However, MYB-related proteins have not been comprehensively investigated in rapeseed (Brassica napus L.). In the present study, a genome-wide analysis of MYB-related transcription factors was performed in rapeseed. We identified 251 Brassica napus MYB (BnMYB)-related members, which were divided phylogenetically into five clades. Evolutionary analysis suggested that whole genome duplication and segmental duplication events have played a significant role in the expansion of BnMYB-related gene family. Selective pressure of BnMYB-related genes was estimated using the Ka/Ks ratio, which indicated that BnMYB-related genes underwent strong purifying selection during evolution. In silico analysis showed that various development-associated, phytohormone-responsive, and stress-related cis-acting regulatory elements were enriched in the promoter regions of BnMYB-related genes. Furthermore, MYB-related genes with tissue or organ-specific, stress-responsive expression patterns were identified in B. napus based on temporospatial and abiotic stress expression profiles. Among the stress-responsive MYB-related genes, BnMRD107 was strongly induced by drought stress, and was therefore selected for functional study. Rapeseed seedlings overexpressing BnMRD107 showed improved resistance to osmotic stress. Our findings not only lay a foundation for further functional characterization of BnMYB-related genes, but also provide valuable clues to determine candidate genes for future genetic improvement of B. napus.

scholarly journals Genome-scale identification of plant defensin (PDF) family genes and molecular characterization of their responses to diverse nutrient stresses in allotetraploid rapeseed

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12007
Author(s):  
Ying Liu ◽  
Ying-peng Hua ◽  
Huan Chen ◽  
Ting Zhou ◽  
Cai-peng Yue ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Stress Resistance ◽  
Cadmium Toxicity ◽  
Expression Patterns ◽  
Defense Responses ◽  
Molecular Characteristics ◽  
Environmental Stress Response ◽  
Promoter Regions ◽  
Genome Wide

Plant defensins (PDFs), short peptides with strong antibacterial activity, play important roles in plant growth, development, and stress resistance. However, there are few systematic analyses on PDFs in Brassica napus. Here, bioinformatics methods were used to identify genome-wide PDFs in Brassica napus, and systematically analyze physicochemical properties, expansion pattern, phylogeny, and expression profiling of BnaPDFs under diverse nutrient stresses. A total of 37 full-length PDF homologs, divided into two subgroups (PDF1s and PDF2s), were identified in the rapeseed genome. A total of two distinct clades were identified in the BnaPDF phylogeny. Clade specific conserved motifs were identified within each clade respectively. Most BnaPDFs were proved to undergo powerful purified selection. The PDF members had enriched cis-elements related to growth and development, hormone response, environmental stress response in their promoter regions. GO annotations indicate that the functional pathways of BnaPDFs are mainly involved in cells killing and plant defense responses. In addition, bna-miRNA164 and bna-miRNA172 respectively regulate the expression of their targets BnaA2.PDF2.5 and BnaC7.PDF2.6. The expression patterns of BnaPDFs were analyzed in different tissues. BnaPDF1.2bs was mainly expressed in the roots, whereas BnaPDF2.2s and BnaPDF2.3s were both expressed in stamen, pericarp, silique, and stem. However, the other BnaPDF members showed low expression levels in various tissues. Differential expression of BnaPDFs under nitrate limitation, ammonium excess, phosphorus starvation, potassium deficiency, cadmium toxicity, and salt stress indicated that they might participate in different nutrient stress resistance. The genome-wide identification and characterization of BnaPDFs will enrich understanding of their molecular characteristics and provide elite gene resources for genetic improvement of rapeseed resistance to nutrient stresses.

Genome-Wide Identification and Characterization of WOX Genes in Cucumis sativus

Genome ◽  
2021 ◽  
Author(s):  
Ni Han ◽  
Rui Tang ◽  
Xueqian Chen ◽  
Zhixuan Xu ◽  
Zhonghai Ren ◽  
...  
Keyword(s):  
Cucumis Sativus ◽  
Stress Responses ◽  
Expression Profiles ◽  
Duplication Event ◽  
Amino Acid Sequences ◽  
Event Analysis ◽  
Promoter Regions ◽  
Element Analysis ◽  
Genome Wide ◽  
Wox Genes

