Comprehensive identification and expression analysis of Hsp90s gene family in Solanum lycopersicum

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.

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Molecular Characterization, Gene Evolution and Expression Analysis of the F-Box Gene Family in Tomato (Solanum lycopersicum)

Genes ◽

10.3390/genes12030417 ◽

2021 ◽

Vol 12 (3) ◽

pp. 417

Author(s):

Fulei Mo ◽

Nian Zhang ◽

Youwen Qiu ◽

Lingjun Meng ◽

Mozhen Cheng ◽

...

Keyword(s):

Abiotic Stress ◽

Cold Stress ◽

Gene Family ◽

Solanum Lycopersicum ◽

Expression Analysis ◽

Gene Evolution ◽

Expression Patterns ◽

Pcr Analysis ◽

Whole Genome ◽

Cis Elements

F-box genes play an important role in the growth and development of plants, but there are few studies on its role in a plant’s response to abiotic stresses. In order to further study the functions of F-box genes in tomato (Solanum lycopersicum, Sl), a total of 139 F-box genes were identified in the whole genome of tomato using bioinformatics methods, and the basic information, transcript structure, conserved motif, cis-elements, chromosomal location, gene evolution, phylogenetic relationship, expression patterns and the expression under cold stress, drought stress, jasmonic acid (JA) treatment and salicylic acid (SA) treatment were analyzed. The results showed that SlFBX genes were distributed on 12 chromosomes of tomato and were prone to TD (tandem duplication) at the ends of chromosomes. WGD (whole genome duplication), TD, PD (proximal duplication) and TRD (transposed duplication) modes seem play an important role in the expansion and evolution of tomato SlFBX genes. The most recent divergence occurred 1.3042 million years ago, between SlFBX89 and SlFBX103. The cis-elements in SlFBX genes’ promoter regions were mainly responded to phytohormone and abiotic stress. Expression analysis based on transcriptome data and qRT-PCR (Real-time quantitative PCR) analysis of SlFBX genes showed that most SlFBX genes were differentially expressed under abiotic stress. SlFBX24 was significantly up-regulated at 12 h under cold stress. This study reported the SlFBX gene family of tomato for the first time, providing a theoretical basis for the detailed study of SlFBX genes in the future, especially the function of SlFBX genes under abiotic stress.

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Cloning, identification, and expression analysis of a Dicer-Like gene family from Solanum lycopersicum

Biologia Plantarum ◽

10.1007/s10535-016-0620-8 ◽

2016 ◽

Vol 60 (3) ◽

pp. 410-418 ◽

Cited By ~ 5

Author(s):

T. Wang ◽

L. You ◽

R. Li ◽

D.-Q. Fu ◽

B.-Z. Zhu ◽

...

Keyword(s):

Gene Family ◽

Solanum Lycopersicum ◽

Expression Analysis

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Genome-wide identification of FK506-binding domain protein gene family, its characterization, and expression analysis in tomato (Solanum lycopersicum L.)

Gene ◽

10.1016/j.gene.2018.08.021 ◽

2018 ◽

Vol 678 ◽

pp. 143-154 ◽

Cited By ~ 3

Author(s):

Muhammad Waseem ◽

Fiaz Ahmad ◽

Sidra Habib ◽

Yanqiang Gao ◽

Zhengguo Li

Keyword(s):

Gene Family ◽

Solanum Lycopersicum ◽

Expression Analysis ◽

Protein Gene ◽

Binding Domain ◽

Solanum Lycopersicum L ◽

Genome Wide ◽

Domain Protein

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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 Profiling of the PDI Gene Family Reveals Their Probable Involvement in Abiotic Stress Tolerance in Tomato (Solanum lycopersicum L.)

Genes ◽

10.3390/genes12010023 ◽

2020 ◽

Vol 12 (1) ◽

pp. 23

Author(s):

Antt Htet Wai ◽

Muhammad Waseem ◽

A B M Mahbub Morshed Khan ◽

Ujjal Kumar Nath ◽

Do Jin Lee ◽

...

Keyword(s):

Abiotic Stress ◽

Gene Family ◽

Stress Tolerance ◽

Solanum Lycopersicum ◽

Expression Profiling ◽

Abiotic Stress Tolerance ◽

Dependent Manner ◽

Solanum Lycopersicum L ◽

Genome Wide ◽

Protein Disulfide

Protein disulfide isomerases (PDI) and PDI-like proteins catalyze the formation and isomerization of protein disulfide bonds in the endoplasmic reticulum and prevent the buildup of misfolded proteins under abiotic stress conditions. In the present study, we conducted the first comprehensive genome-wide exploration of the PDI gene family in tomato (Solanum lycopersicum L.). We identified 19 tomato PDI genes that were unevenly distributed on 8 of the 12 tomato chromosomes, with segmental duplications detected for 3 paralogous gene pairs. Expression profiling of the PDI genes revealed that most of them were differentially expressed across different organs and developmental stages of the fruit. Furthermore, most of the PDI genes were highly induced by heat, salt, and abscisic acid (ABA) treatments, while relatively few of the genes were induced by cold and nutrient and water deficit (NWD) stresses. The predominant expression of SlPDI1-1, SlPDI1-3, SlPDI1-4, SlPDI2-1, SlPDI4-1, and SlPDI5-1 in response to abiotic stress and ABA treatment suggested they play regulatory roles in abiotic stress tolerance in tomato in an ABA-dependent manner. Our results provide new insight into the structure and function of PDI genes and will be helpful for the selection of candidate genes involved in fruit development and abiotic stress tolerance in tomato.

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