Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) gene family in wheat (Triticum aestivum L.)

Abstract Background Plant calmodulin-binding transcription activator (CAMTA) proteins play important roles in hormone signal transduction, developmental regulation, and environmental stress tolerance. However, in wheat, the CAMTA gene family has not been systematically characterized. Results In this work, 15 wheat CAMTA genes were identified using a genome-wide search method. Their chromosome location, physicochemical properties, subcellular localization, gene structure, protein domain, and promoter cis-elements were systematically analyzed. Phylogenetic analysis classified the TaCAMTA genes into three groups (groups A, B, and C), numbered 7, 6, and 2, respectively. The results showed that most TaCAMTA genes contained stress-related cis-elements. Finally, to obtain tissue-specific and stress-responsive candidates, the expression profiles of the TaCAMTAs in various tissues and under biotic and abiotic stresses were investigated. Tissue-specific expression analysis showed that all of the 15 TaCAMTA genes were expressed in multiple tissues with different expression levels, as well as under abiotic stress, the expressions of each TaCAMTA gene could respond to at least one abiotic stress. It also found that 584 genes in wheat genome were predicted to be potential target genes by CAMTA, demonstrating that CAMTA can be widely involved in plant development and growth, as well as coping with stresses. Conclusions This work systematically identified the CAMTA gene family in wheat at the whole-genome-wide level, providing important candidates for further functional analysis in developmental regulation and the stress response in wheat.

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Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) gene family in wheat (Triticum aestivum L.)

10.21203/rs.2.22898/v3 ◽

2020 ◽

Author(s):

Fan Yang ◽

Fushuang Dong ◽

Fanghui Hu ◽

Yongwei Liu ◽

Jianfang Chai ◽

...

Keyword(s):

Abiotic Stress ◽

Gene Family ◽

Expression Analysis ◽

Developmental Regulation ◽

Expression Profiles ◽

Transcription Activator ◽

Tissue Specific ◽

Calmodulin Binding ◽

Genome Wide ◽

A Genome

Abstract Background: Plant calmodulin-binding transcription activator (CAMTA) proteins play important roles in hormone signal transduction, developmental regulation, and environmental stress tolerance. However, in wheat, the CAMTA gene family has not been systematically characterized. Results: In this work, 15 wheat CAMTA genes were identified using a genome-wide search method. Their chromosome location, physicochemical properties, subcellular localization, gene structure, protein domain, and promoter cis-elements were systematically analyzed. Phylogenetic analysis classified the TaCAMTA genes into three groups (groups A, B, and C), numbered 7, 6, and 2, respectively. The results showed that most TaCAMTA genes contained stress-related cis-elements. Finally, to obtain tissue-specific and stress-responsive candidates, the expression profiles of the TaCAMTAs in various tissues and under biotic and abiotic stresses were investigated. Tissue-specific expression analysis showed that all of the 15 TaCAMTA genes were expressed in multiple tissues with different expression levels, as well as under abiotic stress, the expressions of each TaCAMTA gene could respond to at least one abiotic stress. It also found that 584 genes in wheat genome were predicted to be potential target genes by CAMTA, demonstrating that CAMTA can be widely involved in plant development and growth, as well as coping with stresses. Conclusions: This work systematically identified the CAMTA gene family in wheat at the whole-genome-wide level, providing important candidates for further functional analysis in developmental regulation and the stress response in wheat.

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Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) gene family in wheat (Triticum aestivum L.)

10.21203/rs.2.22898/v2 ◽

2020 ◽

Author(s):

Fan Yang ◽

Fushuang Dong ◽

Fanghui Hu ◽

Yongwei Liu ◽

Jianfang Chai ◽

...

Keyword(s):

Abiotic Stress ◽

Gene Family ◽

Expression Analysis ◽

Developmental Regulation ◽

Expression Profiles ◽

Transcription Activator ◽

Tissue Specific ◽

Calmodulin Binding ◽

Genome Wide ◽

A Genome

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Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) gene family in wheat (Triticum aestivum L.)

10.21203/rs.2.22898/v1 ◽

2020 ◽

Author(s):

Fan Yang ◽

Fushuang Dong ◽

Yongwei Liu ◽

Jianfang Chai ◽

He Zhao ◽

...

