Genome-Wide Identification of Key Components of RNA Silencing in Two Phaseolus vulgaris Genotypes of Contrasting Origin and Their Expression Analyses in Response to Fungal Infection

RNA silencing serves key roles in a multitude of cellular processes, including development, stress responses, metabolism, and maintenance of genome integrity. Dicer, Argonaute (AGO), double-stranded RNA binding (DRB) proteins, RNA-dependent RNA polymerase (RDR), and DNA-dependent RNA polymerases known as Pol IV and Pol V form core components to trigger RNA silencing. Common bean (Phaseolus vulgaris) is an important staple crop worldwide. In this study, we aimed to unravel the components of the RNA-guided silencing pathway in this non-model plant, taking advantage of the availability of two genome assemblies of Andean and Meso-American origin. We identified six PvDCLs, thirteen PvAGOs, 10 PvDRBs, 5 PvRDRs, in both genotypes, suggesting no recent gene amplification or deletion after the gene pool separation. In addition, we identified one PvNRPD1 and one PvNRPE1 encoding the largest subunits of Pol IV and Pol V, respectively. These genes were categorized into subgroups based on phylogenetic analyses. Comprehensive analyses of gene structure, genomic localization, and similarity among these genes were performed. Their expression patterns were investigated by means of expression models in different organs using online data and quantitative RT-PCR after pathogen infection. Several of the candidate genes were up-regulated after infection with the fungus Colletotrichum lindemuthianum.

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Genome Wide Identification of Key Components of RNA Silencing in Two Phaseolus vulgaris Genotypes of Contrasting Origin and Their Expression Analyses in Response to Fungal Infection

10.20944/preprints202112.0071.v1 ◽

2021 ◽

Author(s):

Juan Camilo Alvarez-Diaz ◽

Manon Richard ◽

Vincent Thareau ◽

Gianluca Teano ◽

Christine Paysant-Le-Roux ◽

...

Keyword(s):

Phaseolus Vulgaris ◽

Stress Responses ◽

Rna Silencing ◽

Rna Binding ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Colletotrichum Lindemuthianum ◽

Online Data ◽

Pol Iv ◽

Pol V

RNA silencing serves key roles in a multitude of cellular processes, including development, stress responses, metabolism, and maintenance of genome integrity. Dicer, Argonaute (AGO), double-stranded RNA binding (DRB), RNA-dependent RNA polymerase (RDR) and DNA-dependent RNA polymerases known as Pol IV and Pol V form core components to trigger RNA silencing. Common bean (Phaseolus vulgaris) is an important staple crop worldwide. In this study, we aimed to unravel the components of the RNA-guided silencing pathway in this non-model plant taking advantage of the availability of two genome assemblies of Andean and Meso-American origin. We identified six PvDCLs, thirteen PvAGOs, 10 PvDRB, 5 PvRDR, in both genotypes, suggesting no recent gene amplification or deletion after the gene pool separation. In addition, we identified one PvNRPD1 and one PvNRPE1 encoding the largest subunits of Pol IV and Pol V, respectively. These genes were categorized into subgroups based on phylogenetic analyses. Comprehensive analyses of gene structure, genomic localization and similarity among these genes were performed. Their expression patterns were investigated by means of expression models in different organs using online data and quantitative RT-PCR after pathogen infection. Several of the candidate genes were up-regulated after infection with the fungus Colletotrichum lindemuthianum.

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Genome-wide Identification and Expression Analysis of the YTH Domain-containing RNA-binding Protein Family in Citrus Sinensis

Journal of the American Society for Horticultural Science ◽

10.21273/jashs04567-18 ◽

2019 ◽

Vol 144 (2) ◽

pp. 79-91 ◽

Cited By ~ 1

Author(s):

Zhigang Ouyang ◽

Huihui Duan ◽

Lanfang Mi ◽

Wei Hu ◽

Jianmei Chen ◽

...

