Bioinformatic analysis based genome-wide identification, characterization, diversification and regulatory transcription components of RNA silencing machinery genes in wheat (Triticum aestivum L.)

AbstractDicer-Like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) gene families are known as RNA silencing machinery genes or RNAi genes. They have important activities at post-transcriptional and chromatin modification levels. They regulate gene expression relating to different stresses, growth, and development in eukaryotes. A complete cycle of gene silencing is occurred by the collaboration of these three families. However, these gene families are not yet rigorously studied in the economically important wheat genome. Our bioinformatic analysis based genome-wide identification, characterization, diversification and regulatory components of these gene families identified 7 TaDCL, 39 TaAGO and 16 TaRDR genes from wheat genome against RNAi genes of Arabidopsis thaliana. Phylogenetic analysis of wheat genome with Arabidopsis and rice RNAi genes showed that TaDCL, TaAGO and TaRDR proteins are clustered into four, eight and four subgroups respectively. Domain, motif and exon-intron structure analyses showed that the TaDCL, TaAGO and TaRDR proteins conserve identical characteristics within groups while retain diverse differences between groups. GO annotations implied that a number of biological and molecular pathways are linked to RNAi mechanism in wheat. Gene networking between transcription factors and RNAi proteins indicates that ERF is the leading family linked to maximum RNAi genes followed by MIKC-MADS, C2H2, BBR-BPC, MYB, and Dof. Cis-regulatory elements associated to RNAi genes are predicted to act as regulatory components against various environmental conditions. Expressed sequence tag analysis showed that larger numbers of RNAi genes are expressed in different tissues and organs predicted to play roles for healthy plants and grains. Expression analysis of 7 TaDCL genes using qRT-PCR showed that only TaDCL3a and TaDCL3b had root specific significant expression (p-value<0.05) with no expression in leaf validated EST results. Besides, TaDCL3b and TaDCL4 significantly prompted in drought condition indicating their potential role in drought stress tolerance. Overall results would however help researchers for in-depth biological investigation of these RNAi genes in wheat crop improvement.

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Genome-wide identification of DCL, AGO and RDR gene families and their associated functional regulatory elements analyses in banana (Musa acuminata)

PLoS ONE ◽

10.1371/journal.pone.0256873 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0256873

Author(s):

Fee Faysal Ahmed ◽

Md. Imran Hossen ◽

Md. Abdur Rauf Sarkar ◽

Jesmin Naher Konak ◽

Fatema Tuz Zohra ◽

...

Keyword(s):

Transcription Factors ◽

Rna Silencing ◽

Gene Families ◽

Regulatory Elements ◽

Musa Acuminata ◽

Rnai Pathway ◽

Network Analyses ◽

Pathway Gene ◽

Genome Wide

RNA silencing is mediated through RNA interference (RNAi) pathway gene families, i.e., Dicer-Like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) and their cis-acting regulatory elements. The RNAi pathway is also directly connected with the post-transcriptional gene silencing (PTGS) mechanism, and the pathway controls eukaryotic gene regulation during growth, development, and stress response. Nevertheless, genome-wide identification of RNAi pathway gene families such as DCL, AGO, and RDR and their regulatory network analyses related to transcription factors have not been studied in many fruit crop species, including banana (Musa acuminata). In this study, we studied in silico genome-wide identification and characterization of DCL, AGO, and RDR genes in bananas thoroughly via integrated bioinformatics approaches. A genome-wide analysis identified 3 MaDCL, 13 MaAGO, and 5 MaRDR candidate genes based on multiple sequence alignment and phylogenetic tree related to the RNAi pathway in banana genomes. These genes correspond to the Arabidopsis thaliana RNAi silencing genes. The analysis of the conserved domain, motif, and gene structure (exon-intron numbers) for MaDCL, MaAGO, and MaRDR genes showed higher homogeneity within the same gene family. The Gene Ontology (GO) enrichment analysis exhibited that the identified RNAi genes could be involved in RNA silencing and associated metabolic pathways. A number of important transcription factors (TFs), e.g., ERF, Dof, C2H2, TCP, GATA and MIKC_MADS families, were identified by network and sub-network analyses between TFs and candidate RNAi gene families. Furthermore, the cis-acting regulatory elements related to light-responsive (LR), stress-responsive (SR), hormone-responsive (HR), and other activities (OT) functions were identified in candidate MaDCL, MaAGO, and MaRDR genes. These genome-wide analyses of these RNAi gene families provide valuable information related to RNA silencing, which would shed light on further characterization of RNAi genes, their regulatory elements, and functional roles, which might be helpful for banana improvement in the breeding program.

