scholarly journals Genome-Wide Identification and Characterization of Caffeic Acid O-Methyltransferase Gene Family in Soybean

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2816
Author(s):  
Xu Zhang ◽  
Bowei Chen ◽  
Lishan Wang ◽  
Shahid Ali ◽  
Yile Guo ◽  
...  
Keyword(s):  
Gene Family ◽  
Caffeic Acid ◽  
Light Stress ◽  
Comt Gene ◽  
Cis Acting ◽  
Genome Wide ◽  
High Quality Protein ◽  
Methyltransferase Gene ◽  
Salt And Drought Stress

Soybean is one of the most important legumes, providing high-quality protein for humans. The caffeic acid O-methyltransferase (COMT) gene has previously been demonstrated to be a critical gene that regulates lignin production in plant cell walls and plays an important function in plant growth and development. However, the COMT gene family has not been studied in soybeans. In this study, 55 COMT family genes in soybean were identified by phylogenetic analysis and divided into two groups, I and II. The analysis of conserved domains showed that all GmCOMTs genes contained Methyltransferase-2 domains. Further prediction of cis-acting elements showed that GmCOMTs genes were associated with growth, light, stress, and hormonal responses. Eventually, based on the genomic data of soybean under different stresses, the results showed that the expression of GmCOMTs genes was different under different stresses, such as salt and drought stress. This study has identified and characterized the COMT gene family in soybean, which provides an important theoretical basis for further research on the biological functions of COMT genes and promotes revealing the role of GmCOMTs genes under stress resistance.

scholarly journals Genome-Wide Identification and Characterization of the RCI2 Gene Family in Allotetraploid Brassica napus Compared with Its Diploid Progenitors

2022 ◽  
Vol 23 (2) ◽  
pp. 614
Author(s):  
Weiqi Sun ◽  
Mengdi Li ◽  
Jianbo Wang
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Gene Structure ◽  
Stress Responses ◽  
Stress Protein ◽  
Purifying Selection ◽  
Cis Acting ◽  
Genome Wide ◽  
Duplication Events

Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are suitable for studying the problems associated with polyploidization. As an important anti-stress protein, RCI2 proteins widely exist in various tissues of plants, and are crucial to plant growth, development, and stress response. In this study, the RCI2 gene family was comprehensively identified and analyzed, and 9, 9, and 24 RCI2 genes were identified in B. rapa, B. oleracea, and B. napus, respectively. Phylogenetic analysis showed that all of the identified RCI2 genes were divided into two groups, and further divided into three subgroups. Ka/Ks analysis showed that most of the identified RCI2 genes underwent a purifying selection after the duplication events. Moreover, gene structure analysis showed that the structure of RCI2 genes is largely conserved during polyploidization. The promoters of the RCI2 genes in B. napus contained more cis-acting elements, which were mainly involved in plant development and growth, plant hormone response, and stress responses. Thus, B. napus might have potential advantages in some biological aspects. In addition, the changes of RCI2 genes during polyploidization were also discussed from the aspects of gene number, gene structure, gene relative location, and gene expression, which can provide reference for future polyploidization analysis.

scholarly journals Genome-wide identification and analysis of the CNGC gene family in maize

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5816 ◽  
Author(s):  
Lidong Hao ◽  
Xiuli Qiao
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Gene Families ◽  
Regulatory Elements ◽  
Vital Role ◽  
Signal Pathways ◽  
Cis Acting ◽  
Genome Wide ◽  
Gramineous Plant ◽  
Gated Channel

As one of the non-selective cation channel gene families, the cyclic nucleotide-gated channel (CNGC) gene family plays a vital role in plant physiological processes that are related to signal pathways, plant development, and environmental stresses. However, genome-wide identification and analysis of the CNGC gene family in maize has not yet been undertaken. In the present study, twelve ZmCNGC genes were identified in the maize genome, which were unevenly distributed on chromosomes 1, 2, 4, 5, 6, 7, and 8. They were classified into five major groups: Groups I, II, III, IVa, and IVb. Phylogenetic analysis showed that gramineous plant CNGC genes expanded unequally during evolution. Group IV CNGC genes emerged first, whereas Groups I and II appeared later. Prediction analysis of cis-acting regulatory elements showed that 137 putative cis-elements were related to hormone-response, abiotic stress, and organ development. Furthermore, 120 protein pairs were predicted to interact with the 12 ZmCNGC proteins and other maize proteins. The expression profiles of the ZmCNGC genes were expressed in tissue-specific patterns. These results provide important information that will increase our understanding of the CNGC gene family in maize and other plants.

scholarly journals Genome-Wide Identification of WRKY Genes in Artemisia annua: Characterization of a Putative Ortholog of AtWRKY40

