scholarly journals Genome-wide identification and expression analysis of autophagy genes in cucumber

2021 ◽  
Author(s):  
Yuehua Han ◽  
Yue Yang ◽  
Yu Wang ◽  
Nabil Ibrahim Elsheery ◽  
Guohua Ding
Keyword(s):  
Salicylic Acid ◽  
Gene Family ◽  
Expression Analysis ◽  
Growth And Development ◽  
Developmental Process ◽  
Biotic And Abiotic Stress ◽  
Starvation Tolerance ◽  
Meja Treatment ◽  
Cucumber Genome ◽  
Atg Genes

Abstract Background Autophagy is an evolutionarily conserved physiological and developmental process in eukaryotes. In this process, damaged proteins in cells are degraded and cytoplasmic materials recycled. When plants are exposure to stress conditions or their growth and development are blocked, autophagy is induced to maintain the cell homeostasis by degrading long-lived proteins in the cells and organelles that function abnormally due to aging or damage. Cell autophagy has multiple functions in plants, it involved in growth and development, senescence, and responses to biotic and abiotic stress. So far, thirty three autophagy genes (ATG) have been found in rice, and more than 30 autophagy-related genes have been found in Arabidopsis, tobacco and corn, respectively. Four autophagy genes induced by salicylic acid were found in cucumber, but a little still unknown about all of autophagy genes in cucumber genome. Our experiment fully explored the ATG gene family of cucumber genome based on bioinformatics methods and identified 20 CsATG genes. We systematically analyzed the structure, conserved motifs, expression and phylogeny relationship of these ATG genes, which lays the foundation for exploring the function of the genes. Results A total of 20 putative ATG genes were identified in the cucumber genome. Gene duplication analysis showed that both fragmented and tandem duplication played vital roles in the amplification of cucumber ATG gene family. Gene expression analysis showed that 16 CsATG genes were induced by the salicylic acid (SA) treatment, and 16 CsATG genes were down-regulated by Methyl jasmonate (MeJA) treatment. Under high salinity stress, 10 CsATG genes were induced in roots. Under drought stress, 16 CsATG genes were induced in roots. Under carbon starvation stress, all of 20 CsATG genes were induced to express in leaves, suggesting that cell autophagy has a potential role in nutritional starvation tolerance. Conclusion Our results clearly have deepened our understanding of the characteristics and functions of cucumber ATG gene, and also found some new gene resources that can be used for the future development of cucumber and other crop varieties, which can resist stress.

scholarly journals Identification and Expression Analysis of the CsMYB Gene Family in Root Knot Nematode-Resistant and Susceptible Cucumbers

2020 ◽  
Vol 11 ◽  
Author(s):  
Chunyan Cheng ◽  
Qingrong Li ◽  
Xing Wang ◽  
Ying Li ◽  
Chuntao Qian ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Lipid Transfer Protein ◽  
Major Gene ◽  
Regulation Mechanism ◽  
Lipid Transfer ◽  
Biotic And Abiotic Stress ◽  
Root Knot Nematode ◽  
Element Analysis ◽  
Resistance Response

MYB (myeloblastosis) transcription factors (TFs) play important roles in controlling various physiological processes in plants, such as responses to biotic and abiotic stress, metabolism, and defense. A previous study identified a gene, Csa6G410090, encoding a plant lipid transfer protein (LTP), as a possible regulator in cucumber (Cucumis sativus L.) of the resistance response to root-knot nematode (RKN) [Meloidogyne incognita Kofoid and White (Chitwood)]. Myb-type DNA-binding TFs were presumed to regulate downstream genes expression, including LTPs, however, the regulation mechanism remained unclear. To elucidate whether and which MYB TFs may be involved in regulation of the resistance response, this study identified 112 genes as candidate members of the CsMYB gene family by combining CDD and SMART databases, using the Hidden Markov Model (HMM) and manual calibration. Within this group, ten phylogenetic subgroups were resolved according to sequence-based classification, consistent with results from comprehensive investigation of gene structure, conserved motifs, chromosome locations, and cis-element analysis. Distribution and collinearity analysis indicated that amplification of the CsMYB gene family in cucumber has occurred mainly through tandem repeat events. Spatial gene expression analysis showed that 8 CsMYB genes were highly expressed at differing levels in ten different tissues or organs. The roots of RKN-resistant and susceptible cucumbers were inoculated with M. incognita, finding that CsMYB (Csa6G538700, Csa1G021940, and Csa5G641610) genes showed up-regulation coincident with upregulation of the “hub” gene LTP (Csa6G410090) previously implicated as a major gene in the resistance response to RKN in cucumber. Results of this study suggest hypotheses regarding the elements and regulation of the resistant response as well as possible RKN resistance-enhancing strategies in cucumber and perhaps more broadly in plants.

