Genome-wide identification of F-box proteins in Macrophomina phaseolina and comparison with other fungus

AbstractBackgroundIn fungi, like other eukaryotes, protein turnover is an important cellular process for the controlling of various cellular functions. The ubiquitin-proteasome pathway degrades some selected intracellular proteins and F-box proteins are one of the important components controlling protein degradation. F-box proteins are well studied in different model plants however, their functions in the fungi are not clear yet. This study aimed to identify the genes involved in protein degradation for disease development in theMacrophomina phaseolinafungus.ResultsIn this research,in silicostudies were done to understand the distribution of F-box proteins in pathogenic fungi includingMacrophomina phaseolinafungus. Genome-wide analysis indicates thatM. phaseolinafungus contained thirty-one F-box proteins throughout its chromosomes. In addition, there are 17, 37, 16, and 21 F-box proteins have been identified fromPuccinia graminis, Colletotrichum graminicola, Ustilago maydis, andPhytophthora infestans, respectively. Analyses revealed that selective fungal genomes contain several additional functional domains along with F-box domain. Sequence alignment showed the substitution of amino acid in several F-box proteins; however, gene duplication was not found among these proteins. Phylogenetic analysis revealed that F-box proteins having similar functional domain was highly diverse form each other showing the possibility of various function. Analysis also found that MPH_00568 and MPH_05531 were closely related to rice blast fungus F-box protein MGG_00768 and MGG_13065, respectively, may play an important role for blast disease development.ConclusionThis genome-wide analysis of F-box proteins will be useful for characterization of candidate F-box proteins to understand the molecular mechanisms leading to disease development ofM. phaseolinain the host plants.

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Genome-Wide Analysis of the Trihelix Gene Family and Their Response to Cold Stress in Dendrobium officinale

Sustainability ◽

10.3390/su13052826 ◽

2021 ◽

Vol 13 (5) ◽

pp. 2826

Author(s):

Yan Tong ◽

Hui Huang ◽

YuHua Wang

Keyword(s):

Stress Responses ◽

Cold Treatment ◽

Dendrobium Officinale ◽

Functional Domain ◽

Cis Elements ◽

Genome Wide Analysis ◽

Functional Studies ◽

Genome Wide ◽

Growth Development ◽

Chinese Medicinal Plant

Trihelix transcription factors play important roles in plant growth, development and various stress responses. In this study, we identified 32 trihelix family genes (DoGT) in the important Chinese medicinal plant Dendrobium officinale. These trihelix genes could be classified into five different subgroups. The gene structure and conserved functional domain of these trihelix genes were similar in the same subfamily but diverged between different subfamilies. Various stresses responsive cis-elements presented in the promoters of DoGT genes, suggesting that the trihelix genes might respond to the environmental stresses. Expressional changes of DoGT genes in three tissues and under cold treatment suggested that trihelix genes were involved in diverse functions during D. officinale development and cold tolerance. This study provides novel insights into the phylogenetic relationships and functions of the D. officinaletrihelix genes, which will aid future functional studies investigating the divergent roles of trihelix genes belonging to other species.

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Oral Microbiome and Host Health: Review on Current Advances in Genome-Wide Analysis

Applied Sciences ◽

10.3390/app11094050 ◽

2021 ◽

Vol 11 (9) ◽

pp. 4050

Author(s):

Young-Dan Cho ◽

Kyoung-Hwa Kim ◽

Yong-Moo Lee ◽

Young Ku ◽

Yang-Jo Seol

Keyword(s):

Molecular Mechanisms ◽

Close Association ◽

Human Microbiome ◽

Oral Microbiome ◽

Systemic Diseases ◽

Future Directions ◽

Genome Wide Analysis ◽

Host Interaction ◽

Genome Wide ◽

Special Environment

The oral microbiome is an important part of the human microbiome. The oral cavity has the second largest microbiota after the intestines, and its open structure creates a special environment. With the development of technology such as next-generation sequencing and bioinformatics, extensive in-depth microbiome studies have become possible. They can also be applied in the clinical field in terms of diagnosis and treatment. Many microbiome studies have been performed on oral and systemic diseases, showing a close association between the two. Understanding the oral microbiome and host interaction is expected to provide future directions to explore the functional and metabolic changes in diseases, and to uncover the molecular mechanisms for drug development and treatment that facilitate personalized medicine. The aim of this review was to provide comprehension regarding research trends in oral microbiome studies and establish the link between oral microbiomes and systemic diseases based on the latest technique of genome-wide analysis.

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Genome-wide analysis of transcriptional bursting-induced noise in mammalian cells

10.1101/736207 ◽

2019 ◽

Cited By ~ 2

Author(s):

Hiroshi Ochiai ◽

Tetsutaro Hayashi ◽

Mana Umeda ◽

Mika Yoshimura ◽

Akihito Harada ◽

...