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1669
Author(s):  
Angelo De Paolis ◽  
Sofia Caretto ◽  
Angela Quarta ◽  
Gian-Pietro Di Sansebastiano ◽  
Irene Sbrocca ◽  
...  
Keyword(s):  
Artemisia Annua ◽  
Antimalarial Activity ◽  
Regulatory Elements ◽  
Promoter Regions ◽  
Cis Acting ◽  
Protein Motifs ◽  
Genome Wide ◽  
A Genome ◽  
Rapid Amplification

Artemisia annua L. is well-known as the plant source of artemisinin, a sesquiterpene lactone with effective antimalarial activity. Here, a putative ortholog of the Arabidopsis thaliana WRKY40 transcription factor (TF) was isolated via reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends in A. annua and named AaWRKY40. A putative nuclear localization domain was identified in silico and experimentally confirmed by using protoplasts of A. annua transiently transformed with AaWRKY40-GFP. A genome-wide analysis identified 122 WRKY genes in A. annua, and a manually curated database was obtained. The deduced proteins were categorized into the major WRKY groups, with group IIa containing eight WRKY members including AaWRKY40. Protein motifs, gene structure, and promoter regions of group IIa WRKY TFs of A. annua were characterized. The promoter region of AaWRKY group IIa genes contained several abiotic stress cis-acting regulatory elements, among which a highly conserved W-box motif was identified. Expression analysis of AaWRKY40 compared to AaWRKY1 in A. annua cell cultures treated with methyl jasmonate known to enhance artemisinin production, suggested a possible involvement of AaWRKY40 in terpenoid metabolism. Further investigation is necessary to study the role of AaWRKY40 and possible interactions with other TFs in A. annua.

scholarly journals Genome-Wide Identification and Characterization of MLO Gene Family in Octoploid Strawberry (Fragaria ×ananassa)

2020 ◽  
Author(s):  
Ronald R. Tapia ◽  
Christopher R. Barbey ◽  
Saket Chandra ◽  
Kevin M. Folta ◽  
Vance M. Whitaker ◽  
...  
Keyword(s):  
Gene Family ◽  
Genomic Structure ◽  
Resistance Locus ◽  
Fragaria Ananassa ◽  
Loss Of Function ◽  
Genetic Studies ◽  
Genome Wide ◽  
Segregating Population

AbstractPowdery mildew (PM) caused by Podosphaera aphanis is a major fungal disease in cultivated strawberry. Mildew Resistance Locus O (MLO) is a gene family described for having conserved seven-transmembrane domains. Induced loss-of-function in specific MLO genes can confer durable and broad resistance against PM pathogens. However, the underlying biological role of MLO genes in strawberry is still unknown. In the present study, the genomic structure of MLO genes were characterized in both diploid (Fragaria vesca) and octoploid strawberry (Fragaria ×ananassa), and the potential sources of MLO-mediated susceptibility were identified. Twenty MLO-like sequences were identified in F. vesca, with sixty-eight in F. ×ananassa. Phylogenetic analysis divides strawberry MLO genes into eight different clades, in which three FveMLO and ten FaMLO genes were grouped together with the functionally known MLO susceptibility. Out of ten FaMLO genes, FaMLO17-2 and FaMLO17-3 showed the highest similarity to the known susceptibility MLO proteins. Gene expression analysis of FaMLO genes was conducted using a multi-parental segregating population. Three expression quantitative trait loci (eQTL) were substantially associated with MLO transcript levels in mature fruits, suggesting discrete genetic control of susceptibility. These results are a critical first step in understanding allele function of MLO genes, and are necessary for further genetic studies of PM resistance in cultivated strawberry.

scholarly journals Genome-wide characterization of SPL gene family in Codonopsis pilosula reveals the novel roles of CpSPL2 and CpSPL10 in promoting the accumulation of secondary metabolites and growth of C. pilosula hairy root

2020 ◽  
Author(s):  
Jing Yang ◽  
Zhonglong Guo ◽  
Yao Cao ◽  
Rui Chen ◽  
Wentao Wang ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Hairy Root ◽  
Expression Patterns ◽  
Light Stress ◽  
The Novel ◽  
Promoter Regions ◽  
Cis Acting ◽  
Codonopsis Pilosula ◽  
Genome Data ◽  
Genome Wide

