scholarly journals Genome-wide identification and evolution of HECT genes in wheat

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10457
Author(s):  
Xianwen Meng ◽  
Ting Yang ◽  
Jing Liu ◽  
Mingde Zhao ◽  
Jiuli Wang
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Segmental Duplication ◽  
Profile Analysis ◽  
Purifying Selection ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Ubiquitin Proteasome ◽  
Proteasome Pathway

Background As an important class of E3 ubiquitin ligases in the ubiquitin proteasome pathway, proteins containing homologous E6-AP carboxyl terminus (HECT) domains are crucial for growth, development, metabolism, and abiotic and biotic stress responses in plants. However, little is known about HECT genes in wheat (Triticum aestivum L.), one of the most important global crops. Methods Using a genome-wide analysis of high-quality wheat genome sequences, we identified 25 HECT genes classified into six groups based on the phylogenetic relationship among wheat, rice, and Arabidopsis thaliana. Results The predicted HECT genes were distributed evenly in 17 of 21 chromosomes of the three wheat subgenomes. Twenty-one of these genes were hypothesized to be segmental duplication genes, indicating that segmental duplication was significantly associated with the expansion of the wheat HECT gene family. The Ka/Ks ratios of the segmental duplication of these genes were less than 1, suggesting purifying selection within the gene family. The expression profile analysis revealed that the 25 wheat HECT genes were differentially expressed in 15 tissues, and genes in Group II, IV, and VI (UPL8, UPL6, UPL3) were highly expressed in roots, stems, and spikes. This study contributes to further the functional analysis of the HECT gene family in wheat.

scholarly journals Genome-wide identification and expression analysis of the invertase gene family in common wheat

2021 ◽  
Author(s):  
Chao Wang ◽  
Guanghao Wang ◽  
Xiaojian Qu ◽  
Xiangyu Zhang ◽  
pingchuan Deng ◽  
...  
Keyword(s):  
Gene Family ◽  
Segmental Duplication ◽  
Profile Analysis ◽  
Functional Characterization ◽  
Purifying Selection ◽  
Specific Expression ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
Family Based ◽  
Yield Formation

Background: The degradation of sucrose plays an important role in the process of crop biomass allocation and yield formation. Invertase (INV) irreversibly catalyzes the conversion of sucrose into glucose and fructose, which doomed its' important role in plant development and stress tolerance. However, the functions of INV genes in wheat, one of the most important crops, were less studied due to the polyploidy. Results: Here, we systematically analyzed the INV gene family based on the latest published wheat reference genomic information. A total of 126 TaINV genes were identified and classified into three classes based on the phylogenetic relationship and their gene structure. Of which, 11 and 83 gene pairs were identified as tandem and segmental duplication genes respectively, while the Ka/Ks ratios of tandem and segmental duplication TaINV genes were less than 1. Expression profile analysis shows that 18 TaINV genes have tissue-specific expression, and 54 TaINV genes were involved in stress response. Furthermore, RNA-seq showed that 35 genes are differentially expressed in grain weight NILs N0910-81L/N0910-81S, in which 9 TaINVs were stably detected by qRT-PCR at three time-points, 4, 7 and 10 DPA. Four of them (TaCWI47, TaCWI48, TaCWI50 and TaVI27) different expressed between the NILs resided in 4 QTL segments (QTGW.nwafu-5DL.1, QTGW.nwafu-5DL.2, QTGW.nwafu-7AS.1 and QTGW.nwafu-7AS.2). These findings facilitate function investigations of the wheat INV gene family and provide new insights into the grain development mechanism in wheat. Conclusions: Our results showed that allopolyploid events were the main reason for the expansion of the TaINV gene family in hexaploid wheat, and duplication genes might undergo purifying selection. The expression profiling of TaINV genes implied that they are likely to play an important role in wheat growth and development and adaption to stressful environments. And TaCWI47, TaCWI48, TaCWI50 and TaVI27 may have more important roles in grain developments. Our study lay a base for further dissecting the functional characterization of TaINV family members.

scholarly journals Genome-wide identification and functional characterization of the Camelina sativa WRKY gene family in response to abiotic stress