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In silico identification and characterization of AGO, DCL and RDR gene families and their associated regulatory elements in sweet orange (Citrus sinensis L.)

PLoS ONE ◽

10.1371/journal.pone.0228233 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0228233

Author(s):

Md. Parvez Mosharaf ◽

Hafizur Rahman ◽

Md. Asif Ahsan ◽

Zobaer Akond ◽

Fee Faysal Ahmed ◽

...

Keyword(s):

Gene Silencing ◽

Candidate Genes ◽

In Silico ◽

Citrus Sinensis ◽

Rna Silencing ◽

Sweet Orange ◽

Light Stress ◽

Gene Families ◽

Regulatory Elements ◽

Genome Wide

RNA interference (RNAi) plays key roles in post-transcriptional and chromatin modification levels as well as regulates various eukaryotic gene expressions which are involved in stress responses, development and maintenance of genome integrity during developmental stages. The whole mechanism of RNAi pathway is directly involved with the gene-silencing process by the interaction of Dicer-Like (DCL), Argonaute (AGO) and RNA-dependent RNA polymerase (RDR) gene families and their regulatory elements. However, these RNAi gene families and their sub-cellular locations, functional pathways and regulatory components were not extensively investigated in the case of economically and nutritionally important fruit plant sweet orange (Citrus sinensis L.). Therefore, in silico characterization, gene diversity and regulatory factor analysis of RNA silencing genes in C. sinensis were conducted by using the integrated bioinformatics approaches. Genome-wide comparison analysis based on phylogenetic tree approach detected 4 CsDCL, 8 CsAGO and 4 CsRDR as RNAi candidate genes in C. sinensis corresponding to the RNAi genes of model plant Arabidopsis thaliana. The domain and motif composition and gene structure analyses for all three gene families exhibited almost homogeneity within the same group members. The Gene Ontology enrichment analysis clearly indicated that the predicted genes have direct involvement into the gene-silencing and other important pathways. The key regulatory transcription factors (TFs) MYB, Dof, ERF, NAC, MIKC_MADS, WRKY and bZIP were identified by their interaction network analysis with the predicted genes. The cis-acting regulatory elements associated with the predicted genes were detected as responsive to light, stress and hormone functions. Furthermore, the expressed sequence tag (EST) analysis showed that these RNAi candidate genes were highly expressed in fruit and leaves indicating their organ specific functions. Our genome-wide comparison and integrated bioinformatics analyses provided some necessary information about sweet orange RNA silencing components that would pave a ground for further investigation of functional mechanism of the predicted genes and their regulatory factors.

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Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar

BMC Plant Biology ◽

10.1186/s12870-021-02872-3 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zihan Cheng ◽

Xuemei Zhang ◽

Wenjing Yao ◽

Kai Zhao ◽

Lin Liu ◽

...

Keyword(s):