Abstract Background SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors play critical roles in regulating diverse aspects of plant growth and development, including vegetative phase change, plant architecture, anthocyanin accumulation, lateral root growth, etc. Codonopsis pilosula is a famous medicinal plant and its dried root, named Dangshen, is one of the most widely used traditional Chinese medicine. However, little information about SPL genes in this species has been reported. Results In the present study, 15 SPL genes were identified based on the genome data of Codonopsis pilosula. Ten of the 15 CpSPLs were predicted to be the targets of miR156. Phylogenetic analysis clustered CpSPLs into seven groups (G1-G7) along with 16 SPLs from Arabidopsis thaliana. CpSPLs in the same group share similar gene structure and conserved motif composition. Cis-acting elements responding to light, stress, and phytohormone widely exist in their promoter regions. Our qRT-PCR results indicated that 15 CpSPLs were differentially expressed in different tissues (root, stem, leaf, flower, and calyx), different developmental periods (1, 2 and 3 months after germination), and various conditions (NaCl, MeJA and ABA treatment). Compared with the control, overexpression of CpSPL2 or CpSPL10 significantly promoted not only the growth of hairy roots, but also the accumulation of total saponins and lobetyolin. Conclusions The SPL genes in the C. pilosula genome were identified and their expression patterns were analyzed. The novel roles of CpSPL2 and CpSPL10 in promoting the accumulation of secondary metabolites and growth of C. pilosula hairy root were revealed. Our results established a foundation for further investigation of CpSPLs and provided novel insights into their biological functions.

scholarly journals Genome-Wide Identification and Functional Investigation of 1-Aminocyclopropane-1-carboxylic Acid Oxidase (ACO) Genes in Cotton

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1699
Author(s):  
Hengling Wei ◽  
Yujun Xue ◽  
Pengyun Chen ◽  
Pengbo Hao ◽  
Fei Wei ◽  
...  
Keyword(s):  
Tandem Duplication ◽  
Critical Role ◽  
Acid Oxidase ◽  
Comprehensive Overview ◽  
Cis Acting ◽  
Functional Studies ◽  
Genome Wide ◽  
Salt And Drought Stress ◽  
Functional Investigation ◽  
Rate Limiting

ACO is one of the rate-limiting enzymes in the biosynthesis of ethylene, and it plays a critical role in the regulation of plant growth and development. However, the function of ACO genes in cotton is not well studied. In this study, a total of 332 GhACOs, 187 GaACOs, and 181 GrACOs were identified in G. hirsutum, G. arboretum, and G. raimondii, respectively. Gene duplication analysis showed that whole-genome duplication (WGD) and tandem duplication were the major forces driving the generation of cotton ACO genes. In the promoters of GhACOs, there were cis-acting elements responding to stress, phytohormones, light, and circadian factors, indicating the possible involvement of GhACOs in these processes. Expression and co-expression analyses illustrated that most GhACOs were not only widely expressed in various tissues but also coexpressed with other genes in response to salt and drought stress. GhACO106_At overexpression in Arabidopsis promoted flowering and increased salt tolerance. These results provide a comprehensive overview of the ACO genes of cotton and lay the foundation for subsequent functional studies of these genes.

scholarly journals Genome-wide identification and expression profiling of invertase gene family for abiotic stresses tolerance in Poncirus trifoliata

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Bachar Dahro ◽  
Yue Wang ◽  
Ahmed Alhag ◽  
Chunlong Li ◽  
Dayong Guo ◽  
...  
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Family Members ◽  
Physiological Role ◽  
Poncirus Trifoliata ◽  
High Accumulation ◽  
Functional Studies ◽  
Genome Wide ◽  
Cold Tolerant

Abstract Background Sucrose (Suc) hydrolysis is directly associated with plants tolerance to multiple abiotic stresses. Invertase (INV) enzymes irreversibly catalyze Suc degradation to produce glucose (Glc) and fructose (Frc). However, genome-wide identification and function of individual members of the INV gene family in Poncirus trifoliata or its Citrus relatives in response to abiotic stresses are not fully understood. Results In this report, fourteen non-redundant PtrINV family members were identified in P. trifoliata including seven alkaline/neutral INV genes (PtrA/NINV1–7), two vacuolar INV genes (PtrVINV1–2), and five cell wall INV isoforms (PtrCWINV1–5). A comprehensive analysis based on the biochemical characteristics, the chromosomal location, the exon–intron structures and the evolutionary relationships demonstrated the conservation and the divergence of PtrINVs. In addition, expression analysis of INV genes during several abiotic stresses in various tissues indicated the central role of A/NINV7 among INV family members in response to abiotic stresses. Furthermore, our data demonstrated that high accumulation of Suc, Glc, Frc and total sugar contents were directly correlated with the elevated activities of soluble INV enzymes in the cold-tolerant P. trifoliata, C. ichangensis and C. sinensis, demonstrating the potential role of soluble INV enzymes for the cold tolerance of Citrus. Conclusions This work offered a framework for understanding the physiological role of INV genes and laid a foundation for future functional studies of these genes in response to abiotic stresses.

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