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Yanan Song ◽  
Hongli Cui ◽  
Ying Shi ◽  
Jinai Xue ◽  
Chunli Ji ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Stress Resistance ◽  
Segmental Duplication ◽  
Expression Profiles ◽  
High Stress ◽  
Camelina Sativa ◽  
Genome Wide ◽  
A Genome

Abstract Background WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, there is limited knowledge about the WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance for various stresses. Here, a genome-wide characterization of WRKY proteins is performed to examine their gene structures, phylogenetics, expression, conserved motif organizations, and functional annotation to identify candidate WRKYs that mediate stress resistance regulation in camelinas. Results A total of 242 CsWRKY proteins encoded by 224 gene loci distributed unevenly over the chromosomes were identified, and they were classified into three groups by phylogenetic analysis according to their WRKY domains and zinc finger motifs. The 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in the C. sativa and Arabidopsis genomes as well as 282 pairs in the C. sativa and B. napus genomes, respectively. A total of 137 segmental duplication events were observed, but there was no tandem duplication in the camelina genome. Ten major conserved motifs were examined, with WRKYGQK being the most conserved, and several variants were present in many CsWRKYs. Expression analysis revealed that 50% more CsWRKY genes were expressed constitutively, and a set of them displayed tissue-specific expression. Notably, 11 CsWRKY genes exhibited significant expression changes in seedlings under cold, salt, and drought stresses, showing a preferentially inducible expression pattern in response to the stress. Conclusions The present article describes a detailed analysis of the CsWRKY gene family and its expression profiles in 12 tissues and under several stress conditions. Segmental duplication is the major force underlying the broad expansion of this gene family, and a strong purifying pressure occurred for CsWRKY proteins during their evolution. CsWRKY proteins play important roles in plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms, were found to be the possible key players in mediating plant responses to various stresses. Overall, our results provide a foundation for understanding the roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance as well as the development of stress tolerance cultivars among Cruciferae crops.

scholarly journals Expression profiling of the Dof gene family under abiotic stresses in spinach

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hongying Yu ◽  
Yaying Ma ◽  
Yijing Lu ◽  
Jingjing Yue ◽  
Ray Ming
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Profiling ◽  
Abiotic Stresses ◽  
Spinacia Oleracea ◽  
Purifying Selection ◽  
Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

AbstractDNA-binding with one finger (Dof) are plant-specific transcription factors involved in numerous pathways of plant development, such as abiotic stresses responses. Although genome-wide analysis of Dof genes has been performed in many species, but these genes in spinach have not been analyzed yet. We performed a genome-wide analysis and characterization of Dof gene family in spinach (Spinacia oleracea L.). Twenty-two Dof genes were identified and classified into four groups with nine subgroups, which was further corroborated by gene structure and motif analyses. Ka/Ks analysis revealed that SoDofs were subjected to purifying selection. Using cis-acting elements analysis, SoDofs were involved in plant growth and development, plant hormones, and stress responses. Expression profiling demonstrated that SoDofs expressed in leaf and inflorescence, and responded to cold, heat, and drought stresses. SoDof22 expressed the highest level in male flowers and under cold stress. These results provided a genome-wide analysis of SoDof genes, their gender- and tissue-specific expression, and response to abiotic stresses. The knowledge and resources gained from these analyses will benefit spinach improvement.

scholarly journals Genome-Wide Analysis Elucidates the Role of CONSTANS-like Genes in Stress Responses of Cotton

2018 ◽  
Vol 19 (9) ◽  
pp. 2658 ◽  
Author(s):  
Wenqiang Qin ◽  
Ya Yu ◽  
Yuying Jin ◽  
Xindong Wang ◽  
Ji Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Segmental Duplication ◽  
Purifying Selection ◽  
Phylogenetic Tree Analysis ◽  
Group Iii ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Drought And Salt Stress

