scholarly journals The Hsp70 Gene Family in Boleophthalmus pectinirostris: Genome-Wide Identification and Expression Analysis under High Ammonia Stress

Animals ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 36
Author(s):  
Zhaochao Deng ◽  
Shanxiao Sun ◽  
Tianxiang Gao ◽  
Zhiqiang Han
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Expression Patterns ◽  
Large Body ◽  
Hypoxic Condition ◽  
Hsp70 Gene ◽  
High Concentration ◽  
Genome Wide ◽  
Boleophthalmus Pectinirostris ◽  
Shock Proteins

Heat shock proteins 70 have triggered a remarkable large body of research in various fishes; however, no genome-wide identification and expression analysis has been performed on the Hsp70 gene family of Boleophthalmus pectinirostris. In this study, we identified 20 Hsp70 genes within the genome of B. pectinirostris and provided insights into their response to high environmental ammonia (HEA) stress. Positive selection on stress response genes and expansion of hspa1a and hspa1a-like genes might be related to terrestrial adaptations in this species. The expression patterns of the Hsp70 gene family in the gill and liver of B. pectinirostris under HEA stress were studied by examining transcriptome data. The results showed that most Hsp70 genes were downregulated after high concentration ammonia exposure. The downregulation may be related to the hypoxic condition of the tissues.

scholarly journals The Hsp70 Gene Family in Solanum tuberosum: Genome-Wide Identification, Phylogeny, and Expression Patterns

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Jia Liu ◽  
Xin Pang ◽  
Yuan Cheng ◽  
Yuhe Yin ◽  
Qiang Zhang ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Gene Family ◽  
Expression Patterns ◽  
Hsp70 Gene ◽  
Genome Wide

scholarly journals The Hsp70 Gene family in Solanum Lycopersicum; Genome-wide Identification and Expression Analysis Under Heavy Metals Stresses

2021 ◽  
Author(s):  
Ahmed El Sappah ◽  
Manzar Abbas ◽  
Ahmed S. Elrys ◽  
Vivek Yadav ◽  
Hamza H. El-Sappah ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Gene Ontology ◽  
Gene Family ◽  
Candidate Genes ◽  
Solanum Lycopersicum ◽  
Expression Analysis ◽  
Hsp70 Gene ◽  
Rna Seq ◽  
Genome Wide

Abstract The Heat shock protein-70 (Hsp70) gene family is one of the protective mechanisms; however, it has not been widely studied in tomatoes. Therefore, the current study provides the first report genome-wide analysis of the Hsp70 gene family in tomato (Solanum lycopersicum L.) under five heavy metals (Cd2+, Co2+, Mn2+, Zn2+, and Fe2+) stresses. We identified 23 candidate genes of the Hsp70 gene family based on the PF00012 domain through bioinformatics studies, including gene structure, distribution, synteny, phylogenetic tree, protein-protein interactions, gene ontology, and previous RNA-seq data analysis followed by qRT-PCR analysis. Based on the phylogenetic analysis, the 23 candidate genes were classified into five subfamilies where the same subfamily contains similar SlHsp70 proteins. Many pairs of SlHsp70 gene duplications have appeared, consisting of tandem and segment duplication. In addition, analysis of previous RNA-seq besides the gene ontology gave us significant evidence about the vital roles of these genes during tomato development and growth. The SlHsp7s showed different responses, which were varied depend on different plant tissues and types of heavy metal. Some of the SlHsp70s were up-regulated after heavy metal exposure, such as Cd2+/SlHsp70-23 and Mn2+/ SlHsp70-8. Still, down-regulated others such as Fe2+/ SlHsp70-18. Finally, our gene expression analysis revealed the significant roles of the Hsp70s, especially, SlHsp70- 3, SlHsp70-8, SlHsp70-12, SlHsp70-19, and SlHsp70-23, with the different heavy metals treatments.

scholarly journals Genome-wide analysis of HSP70 gene superfamily in Pyropia yezoensis (Bangiales, Rhodophyta): identification, characterization and expression profiles in response to dehydration stress

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xinzi Yu ◽  
Zhaolan Mo ◽  
Xianghai Tang ◽  
Tian Gao ◽  
Yunxiang Mao
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Dehydration Stress ◽  
Pyropia Yezoensis ◽  
Genome Wide ◽  
Regulated Expression ◽  
Relative Conservation ◽  
Shock Proteins ◽  
Insight Into