Keyword(s):

Stress Response ◽

Gene Family ◽

Expression Analysis ◽

Developmental Regulation ◽

Cis Elements ◽

Transcription Activator ◽

Tissue Specific ◽

Calmodulin Binding ◽

Genome Wide ◽

A Genome

Abstract Plant calmodulin-binding transcription activator (CAMTA) proteins play important roles in hormone signal transduction, developmental regulation, and environmental stress tolerance. However, in wheat, the CAMTA gene family has not been systematically characterized. In this work, 15 wheat CAMTA genes were identified using a genome-wide search method. Their chromosome location, physicochemical properties, subcellular localization, gene structure, protein domain, and promoter cis-elements were systematically analyzed. Phylogenetic analysis classified the TaCAMTA genes into three groups (groups A, B, and C), numbered 7, 6, and 2, respectively. The results showed that most TaCAMTA genes contained stress-related cis-elements. Finally, to obtain tissue-specific and stress-responsive candidates, the expression profiles of the TaCAMTAs in various tissues and under biotic and abiotic stresses were investigated. Tissue-specific expression analysis showed that all of the TaCAMTA genes were expressed in multiple tissues, suggesting that the wheat CAMTA genes may play important roles in growth and development. Under abiotic stress, TaCAMTA1, 3, and 6 were up-regulated after drought treatment, while the expression levels of TaCAMTA1 and 3 were induced after cold treatment, indicating that they may be involved in drought and cold stress response. This work systematically identified the CAMTA gene family in wheat at the whole-genome-wide level, providing important candidates for further functional analysis in developmental regulation and the stress response in wheat.

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Genome-Wide Analysis and Expression Profile of Superoxide Dismutase (SOD) Gene Family in Rapeseed (Brassica napus L.) under Different Hormones and Abiotic Stress Conditions

Antioxidants ◽

10.3390/antiox10081182 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1182

Author(s):

Wei Su ◽

Ali Raza ◽

Ang Gao ◽

Ziqi Jia ◽

Yi Zhang ◽

...

Keyword(s):

Superoxide Dismutase ◽

Abiotic Stress ◽

Brassica Napus ◽

Gene Family ◽

Expression Profiles ◽

Protein Structures ◽

Brassica Napus L ◽

Genome Wide ◽

A Genome ◽

Sod Gene Family

Superoxide dismutase (SOD) is an important enzyme that acts as the first line of protection in the plant antioxidant defense system, involved in eliminating reactive oxygen species (ROS) under harsh environmental conditions. Nevertheless, the SOD gene family was yet to be reported in rapeseed (Brassica napus L.). Thus, a genome-wide investigation was carried out to identify the rapeseed SOD genes. The present study recognized 31 BnSOD genes in the rapeseed genome, including 14 BnCSDs, 11 BnFSDs, and six BnMSDs. Phylogenetic analysis revealed that SOD genes from rapeseed and other closely related plant species were clustered into three groups based on the binding domain with high bootstrap values. The systemic analysis exposed that BnSODs experienced segmental duplications. Gene structure and motif analysis specified that most of the BnSOD genes displayed a relatively well-maintained exon–intron and motif configuration within the same group. Moreover, we identified five hormones and four stress- and several light-responsive cis-elements in the promoters of BnSODs. Thirty putative bna-miRNAs from seven families were also predicted, targeting 13 BnSODs. Gene ontology annotation outcomes confirm the BnSODs role under different stress stimuli, cellular oxidant detoxification processes, metal ion binding activities, SOD activity, and different cellular components. Twelve BnSOD genes exhibited higher expression profiles in numerous developmental tissues, i.e., root, leaf, stem, and silique. The qRT-PCR based expression profiling showed that eight genes (BnCSD1, BnCSD3, BnCSD14, BnFSD4, BnFSD5, BnFSD6, BnMSD2, and BnMSD10) were significantly up-regulated under different hormones (ABA, GA, IAA, and KT) and abiotic stress (salinity, cold, waterlogging, and drought) treatments. The predicted 3D structures discovered comparable conserved BnSOD protein structures. In short, our findings deliver a foundation for additional functional investigations on the BnSOD genes in rapeseed breeding programs.

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Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle

BMC Genomics ◽

10.1186/s12864-021-07653-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Cuili Pan ◽

Zhaoxiong Lei ◽

Shuzhe Wang ◽

Xingping Wang ◽

Dawei Wei ◽

...