Gene Family ◽

Higher Plants ◽

Abiotic Stress Tolerance ◽

Gene Families ◽

Regulatory Elements ◽

Late Embryogenesis Abundant ◽

Genome Wide ◽

Lea Gene ◽

Late Embryogenesis ◽

Genome Wide Search

Abstract Background The Late Embryogenesis-Abundant (LEA) gene families, which play significant roles in regulation of tolerance to abiotic stresses, widely exist in higher plants. Poplar is a tree species that has important ecological and economic values. But systematic studies on the gene family have not been reported yet in poplar. Results On the basis of genome-wide search, we identified 88 LEA genes from Populus trichocarpa and renamed them as PtrLEA. The PtrLEA genes have fewer introns, and their promoters contain more cis-regulatory elements related to abiotic stress tolerance. Our results from comparative genomics indicated that the PtrLEA genes are conserved and homologous to related genes in other species, such as Eucalyptus robusta, Solanum lycopersicum and Arabidopsis. Using RNA-Seq data collected from poplar under two conditions (with and without salt treatment), we detected 24, 22 and 19 differentially expressed genes (DEGs) in roots, stems and leaves, respectively. Then we performed spatiotemporal expression analysis of the four up-regulated DEGs shared by the tissues, constructed gene co-expression-based networks, and investigated gene function annotations. Conclusion Lines of evidence indicated that the PtrLEA genes play significant roles in poplar growth and development, as well as in responses to salt stress.

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Genome-wide identification and analysis of the CNGC gene family in maize

PeerJ ◽

10.7717/peerj.5816 ◽

2018 ◽

Vol 6 ◽

pp. e5816 ◽

Cited By ~ 4

Author(s):

Lidong Hao ◽

Xiuli Qiao

Keyword(s):

Gene Family ◽

Expression Profiles ◽

Gene Families ◽

Regulatory Elements ◽

Vital Role ◽

Signal Pathways ◽

Cis Acting ◽

Genome Wide ◽

Gramineous Plant ◽

Gated Channel

As one of the non-selective cation channel gene families, the cyclic nucleotide-gated channel (CNGC) gene family plays a vital role in plant physiological processes that are related to signal pathways, plant development, and environmental stresses. However, genome-wide identification and analysis of the CNGC gene family in maize has not yet been undertaken. In the present study, twelve ZmCNGC genes were identified in the maize genome, which were unevenly distributed on chromosomes 1, 2, 4, 5, 6, 7, and 8. They were classified into five major groups: Groups I, II, III, IVa, and IVb. Phylogenetic analysis showed that gramineous plant CNGC genes expanded unequally during evolution. Group IV CNGC genes emerged first, whereas Groups I and II appeared later. Prediction analysis of cis-acting regulatory elements showed that 137 putative cis-elements were related to hormone-response, abiotic stress, and organ development. Furthermore, 120 protein pairs were predicted to interact with the 12 ZmCNGC proteins and other maize proteins. The expression profiles of the ZmCNGC genes were expressed in tissue-specific patterns. These results provide important information that will increase our understanding of the CNGC gene family in maize and other plants.

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Comparative Genome-wide Analysis and Expression Profiling of Histone Acetyltransferases and Histone Deacetylases Involved in the Response to Drought in Wheat

10.21203/rs.3.rs-123885/v1 ◽

2020 ◽

Author(s):

Hua Li ◽

Huajie Liu ◽

Xinxin Pei ◽

Hongyu Chen ◽

Xiao Li ◽

...

Keyword(s):

Drought Stress ◽

Stress Responses ◽

Histone Deacetylases ◽

Gene Expression Analysis ◽

Regulatory Elements ◽

Wheat Genome ◽

Histone Acetyltransferases ◽

Promoter Regions ◽

Conserved Domain ◽

Genome Wide

Abstract Background: Histone acetyltransferases (HATs) and histone deacetylases (HDACs) contribute to plant growth, development, and stress responses. A number of HAT and HDAC genes have been identified in several plants. However, wheat HATs and HDACs have not been comprehensively characterized. In this study, we identified TaHATs and TaHDACs in the wheat genome using bioinformatics tools. Result: In total, 30 TaHAT genes and 53 TaHDAC genes were detected in the wheat genome. As described in other plants, TaHATs were classified into four subfamilies (i.e., GNAT, p300/CBP, MYST, and TAFII250) and TaHDACs were divided into three subfamilies (i.e., RPD3/HDA1, HD2, and SIR2). Phylogenetic and conserved domain analyses showed that TaHATs and TaHDACs are highly similar to those in Arabidopsis and rice; however, divergence and expansion from Arabidopsis and rice were also observed. We detected many stress-related cis-regulatory elements in the promoter regions of these genes (i.e., ABRE, STRE, MYB et al.). Further, based on a comparative expression analyses of three varieties with different degrees of drought resistance under drought stress, we found that TaHAG2, TaHAG3, TaHAC2, TaHDA18, TaHDT1, and TaHDT2 are likely regulate drought stress in wheat. Conclusions: In this study, TaHATs and TaHDACs from the wheat genome were identified. Three TaHATs and three TaHDACs were very likely to regulate drought stress based on a promoter analysis and gene expression analysis. These results provide a foundation for further research on the regulation of acetylation in wheat and its role in the response to drought stress.