Keyword(s):

Stress Responses ◽

Messenger Rna ◽

Citrus Sinensis ◽

Rna Binding ◽

Developmental Stages ◽

Rna Binding Proteins ◽

Expression Profiles ◽

Expression Patterns ◽

Genome Wide ◽

Yth Domain

In eukaryotic systems, messenger RNA regulations, including splicing, 3′-end formation, editing, localization, and translation, are achieved by different RNA-binding proteins and noncoding RNAs. The YTH domain is a newly identified RNA-binding domain that was identified by comparing its sequence with that of splicing factor YT521-B. Previous study showed that the YTH gene plays an important role in plant resistance to abiotic and biotic stress. In this study, 211 YTH genes were identified in 26 species that represent four major plant lineages. Phylogenetic analysis revealed that these genes could be divided into eight subgroups. All of the YTH genes contain a YT521 domain and have different structures. Ten YTH genes were identified in navel orange (Citrus sinensis). The expression profiles of these CitYTH genes were analyzed in different tissues and at different fruit developmental stages, and CitYTH genes displayed distinct expression patterns under heat, cold, salt, and drought stress. Furthermore, expression of the CitYTH genes in response to exogenous hormones was measured. Nuclear localization was also confirmed for five of the proteins encoded by these genes after transient expression in Nicotiana benthamiana cells. This study provides valuable information on the role of CitYTHs in the signaling pathways involved in environmental stress responses in Citrus.

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Preliminary Classification of the ABC Transporter Family in Betula halophila and Expression Patterns in Response to Exogenous Phytohormones and Abiotic Stresses

Forests ◽

10.3390/f10090722 ◽

2019 ◽

Vol 10 (9) ◽

pp. 722

Author(s):

An ◽

Ma ◽

Du ◽

Yu ◽

Li ◽

...

Keyword(s):

Abiotic Stress ◽

Abc Transporters ◽

Stress Responses ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Pcr Analysis ◽

Structural Domain ◽

Transcriptional Responses ◽

Hormone Transport ◽

Transporter Family

ATP-binding cassette (ABC) transporters comprise a transport system superfamily which is ubiquitous in eukaryotic and prokaryotic cells. In plants, ABC transporters play important roles in hormone transport and stress tolerance. In this study, 15 BhABC transporters encoded by genes identified from the transcriptome of Betula halophila were categorized into four subfamilies (ABCB, ABCF, ABCG, and ABCI) using structural domain and phylogenetic analyses. Upon B. halophila exposure to exogenous phytohormones and abiotic stressors, gene expression patterns and transcriptional responses for each subfamily of genes were obtained using semi-quantitative RT-PCR analysis. The results demonstrated that expression of most genes belonging to ABCB and ABCG subfamilies changed in response to exogenous phytohormone exposures and abiotic stress. These results suggest that BhABC genes may participate in hormone transport and that their expression may be influenced by ABA-dependent signaling pathways involved in abiotic stress responses to various stressors.

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Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II

Molecular Cell ◽

10.1016/j.molcel.2008.12.015 ◽

2009 ◽

Vol 33 (2) ◽

pp. 192-203 ◽

Cited By ~ 149

Author(s):

Thomas S. Ream ◽

Jeremy R. Haag ◽

Andrzej T. Wierzbicki ◽

Carrie D. Nicora ◽

Angela D. Norbeck ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Rna Silencing ◽

Pol Iv ◽

Pol V

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Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

10.21203/rs.3.rs-17430/v2 ◽

2020 ◽

Author(s):

Chong Yang ◽

Juanjuan Li ◽

Faisal Islam ◽

Luyang Hu ◽

Jiansu Wang ◽

...

Keyword(s):

Helianthus Annuus ◽

Stress Responses ◽

Abiotic Stresses ◽

Expression Profiles ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Crop Improvement ◽

Plant Tolerance ◽

Biotic And Abiotic Stresses

Abstract Background: WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. However, the information about WRKY genes in Helianthus annuus L. (common sunflower) is limited. Results: Ninety WRKY (HaWRKY) genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group and HaWRKY genes within same group or subgroup generally showed similar exon-intron structures and motif compositions. The tandem and segmental duplication possibly contributed to the diversity and expansion of HaWRKY gene families. Synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses. Conclusions: Ninety WRKY (HaWRKY) genes were identified from H. annuus L. and classified into four groups. Structures of HaWRKY proteins and their evolutionary characteristics were also investigated. The characterization of HaWRKY genes and their expression profiles under biotic and abiotic stresses in this study provide a foundation for further functional analyses of these genes. Therefore, these functional genes related to increasing the plant tolerance or improving the crop quality, could be applied for the crop improvement..