Keyword(s):

Gene Family ◽

Expression Analysis ◽

Adipocyte Differentiation ◽

Bos Taurus ◽

Adipogenic Differentiation ◽

Critical Role ◽

Bos Indicus ◽

Specific Expression ◽

Genome Wide ◽

A Genome

Abstract Background Cyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but the role of CDK gene family in regulating bovine adipocyte differentiation has not been studied. Therefore, the present study aims to characterize the CDK gene family in bovine and study their expression pattern during adipocyte differentiation. Results We performed a genome-wide analysis and identified a number of CDK genes in several bovine species. The CDK genes were classified into 8 subfamilies through phylogenetic analysis. We found that 25 bovine CDK genes were distributed in 16 different chromosomes. Collinearity analysis revealed that the CDK gene family in Bos taurus is homologous with Bos indicus, Hybrid-Bos taurus, Hybrid Bos indicus, Bos grunniens and Bubalus bubalis. Several CDK genes had higher expression levels in preadipocytes than in differentiated adipocytes, as shown by RNA-seq analysis and qPCR, suggesting a role in the growth of emerging lipid droplets. Conclusion In this research, 185 CDK genes were identified and grouped into eight distinct clades in Bovidae, showing extensively homology. Global expression analysis of different bovine tissues and specific expression analysis during adipocytes differentiation revealed CDK4, CDK7, CDK8, CDK9 and CDK14 may be involved in bovine adipocyte differentiation. The results provide a basis for further study to determine the roles of CDK gene family in regulating adipocyte differentiation, which is beneficial for beef quality improvement.

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Genome-wide identification and expression analysis of the GA2ox gene family in maize (Zea mays L.) under various abiotic stress conditions

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2021.06.043 ◽

2021 ◽

Author(s):

Yidan Li ◽

Xiaohui Shan ◽

Zhilei Jiang ◽

Lei Zhao ◽

Fengxue Jin

Keyword(s):

Zea Mays ◽

Abiotic Stress ◽

Gene Family ◽

Expression Analysis ◽

Zea Mays L ◽

Stress Conditions ◽

Genome Wide

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Genome-wide identification and analysis of cystatin family genes in Sorghum (Sorghum bicolor (L.) Moench)

PeerJ ◽

10.7717/peerj.10617 ◽

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.

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Genome-wide identification and expression analysis of calmodulin-binding transcription activator genes in banana under drought stress

Scientia Horticulturae ◽

10.1016/j.scienta.2018.09.022 ◽

2019 ◽

Vol 244 ◽

pp. 10-14 ◽

Cited By ~ 4

Author(s):

Laraib Meer ◽

Sana Mumtaz ◽

Abdullahi Muhammad Labbo ◽

Muhammad Jawad Khan ◽

Irfan Sadiq

Keyword(s):

Drought Stress ◽

Expression Analysis ◽

Transcription Activator ◽

Calmodulin Binding ◽

Genome Wide

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Genome-Wide Analysis of the TCP Gene Family in Switchgrass (Panicum virgatum L.)

International Journal of Genomics ◽

10.1155/2019/8514928 ◽

2019 ◽

Vol 2019 ◽

pp. 1-13 ◽

Cited By ~ 2

Author(s):

Yuzhu Huo ◽

Wangdan Xiong ◽

Kunlong Su ◽

Yu Li ◽

Yawen Yang ◽

...

Keyword(s):

Salt Stress ◽

Plant Growth ◽

Gene Family ◽

Stress Responses ◽

Panicum Virgatum ◽

Expression Profiles ◽

Specific Expression ◽

Genome Wide Analysis ◽

Genome Wide ◽

A Genome

The plant-specific transcription factor TCPs play multiple roles in plant growth, development, and stress responses. However, a genome-wide analysis of TCP proteins and their roles in salt stress has not been declared in switchgrass (Panicum virgatum L.). In this study, 42 PvTCP genes (PvTCPs) were identified from the switchgrass genome and 38 members can be anchored to its chromosomes unevenly. Nine PvTCPs were predicted to be microRNA319 (miR319) targets. Furthermore, PvTCPs can be divided into three clades according to the phylogeny and conserved domains. Members in the same clade have the similar gene structure and motif localization. Although all PvTCPs were expressed in tested tissues, their expression profiles were different under normal condition. The specific expression may indicate their different roles in plant growth and development. In addition, approximately 20 cis-acting elements were detected in the promoters of PvTCPs, and 40% were related to stress response. Moreover, the expression profiles of PvTCPs under salt stress were also analyzed and 29 PvTCPs were regulated after NaCl treatment. Taken together, the PvTCP gene family was analyzed at a genome-wide level and their possible functions in salt stress, which lay the basis for further functional analysis of PvTCPs in switchgrass.

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