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Comparative bioinformatic analysis of genes expressed in common bean (Phaseolus vulgaris L.) seedlings

Genome ◽

10.1139/g05-010 ◽

2005 ◽

Vol 48 (3) ◽

pp. 562-570 ◽

Cited By ~ 31

Author(s):

Maeli Melotto ◽

Claudia B Monteiro-Vitorello ◽

Adriano G Bruschi ◽

Luis E.A Camargo

Keyword(s):

Phaseolus Vulgaris ◽

Common Bean ◽

Expressed Sequence Tag ◽

Gene Families ◽

Bioinformatic Analysis ◽

Colletotrichum Lindemuthianum ◽

Cdna Libraries ◽

Nucleotide Polymorphisms ◽

Phaseolus Vulgaris L ◽

Single Nucleotide

To rapidly and cost-effectively generate gene expression data, we developed an annotated unigene database of common bean (Phaseolus vulgaris L.). In this study, 3 cDNA libraries were constructed from the bean breeding line SEL1308, 1 from young leaf and 2 from seedlings inoculated or not inoculated with the fungal pathogen Colletotrichum lindemuthianum (Sacc. & Magnus) Briosi & Cavara, which causes anthracnose in common bean. To this date, 5255 single-pass sequences have been included in the database after selection based on sequence quality. These ESTs were trimmed and clustered using the computer programs Phred and CAP3 to form a unigene collection of 3126 unique sequences. Within clusters, 318 single nucleotide polymorphisms (SNPs) and 68 insertions–deletions (indels) were found, indicating the presence of paralogous gene families in our database. Each unigene sequence was analyzed for possible function using their similarity to known genes represented in the GenBank database and classified into 14 categories. Only 314 unigenes showed significant similarities to Phaseolus genomic sequences and P. vulgaris ESTs, which indicates that 90% (2818 unigenes) of our database represent newly discovered common bean genes. In addition, 12% (387 unigenes) were shown to be specific to common bean. This study represents a first step towards the discovery of novel genes in beans and a valuable source of molecular markers for expressed gene tagging and mapping.Key words: expressed sequence tag (EST), Colletotrichum lindemuthianum, Phaseolus vulgaris, simple sequence repeat (SSR), single nucleotide polymorphism (SNP).

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In Silico Identification, Characterization and Diversity Analysis of RNAi Genes and their Associated Regulatory Elements in Sweet Orange (Citrus sinensis L)

10.1101/2020.01.13.904128 ◽

2020 ◽

Author(s):

Md. Parvez Mosharaf ◽

Md. Asif Ahsan ◽

Hafizur Rahman ◽

Zobaer Akond ◽

Fee Faysal Ahmed ◽

...

Keyword(s):