Abstract Background Heat shock proteins (HSPs) perform a fundamental role in protecting plants against abiotic stresses. Individual family members have been analyzed in previous studies, but there has not yet been a comprehensive analysis of the HSP70 gene family in Pyropia yezoensis. Results We investigated 15 putative HSP70 genes in Py. yezoensis. These genes were classified into two sub-families, denoted as DnaK and Hsp110. In each sub-family, there was relative conservation of the gene structure and motif. Synteny-based analysis indicated that seven and three PyyHSP70 genes were orthologous to HSP70 genes in Pyropia haitanensis and Porphyra umbilicalis, respectively. Most PyyHSP70s showed up-regulated expression under different degrees of dehydration stress. PyyHSP70-1 and PyyHSP70-3 were expressed in higher degrees compared with other PyyHSP70s in dehydration treatments, and then expression degrees somewhat decreased in rehydration treatment. Subcellular localization showed PyyHSP70-1-GFP and PyyHSP70-3-GFP were in the cytoplasm and nucleus/cytoplasm, respectively. Similar expression patterns of paired orthologs in Py. yezoensis and Py. haitanensis suggest important roles for HSP70s in intertidal environmental adaptation during evolution. Conclusions These findings provide insight into the evolution and modification of the PyyHSP70 gene family and will help to determine the functions of the HSP70 genes in Py. yezoensis growth and development.

scholarly journals Genome-Wide Identification of Hsp70 Genes in the Large Yellow Croaker (Larimichthys crocea) and Their Regulated Expression Under Cold and Heat Stress

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 590 ◽  
Author(s):  
Kaida Xu ◽  
Hanxiang Xu ◽  
Zhiqiang Han
Keyword(s):  
Heat Stress ◽  
Gene Family ◽  
Environmental Changes ◽  
Expression Patterns ◽  
Cold Treatment ◽  
Large Yellow Croaker ◽  
Hsp70 Gene ◽  
Larimichthys Crocea ◽  
Stress Dependent ◽  
Shock Proteins

Heat shock proteins 70 (Hsp70) are required for key cellular processes and responses to environmental changes, however, there are an unknown number of hsp70 gene family members in the large yellow croaker (Larimichthys crocea). In the present study, 17 hsp70 genes were identified through the genome of the large yellow croaker. These genes are divided into seven evolutionarily distinct groups according to a phylogenetic tree. The orthologs of these hsp70 genes were found in humans and zebrafish. The expression patterns of the hsp70 gene family in the large yellow croaker under cold and heat stress were studied by examining transcriptome data. Six out of 17 genes were significantly unregulated or downregulated after cold or heat stress. There were two genes significantly upregulated and two genes downregulated in the liver after cold treatment, while after heat treatment, five genes were significantly upregulated, and no genes were significantly downregulated. Three expression patterns were detected: strictly heat-inducible hsp70, constitutively expressed and moderately heat-inducible hsp70, and constitutively expressed and less stress-dependent hsp70 genes. All the findings will contribute to a better understanding of the biological function of hsp70s in defending against thermal challenges.

scholarly journals Genome-Wide Identification, Characterization, and Expression Analysis of the Grapevine Superoxide Dismutase (SOD) Family

2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
Xiaoxuan Hu ◽  
Chenyu Hao ◽  
Zong-Ming Cheng ◽  
Yan Zhong
Keyword(s):  
Superoxide Dismutase ◽  
Gene Family ◽  
Expression Analysis ◽  
Gene Pair ◽  
Expression Patterns ◽  
Protein Motifs ◽  
Genome Wide ◽  
Copper Zinc ◽  
Essential Enzyme ◽  
Sod Gene Family

Superoxide dismutase (SOD) is an essential enzyme of the plant antioxidant system that responds to oxidative damage caused by adverse conditions. However, little is known about the SOD gene family in Vitis vinifera (Vv). In the present study, ten SOD genes, including 6 copper/zinc SODs, 2 iron SODs, and 2 manganese SODs, were identified in the grapevine genome where they were unevenly distributed on 12 chromosomes. Ten VvSOD genes were divided into three main groups based on phylogenetic analysis, subcellular localization, and the distribution of conserved protein motifs. Additionally, many cis-elements related to different stresses were found in the promoters of the 10 VvSOD genes. Syntenic analysis revealed that VvMSD1 and VvMSD2 were derived from segmental duplication, and VvCSD4 and VvCSD5 belong to a pair of tandemly duplicated genes. Gene expression analysis based on microarray data showed that the 10 VvSOD genes were expressed in all the tested tissues. Interestingly, the segmentally duplicated gene pair (VvMSD1 and VvMSD2) exhibited differential expression patterns in various organs. In contrast, the tandemly duplicated gene pair (VvCSD4 and VvCSD5) displayed similar expression patterns in the tested organs. Our results provide a basis for further functional research on the SOD gene family in grapevine.