Keyword(s):

Gene Expression ◽

Mammalian Cells ◽

Molecular Mechanisms ◽

Transcription Elongation ◽

Mapk Signaling ◽

Kinetic Properties ◽

Genome Wide Analysis ◽

Genome Wide ◽

A Genome ◽

Transcriptional Bursting

AbstractTranscriptional bursting is stochastic activation and inactivation of promoters, leading to discontinuous production of mRNA, and is considered to be a contributing factor to cell-to-cell heterogeneity in gene expression. However, it remains elusive how the kinetic properties of transcriptional bursting (e.g., burst size, burst frequency, and noise induced by transcriptional bursting) are regulated in mammalian cells. In this study, we performed a genome-wide analysis of transcriptional bursting in mouse embryonic stem cells (mESCs) using single-cell RNA-sequencing. We found that the kinetics of transcriptional bursting was determined by a combination of promoter and gene body binding proteins, including polycomb repressive complex 2 and transcription elongation-related factors. Furthermore, large-scale CRISPR-Cas9-based screening and functional analysis revealed that the Akt/MAPK signaling pathway regulated bursting kinetics by modulating transcription elongation efficiency. These results uncover key molecular mechanisms underlying transcriptional bursting and cell-to-cell gene expression noise in mammalian cells.

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Genome-wide functional analysis reveals that infection-associated fungal autophagy is necessary for rice blast disease

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0901477106 ◽

2009 ◽

Vol 106 (37) ◽

pp. 15967-15972 ◽

Cited By ~ 159

Author(s):

Michael J. Kershaw ◽

Nicholas J. Talbot

Keyword(s):

Functional Analysis ◽

Rice Blast ◽

Rice Blast Disease ◽

Blast Disease ◽

Deletion Mutants ◽

Targeted Deletion ◽

Genome Wide Analysis ◽

Plant Infection ◽

Genome Wide ◽

A Genome

To cause rice blast disease, the fungus Magnaporthe oryzae elaborates specialized infection structures called appressoria, which use enormous turgor to rupture the tough outer cuticle of a rice leaf. Here, we report the generation of a set of 22 isogenic M. oryzae mutants each differing by a single component of the predicted autophagic machinery of the fungus. Analysis of this set of targeted deletion mutants demonstrated that loss of any of the 16 genes necessary for nonselective macroautophagy renders the fungus unable to cause rice blast disease, due to impairment of both conidial programmed cell death and appressorium maturation. In contrast, genes necessary only for selective forms of autophagy, such as pexophagy and mitophagy, are dispensable for appressorium-mediated plant infection. A genome-wide analysis therefore demonstrates the importance of infection-associated, nonselective autophagy for the establishment of rice blast disease.

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Genome-Wide Characterization and Expression Analysis Provide Basis to the Biological Function of Cotton FBA Genes

Frontiers in Plant Science ◽

10.3389/fpls.2021.696698 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zhong-Qing Li ◽

Yao Zhang ◽

He Li ◽

Ting-Ting Su ◽

Cheng-Gong Liu ◽

...

Keyword(s):

Abiotic Stress ◽

Stress Responses ◽

Function Analysis ◽

Pcr Analysis ◽

Functional Domain ◽

Systematic Analysis ◽

Genome Wide ◽

A Genome ◽

Identification And Characterization

Fructose-1,6-biphosphate aldolase (FBA) is a multifunctional enzyme in plants, which participates in the process of Calvin-Benson cycle, glycolysis and gluconeogenesis. Despite the importance of FBA genes in regulating plant growth, development and abiotic stress responses, little is known about their roles in cotton. In the present study, we performed a genome-wide identification and characterization of FBAs in Gossypium hirsutum. Totally seventeen GhFBA genes were identified. According to the analysis of functional domain, phylogenetic relationship, and gene structure, GhFBA genes were classified into two subgroups. Furthermore, nine GhFBAs were predicted to be in chloroplast and eight were located in cytoplasm. Moreover, the promoter prediction showed a variety of abiotic stresses and phytohormone related cis-acting elements exist in the 2k up-stream region of GhFBA. And the evolutionary characteristics of cotton FBA genes were clearly presented by synteny analysis. Moreover, the results of transcriptome and qRT-PCR analysis showed that the expression of GhFBAs were related to the tissue distribution, and further analysis suggested that GhFBAs could respond to various abiotic stress and phytohormonal treatments. Overall, our systematic analysis of GhFBA genes would not only provide a basis for the understanding of the evolution of GhFBAs, but also found a foundation for the further function analysis of GhFBAs to improve cotton yield and environmental adaptability.

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