Identification and expression analysis of LEA gene family members in cucumber genome

2016 ◽  
Vol 80 (2) ◽  
pp. 225-241 ◽  
Author(s):  
Yasemin Celik Altunoglu ◽  
Pinar Baloglu ◽  
Esra Nurten Yer ◽  
Sefa Pekol ◽  
Mehmet Cengiz Baloglu
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Family Members ◽  
Lea Gene ◽  
Cucumber Genome

scholarly journals Genome-Wide Characterization of HSP90 Gene Family in Cucumber and Their Potential Roles in Response to Abiotic and Biotic Stresses

2021 ◽  
Vol 12 ◽  
Author(s):  
Kaijing Zhang ◽  
Shuaishuai He ◽  
Yihu Sui ◽  
Qinghai Gao ◽  
Shuangshuang Jia ◽  
...  
Keyword(s):  
Gene Family ◽  
Growth And Development ◽  
Structural Characteristics ◽  
Heat Shock Protein 90 ◽  
The Other ◽  
Specific Expression ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Genome Wide ◽  
Cucumber Genome

Heat shock protein 90 (HSP90) possesses critical functions in plant developmental control and defense reactions. The HSP90 gene family has been studied in various plant species. However, the HSP90 gene family in cucumber has not been characterized in detail. In this study, a total of six HSP90 genes were identified from the cucumber genome, which were distributed to five chromosomes. Phylogenetic analysis divided the cucumber HSP90 genes into two groups. The structural characteristics of cucumber HSP90 members in the same group were similar but varied among different groups. Synteny analysis showed that only one cucumber HSP90 gene, Csa1G569290, was conservative, which was not collinear with any HSP90 gene in Arabidopsis and rice. The other five cucumber HSP90 genes were collinear with five Arabidopsis HSP90 genes and six rice HSP90 genes. Only one pair of paralogous genes in the cucumber HSP90 gene family, namely one pair of tandem duplication genes (Csa1G569270/Csa1G569290), was detected. The promoter analysis showed that the promoters of cucumber HSP90 genes contained hormone, stress, and development-related cis-elements. Tissue-specific expression analysis revealed that only one cucumber HSP90 gene Csa3G183950 was highly expressed in tendril but low or not expressed in other tissues, while the other five HSP90 genes were expressed in all tissues. Furthermore, the expression levels of cucumber HSP90 genes were differentially induced by temperature and photoperiod, gibberellin (GA), downy mildew, and powdery mildew stimuli. Two cucumber HSP90 genes, Csa1G569270 and Csa1G569290, were both differentially expressed in response to abiotic and biotic stresses, which means that these two HSP90 genes play important roles in the process of cucumber growth and development. These findings improve our understanding of cucumber HSP90 family genes and provide preliminary information for further studies of cucumber HSP90 gene functions in plant growth and development.

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

BMC Genomics ◽  
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.

scholarly journals Stress-Induced Changes in Alternative Splicing Landscape in Rice: Functional Significance of Splice Isoforms in Stress Tolerance

Biology ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 309
Author(s):  
Showkat Ahmad Ganie ◽  
Anireddy S. N. Reddy
Keyword(s):  
Abiotic Stress ◽  
Alternative Splicing ◽  
Stress Tolerance ◽  
Functional Significance ◽  
Growth And Development ◽  
Regulatory Mechanism ◽  
Pathogen Resistance ◽  
Biotic And Abiotic Stress ◽  
Rice Varieties ◽  
Rice Growth

Improvements in yield and quality of rice are crucial for global food security. However, global rice production is substantially hindered by various biotic and abiotic stresses. Making further improvements in rice yield is a major challenge to the rice research community, which can be accomplished through developing abiotic stress-resilient rice varieties and engineering durable agrochemical-independent pathogen resistance in high-yielding elite rice varieties. This, in turn, needs increased understanding of the mechanisms by which stresses affect rice growth and development. Alternative splicing (AS), a post-transcriptional gene regulatory mechanism, allows rapid changes in the transcriptome and can generate novel regulatory mechanisms to confer plasticity to plant growth and development. Mounting evidence indicates that AS has a prominent role in regulating rice growth and development under stress conditions. Several regulatory and structural genes and splicing factors of rice undergo different types of stress-induced AS events, and the functional significance of some of them in stress tolerance has been defined. Both rice and its pathogens use this complex regulatory mechanism to devise strategies against each other. This review covers the current understanding and evidence for the involvement of AS in biotic and abiotic stress-responsive genes, and its relevance to rice growth and development. Furthermore, we discuss implications of AS for the virulence of different rice pathogens and highlight the areas of further research and potential future avenues to develop climate-smart and disease-resistant rice varieties.

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