WUSCHEL-related homeobox (WOX) proteins are plant-specific transcription factors that are profoundly involved in regulation of plant development and stress responses. In this study, we totally identified 11 WOX transcription factor family members in cucumber (Cucumis sativus, CsWOXs) genome and classified them into three clades with nine subclades based on phylogenetic analysis results. Alignment of amino acid sequences revealed that all WOX members in cucumber contained the typical homeodomain, which consists of 60-66 amino acids and is folded into a helix-turn-helix structure. Gene duplication event analysis indicated that CsWOX1a and CsWOX1b were a segment duplication pair, which might affect the number of WOX members in cucumber genome. The expression profiles of CsWOX genes in different tissues demonstrated that the members sorted into the ancient clade (CsWOX13a and CsWOX13b) were constitutively expressed at higher levels in comparison to the others. Cis-element analysis in promoter regions suggested that the expression of CsWOX genes was associated with phytohormone pathways and stress responses, which was further supported by RNA-seq data. Taken together, our results provide new insights into the evolution of cucumber WOX genes and improve our understanding about the biological functions of CsWOX family.

scholarly journals Genome-wide in silico identification and expression analysis of beta-galactosidase family members in sweetpotato [Ipomoea batatas (L.) Lam]

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Fuyun Hou ◽  
Taifeng Du ◽  
Zhen Qin ◽  
Tao Xu ◽  
Aixian Li ◽  
...  
Keyword(s):  
Plant Development ◽  
Stress Responses ◽  
Ipomoea Batatas ◽  
Expression Profiles ◽  
Glycosyl Hydrolase ◽  
Expression Patterns ◽  
Human Beings ◽  
Promoter Regions ◽  
Cell Wall Modification ◽  
Biotic Stresses

Abstract Background Sweetpotato (Ipomoea batatas (L.) Lam.) serves as an important food source for human beings. β-galactosidase (bgal) is a glycosyl hydrolase involved in cell wall modification, which plays essential roles in plant development and environmental stress adaptation. However, the function of bgal genes in sweetpotato remains unclear. Results In this study, 17 β-galactosidase genes (Ibbgal) were identified in sweetpotato, which were classified into seven subfamilies using interspecific phylogenetic and comparative analysis. The promoter regions of Ibbgals harbored several stress, hormone and light responsive cis-acting elements. Quantitative real-time PCR results displayed that Ibbgal genes had the distinct expression patterns across different tissues and varieties. Moreover, the expression profiles under various hormonal treatments, abiotic and biotic stresses were highly divergent in leaves and root. Conclusions Taken together, these findings suggested that Ibbgals might play an important role in plant development and stress responses, which provided evidences for further study of bgal function and sweetpotato breeding.

scholarly journals Genome-Wide Identification and Expression Analyses of CONSTANS-Like Family Genes in Cucumber (Cucumis sativus L.)

2021 ◽  
Author(s):  
Zhen Tian ◽  
Xiaodong Qin ◽  
Hui Wang ◽  
Ji Li ◽  
Jinfeng Chen
Keyword(s):  
Floral Induction ◽  
Structural Characteristics ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Biological Functions ◽  
Promoter Regions ◽  
Cucumis Sativus L ◽  
Cis Acting ◽  
Genome Wide ◽  
Induction Process

AbstractThe CONSTANS-like (COL) gene family is one of the plant-specific transcription factor families that play important roles in plant growth and development. However, the knowledge of COLs related in cucumber is limited, and their biological functions, especially in the photoperiod-dependent flowering process, are still unclear. In this study, twelve CsaCOL genes were identified in the cucumber genome. Phylogenetic and conserved motif analyses provided insights into the evolutionary relationship between the CsaCOLs. Further, the comparative genome analysis revealed that COL genes are conserved in different plant species, especially collinearity gene pairs related to CsaCOL5. Ten kinds of cis-acting elements were vividly detected in CsaCOLs promoter regions, including five light-responsive elements, which echo the diurnal rhythm expression patterns of seven CsaCOL genes under SD and LD photoperiod regimes. Combined with the expression data of developmental stage, three CsaCOL genes are involved in the flowering network and play pivotal roles for the floral induction process. Our results provide useful information for further elucidating the structural characteristics, expression patterns, and biological functions of COL family genes in many plants

scholarly journals Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhixuan Du ◽  
Qitao Su ◽  
Zheng Wu ◽  
Zhou Huang ◽  
Jianzhong Bao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Tandem Repeats ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Genome Wide ◽  
Comprehensive Information ◽  
Family Gene

AbstractMultidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

Sign in / Sign up

Export Citation Format

Share Document