Stress Responses ◽

Citrus Sinensis ◽

Expressed Sequence Tag ◽

Sweet Orange ◽

Gene Families ◽

Regulatory Elements ◽

Rnai Pathway ◽

Composition Analysis ◽

Diversity Analysis ◽

Regulatory Pathways

AbstractRNA interference (RNAi) plays key roles in post-transcriptional and chromatin modification levels as well as regulates various eukaryotic gene expressions which involved in stress responses, development and maintenance of genome integrity during developmental stages. The whole mechanism of RNAi pathway is directly involved with the gene-silencing process by the interaction of Dicer-Like (DCL), Argonaute (AGO) and RNA-dependent RNA polymerase (RDR) gene families. However, the genes of these three RNAi families are largely unknown yet in sweet orange (Citrus sinensis), though it is an economically important fruit plant all over the world. Therefore, a comprehensive investigation for genome-wide identification, characterization and diversity analysis of RNA silencing genes in C. sinensis was conducted and identified 4 CsDCL, 8 CsAGO and 4 CsRDR as RNAi genes. To characterize and validate the predicted genes of RNAi families, various bioinformatics analysis was conducted. Phylogenetic analysis clustered the predicted CsDCLs, CsAGOs and CsRDRs genes into four, six and four subgroups with the relevant genes of Arabidopsis respectively. The domain and motif composition analysis, the gene structure for all three-gene families exhibited almost homogeneity within the same group members while showed significant differences in between groups. The GO enrichment analysis results clearly indicated that the predicted genes have direct involvement into the RNAi process as expected in C. sinensis. Moreover, Cis-regulatory elements and regulatory transcription factor analysis of the reported RNAi genes demonstrated the diverse connection to the huge biological functions and regulatory pathways. The expressed sequence tag (EST) analysis showed that these genes are highly expressed in fruit and leaves which indicate that these reported genes have great involvement in C. sinensis food, flowering and fruit production. The expression analysis of the reported RNAi genes might be more useful to explore the most effective RNAi genes in C. sinensis for further biotechnological application.

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Genome-wide identification, evolutionary relationship and expression analysis of AGO, DCL and RDR family genes in tea

Scientific Reports ◽

10.1038/s41598-021-87991-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Debasish B. Krishnatreya ◽

Pooja Moni Baruah ◽

Bhaskar Dowarah ◽

Soni Chowrasia ◽

Tapan Kumar Mondal ◽

...

Keyword(s):

Expression Analysis ◽

Small Rna ◽

Expression Patterns ◽

Crop Improvement ◽

Evolutionary Relationship ◽

Constitutive Expression ◽

Gene Families ◽

Tea Plant ◽

Variable Expression ◽

Genome Wide

AbstractThree gene families in plants viz. Argonaute (AGOs), Dicer-like (DCLs) and RNA dependent RNA polymerase (RDRs) constitute the core components of small RNA mediated gene silencing machinery. The present study endeavours to identify members of these gene families in tea and to investigate their expression patterns in different tissues and various stress regimes. Using genome-wide analysis, we have identified 18 AGOs, 5 DCLs and 9 RDRs in tea, and analyzed their phylogenetic relationship with orthologs of Arabidopsis thaliana. Gene expression analysis revealed constitutive expression of CsAGO1 in all the studied tissues and stress conditions, whereas CsAGO10c showed most variable expression among all the genes. CsAGO10c gene was found to be upregulated in tissues undergoing high meristematic activity such as buds and roots, as well as in Exobasidium vexans infected samples. CsRDR2 and two paralogs of CsAGO4, which are known to participate in biogenesis of hc-siRNAs, showed similarities in their expression levels in most of the tea plant tissues. This report provides first ever insight into the important gene families involved in biogenesis of small RNAs in tea. The comprehensive knowledge of these small RNA biogenesis purveyors can be utilized for tea crop improvement aimed at stress tolerance and quality enhancement.

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Genome-wide analysis of AGO, DCL and RDR gene families reveals RNA-directed DNA methylation is involved in fruit abscission in Citrus sinensis

BMC Plant Biology ◽

10.1186/s12870-019-1998-1 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 2

Author(s):

Agustín Sabbione ◽

Lucas Daurelio ◽

Abelardo Vegetti ◽

Manuel Talón ◽

Francisco Tadeo ◽

...