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 Roles of the 14-3-3 gene family in cotton flowering

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Na Sang ◽  
Hui Liu ◽  
Bin Ma ◽  
Xianzhong Huang ◽  
Lu Zhuo ◽  
...  
Keyword(s):  
Gene Family ◽  
Protein Interactions ◽  
Leucine Zipper ◽  
Expression Patterns ◽  
Bimolecular Fluorescence Complementation ◽  
Structural Motif ◽  
Virus Induced Gene Silencing ◽  
Protein Protein Interactions ◽  
Basic Leucine Zipper ◽  
Genome Wide

Abstract Background In plants, 14-3-3 proteins, also called GENERAL REGULATORY FACTORs (GRFs), encoded by a large multigene family, are involved in protein–protein interactions and play crucial roles in various physiological processes. No genome-wide analysis of the GRF gene family has been performed in cotton, and their functions in flowering are largely unknown. Results In this study, 17, 17, 31, and 17 GRF genes were identified in Gossypium herbaceum, G. arboreum, G. hirsutum, and G. raimondii, respectively, by genome-wide analyses and were designated as GheGRFs, GaGRFs, GhGRFs, and GrGRFs, respectively. A phylogenetic analysis revealed that these proteins were divided into ε and non-ε groups. Gene structural, motif composition, synteny, and duplicated gene analyses of the identified GRF genes provided insights into the evolution of this family in cotton. GhGRF genes exhibited diverse expression patterns in different tissues. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that the GhGRFs interacted with the cotton FLOWERING LOCUS T homologue GhFT in the cytoplasm and nucleus, while they interacted with the basic leucine zipper transcription factor GhFD only in the nucleus. Virus-induced gene silencing in G. hirsutum and transgenic studies in Arabidopsis demonstrated that GhGRF3/6/9/15 repressed flowering and that GhGRF14 promoted flowering. Conclusions Here, 82 GRF genes were identified in cotton, and their gene and protein features, classification, evolution, and expression patterns were comprehensively and systematically investigated. The GhGRF3/6/9/15 interacted with GhFT and GhFD to form florigen activation complexs that inhibited flowering. However, GhGRF14 interacted with GhFT and GhFD to form florigen activation complex that promoted flowering. The results provide a foundation for further studies on the regulatory mechanisms of flowering.

Genome-wide identification and analysis of the MADS-box gene family and its potential role in fruit ripening in black raspberry (Rubus occidentalis L.)

2021 ◽  
pp. 1-15
Author(s):  
Yaqiong Wu ◽  
Chunhong Zhang ◽  
Wenlong Wu ◽  
Weilin Li ◽  
Lianfei Lyu
Keyword(s):  
Gene Family ◽  
Fruit Ripening ◽  
Fruit Development ◽  
Expression Patterns ◽  
Type I ◽  
Black Raspberry ◽  
Mads Box ◽  
Mads Box Genes ◽  
Genome Wide ◽  
Mads Box Gene

BACKGROUND: Black raspberry is a vital fruit crop with a high antioxidant function. MADS-box genes play an important role in the regulation of fruit development in angiosperms. OBJECTIVE: To understand the regulatory role of the MADS-box family, a total of 80 MADS-box genes were identified and analyzed. METHODS: The MADS-box genes in the black raspberry genome were analyzed using bioinformatics methods. Through an analysis of the promoter elements, the possible functions of different members of the family were predicted. The spatiotemporal expression patterns of members of the MADS-box family during black raspberry fruit development and ripening were systematically analyzed. RESULTS: The genes were classified into type I (Mα: 33; Mβ: 6; Mγ: 10) and type II (MIKC *: 2; MIKCC: 29) genes. We also obtained a complete overview of the RoMADS-box gene family through phylogenetic, gene structure, conserved motif, and cis element analyses. The relative expression analysis showed different expression patterns, and most RoMADS-box genes were more highly expressed in fruit than in other tissues of black raspberry. CONCLUSIONS: This finding indicates that the MADS-box gene family is involved in the regulation of fruit ripening processes in black raspberry.

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