The CONSTANS (CO)-like gene family has been well studied for its role in the regulation of plant flowering time. However, their role remains poorly understood in cotton. To better understand the possible roles of CO-like in cotton, we performed a comprehensive genome-wide analysis of CO-like genes in cotton. Phylogenetic tree analysis showed that CO-like genes naturally clustered into three groups. Segmental duplication and whole genome duplication (WGD), which occurred before polyploidy, were important contributors to its expansion within the At (“t” indicates tetraploid) and Dt subgenomes, particularly in Group III. Long-terminal repeat retroelements were identified as the main transposable elements accompanying 18 genes. The genotype of GhCOL12_Dt displayed low diversity; it was a candidate involved in domestication. Selection pressure analyses indicated that relaxed purifying selection might have provided the main impetus during the evolution of CO-like genes in upland cotton. In addition, the high expression in the torus and calycle indicated that CO-like genes might affect flowering. The genes from Group II, and those from Group III involved in segmental duplication or WGD, might play important roles in response to drought and salt stress. Overall, this comprehensive genome-wide study of the CO-like gene family would facilitate further detailed studies in cotton.

scholarly journals Genome-wide identification and functional characterization of the Camelina sativa WRKY gene family in response to abiotic stress 

2020 ◽  
Author(s):  
Yanan Song ◽  
Hongli Cui ◽  
Ying Shi ◽  
Jinai Xue ◽  
Chunli Ji ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Stress Resistance ◽  
Segmental Duplication ◽  
Expression Profiles ◽  
High Stress ◽  
Camelina Sativa ◽  
Genome Wide ◽  
A Genome

Abstract Background: WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, there is limited knowledge about the WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance for various stresses. Here, a genome-wide characterization of WRKY proteins is performed to examine their gene structures, phylogenetics, expression, conserved motif organizations, and functional annotation to identify candidate WRKYs that mediate stress resistance regulation in camelinas. Results: A total of 242 CsWRKY proteins encoded by 224 gene loci distributed unevenly over the chromosomes were identified, and they were classified into three groups by phylogenetic analysis according to their WRKY domains and zinc finger motifs. The 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in the C. sativa and Arabidopsis genomes as well as 282 pairs in the C. sativa and B. napus genomes, respectively. A total of 137 segmental duplication events were observed, but there was no tandem duplication in the camelina genome. Ten major conserved motifs were examined, with WRKYGQK being the most conserved, and several variants were present in many CsWRKYs. Expression analysis revealed that 50% more CsWRKY genes were expressed constitutively, and a set of them displayed tissue-specific expression. Notably, 11 CsWRKY genes exhibited significant expression changes in seedlings under cold, salt, and drought stresses, showing a preferentially inducible expression pattern in response to the stress. Conclusions: The present article describes a detailed analysis of the CsWRKY gene family and its expression profiles in twelve tissues and under several stress conditions. Segmental duplication is the major force underlying the broad expansion of this gene family, and a strong purifying pressure occurred for CsWRKY proteins during their evolution. CsWRKY proteins play important roles in plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms, were found to be the possible key players in mediating plant responses to various stresses. Overall, our results provide a foundation for understanding the roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance as well as the development of stress tolerance cultivars among Cruciferae crops.

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 cystatin family genes in Sorghum (Sorghum bicolor (L.) Moench)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10617
Author(s):  
Jie Li ◽  
Xinhao Liu ◽  
Qingmei Wang ◽  
Junyan Sun ◽  
Dexian He
Keyword(s):  
Gene Family ◽  
Seed Development ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Seed Formation ◽  
Aphid Infestation ◽  
Genome Wide ◽  
A Genome ◽  
Cystatin Family

To set a systematic study of the Sorghum cystatins (SbCys) gene family, a genome-wide analysis of the SbCys family genes was performed by bioinformatics-based methods. In total, 18 SbCys genes were identified in Sorghum, which were distributed unevenly on chromosomes, and two genes were involved in a tandem duplication event. All SbCys genes had similar exon/intron structure and motifs, indicating their high evolutionary conservation. Transcriptome analysis showed that 16 SbCys genes were expressed in different tissues, and most genes displayed higher expression levels in reproductive tissues than in vegetative tissues, indicating that the SbCys genes participated in the regulation of seed formation. Furthermore, the expression profiles of the SbCys genes revealed that seven cystatin family genes were induced during Bipolaris sorghicola infection and only two genes were responsive to aphid infestation. In addition, quantitative real-time polymerase chain reaction (qRT-PCR) confirmed that 17 SbCys genes were induced by one or two abiotic stresses (dehydration, salt, and ABA stresses). The interaction network indicated that SbCys proteins were associated with several biological processes, including seed development and stress responses. Notably, the expression of SbCys4 was up-regulated under biotic and abiotic stresses, suggesting its potential roles in mediating the responses of Sorghum to adverse environmental impact. Our results provide new insights into the structural and functional characteristics of the SbCys gene family, which lay the foundation for better understanding the roles and regulatory mechanism of Sorghum cystatins in seed development and responses to different stress conditions.