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Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

10.21203/rs.3.rs-17430/v1 ◽

2020 ◽

Author(s):

Chong Yang ◽

Juanjuan Li ◽

Faisal Islam ◽

Luyang Hu ◽

Jiansu Wang ◽

...

Keyword(s):

Helianthus Annuus ◽

Stress Responses ◽

Abiotic Stresses ◽

Expression Profiles ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Crop Improvement ◽

Gene Families ◽

Biotic And Abiotic Stresses

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RNA-Silencing Enzymes Pol IV and Pol V in Maize: More than one Flavor?

PLoS Genetics ◽

10.1371/journal.pgen.1000736 ◽

2009 ◽

Vol 5 (11) ◽

pp. e1000736 ◽

Cited By ~ 10

Author(s):

Craig S. Pikaard ◽

Sarah Tucker

Keyword(s):

Rna Silencing ◽

Pol Iv ◽

Pol V

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Genome-wide Characterization of GRAS Transcription Factors and Their Potential Roles in Development and Drought Resilience in Rose (Rosa chinensis)

10.21203/rs.3.rs-312426/v1 ◽

2021 ◽

Author(s):

Priya Kumari ◽

Vijay Gahlaut ◽

Ekjot Kaur ◽

Sanatsujat Singh ◽

Sanjay Kumar ◽

...

Keyword(s):

Transcription Factors ◽

Stress Responses ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Specific Gene ◽

Biological Processes ◽

Rosa Chinensis ◽

Genome Wide ◽

Am Symbiosis ◽

Hormone Responses

Abstract In the past few years, plant-specific GRAS transcription factors (TFs) were reported to play an essential role in regulating several biological processes, such as plant growth and development, phytochrome signal, arbuscular mycorrhiza (AM) symbiosis, environmental stress responses. GRAS genes have been thoroughly studied in several plant species, but unexplored in Rosa chinensis (rose). In this study, 59 rose GRAS genes (RcGRAS) were identified. Phylogenetic analyses grouped RcGRAS genes into 17 subfamilies, of which subfamily Rc2 was Rosaceae family-specific. Gene structure analyses showed that most of the RcGRAS genes were intronless and were relatively conserved. Cis-element analyses suggested that RcGRAS genes may involve in distinct biological processes and responsive to diverse abiotic stresses. Most of the genes were localized in the nucleus, except for a few in the cytoplasm. Gene expression analysis was also performed in various tissues, during gibberellin (GA) and drought stress treatment. The expression patterns of RcGRAS genes during GA treatment and in response to drought stresses suggested the potential functions of these genes in regulating stress and hormone responses. In summary, a comprehensive exploration of the rose GRAS gene family was performed, and the generated information can be utilized for further functional-based studies on this family.

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Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

PLoS ONE ◽

10.1371/journal.pone.0241965 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0241965

Author(s):

Juanjuan Li ◽

Faisal Islam ◽

Qian Huang ◽

Jian Wang ◽

Weijun Zhou ◽

...

Keyword(s):

Helianthus Annuus ◽

Stress Responses ◽

Expression Profiles ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Gene Families ◽

Biotic Stresses ◽

Gene Pairs ◽

Duplication Events ◽

Species Specific

WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. Sunflower (Helianthus annuus L.) is one of the important vegetable oil supplies in the world. However, the information about WRKY genes in sunflower is limited. In this study, ninety HaWRKY genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group. Besides, HaWRKY genes within the same group or subgroup generally showed similar exon-intron structures and motif compositions. The gene duplication analysis showed that five pairs of HaWRKY genes (HaWRKY8/9, HaWRKY53/54, HaWRKY65/66, HaWRKY66/67 and HaWRKY71/72) are tandem duplicated and four HaWRKY gene pairs (HaWRKY15/82, HaWRKY25/65, HaWRKY28/55 and HaWRKY50/53) are also identified as segmental duplication events, indicating that these duplication genes were contribute to the diversity and expansion of HaWRKY gene families. The dN/dS ratio of these duplicated gene pairs were also calculated to understand the evolutionary constraints. In addition, synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses, which provide a foundation for further functional analyses of these genes. Those functional genes related to stress tolerance and quality improvement could be applied in marker assisted breeding of the crop.

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