Keyword(s):

Dna Methylation ◽

Small Rnas ◽

Citrus Sinensis ◽

Rna Silencing ◽

Expression Patterns ◽

Gene Families ◽

Rna Seq ◽

Fruit Abscission ◽

Methylation Pathway ◽

Genome Wide

Abstract Background Small RNAs regulate a wide variety of processes in plants, from organ development to both biotic and abiotic stress response. Being master regulators in genetic networks, their biogenesis and action is a fundamental aspect to characterize in order to understand plant growth and development. Three main gene families are critical components of RNA silencing: DICER-LIKE (DCL), ARGONAUTE (AGO) and RNA-DEPENDENT RNA POLYMERASE (RDR). Even though they have been characterized in other plant species, there is no information about these gene families in Citrus sinensis, one of the most important fruit species from both economical and nutritional reasons. While small RNAs have been implicated in the regulation of multiple aspects of plant growth and development, their role in the abscission process has not been characterized yet. Results Using genome-wide analysis and a phylogenetic approach, we identified a total of 13 AGO, 5 DCL and 7 RDR genes. We characterized their expression patterns in root, leaf, flesh, peel and embryo samples using RNA-seq data. Moreover, we studied their role in fruit abscission through gene expression analysis in fruit rind compared to abscission zone from samples obtained by laser capture microdissection. Interestingly, we determined that the expression of several RNA silencing factors are down-regulated in fruit abscission zone, being particularly represented gene components of the RNA-dependent DNA Methylation pathway, indicating that repression of this process is necessary for fruit abscission to take place in Citrus sinensis. Conclusions The members of these 3 families present characteristic conserved domains and distinct expression patterns. We provide a detailed analysis of the members of these families and improved the annotation of some of these genes based on RNA-seq data. Our data suggests that the RNA-dependent DNA Methylation pathway is involved in the important fruit abscission process in C. sinensis.

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Polyamine and Ethylene pathways crosstalk revisited on a genome wide and gene function scale

10.21203/rs.2.11103/v1 ◽

2019 ◽

Author(s):

BLAISE PASCAL MUVUNYI ◽

Fan Wu ◽

Qi Yan ◽

Gisele Kanzana ◽

Yufei Zhang ◽

...

Keyword(s):

Salt Stress ◽

Stress Tolerance ◽

Abiotic Stresses ◽

Primary Root ◽

Evolutionary Relationship ◽

Gene Families ◽

Regulatory Elements ◽

Pathway Gene ◽

Genome Wide ◽

A Genome

Abstract Background Polyamine and ethylene biosynthesis pathway genes are widely involved in the regulation of plant abiotic stresses. For their biosynthesis, both pathways require the same precursor, Synthase Adenosyl Methionine (SAM) enzyme. Whether they function as competitors or collaborators to regulate plant abiotic stress tolerance is still an elusive topic. Genome wide analysis of Cleistogenes songorica polyamine and ethylene pathway gene families was conducted to study their evolutionary relationship. And, using Arabidopsis plants transformed with a polyamine gene SAMDC2 from C. songorica, the expression of key genes from both pathways, and other previously well-studied stress responsive genes was investigated under salt or drought stress. Further, the ABA’s role on this interaction salt stress was also studied. Results 17 polyamine, 12 ethylene and 6 SAM biosynthesis related genes were identified at genome wide level in C. songorica. Phylogenetic analysis revealed close evolutionary similarities between gene families from both pathways. Also, analysis of cis regulatory elements indicated that SAM family genes promoters were rich into both ABA and ethylene related cis regulatory elements. Transcriptomic analysis, qRT-PCR validation, and confirmation using transgenic Arabidopsis showed that polyamine and ethylene key pathway genes can be concurrently expressed during abiotic stresses. Arabidopsis plants expressing a polyamine gene CsSAMDC2 driven by RD29A showed an improved drought and salt stress tolerance, and an increased expression of key polyamine and ethylene pathway genes. These plants maintained higher chlorophyll content and photosynthetic capacity. Morphological analysis of transgenic seedlings showed that leaves of these lines exhibited a more compact architecture following salt stress exposure. Application of ABA on transgenic lines under salt stress further improved the expression of polyamine and ethylene pathway genes. Further, lateral and primary root development were found improved during salt stress and ABA treatments. Interestingly, the expression of ethylene pathway genes was not reversed by exogenous ABA during salt stress treatment. Conclusion In silico and gene functional analysis assays revealed potential evolutionary and functional similarities between polyamine and ethylene pathway gene families. Such findings imply a synergetic interaction between polyamine and ethylene pathways, and the significant role of ABA on this crosstalk.

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