scholarly journals Genome-wide identification and functional characterization of Camelina sativa WRKY gene family in response to abiotic stress

2020 ◽  
Author(s):  
Yanan Song ◽  
Hongli Cui ◽  
Ying Shi ◽  
Jinai Xue ◽  
Chunli Ji ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Stress Resistance ◽  
Segmental Duplication ◽  
Functional Characterization ◽  
High Stress ◽  
Camelina Sativa ◽  
Genome Wide ◽  
Large Expansion

Abstract Background: WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, knowledge is limited for WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance against various stresses. Here, genome-wide characterization of WRKY proteins is performed to examine their gene-structures, phylogenetics, expressions, conserved motif organizations, and functional annotation to identify candidate WRKYs mediating regulation of stress resistance in camelina.Results: Total of 242 CsWRKY proteins encoded by 224 gene loci distributed uneven on chromosomes were identified, and classified into three groups via phylogenetic analysis according to their WRKY domains and zinc finger motifs. 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in C. sativa and Arabidopsis genomes as well as 282 pairs for C. sativa and B. napus, respectively. 137 segmental duplication events were observed but no tandem duplication in camelina genome. Ten major conserved motifs were examined, with WRKYGQK as the most conserved and several variants existed in many CsWRKYs. Expression analysis revealed that half more CsWRKY genes were expressed constitutively, and a set of them had a tissue-specific expression. Notably, 11 CsWRKY genes exhibited significantly expression changes in plant seedlings under cold, salt, and drought stress, respectively, having preferentially inducible expression pattern in response to the stress.Conclusions: The present described a detail analysis of CsWRKY gen family and their expression profiled in twelve tissues and under several stress conditions. Segmental duplication is the major force for large expansion of this gene family, and a strong purifying pressure happened for CsWRKY proteins evolutionally. CsWRKY proteins play important roles for plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms were found to be the key players possibly in mediating plant response to various stresses. Overall, our results provide a foundation for understanding roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance to stress as well as development of stress tolerance cultivars for Cruciferae crops.

scholarly journals Genome-Wide Identification of Barley ABC Genes and Their Expression in Response to Abiotic Stress Treatment

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1281
Author(s):  
Ziling Zhang ◽  
Tao Tong ◽  
Yunxia Fang ◽  
Junjun Zheng ◽  
Xian Zhang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Amino Acid ◽  
Stress Responses ◽  
Transmembrane Domain ◽  
Profile Analysis ◽  
Tissue Expression ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
Tissue Expression Profile ◽  
Amino Acid Length

Adenosine triphosphate-binding cassette transporters (ABC transporters) participate in various plant growth and abiotic stress responses. In the present study, 131 ABC genes in barley were systematically identified using bioinformatics. Based on the classification method of the family in rice, these members were classified into eight subfamilies (ABCA–ABCG, ABCI). The conserved domain, amino acid composition, physicochemical properties, chromosome distribution, and tissue expression of these genes were predicted and analyzed. The results showed that the characteristic motifs of the barley ABC genes were highly conserved and there were great diversities in the homology of the transmembrane domain, the number of exons, amino acid length, and the molecular weight, whereas the span of the isoelectric point was small. Tissue expression profile analysis suggested that ABC genes possess non-tissue specificity. Ultimately, 15 differentially expressed genes exhibited diverse expression responses to stress treatments including drought, cadmium, and salt stress, indicating that the ABCB and ABCG subfamilies function in the response to abiotic stress in barley.

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