Genome-Wide Analysis of DCL, AGO, and RDR Gene Families in Pepper (Capsicum Annuum L.)

Qin, Lei; Mo, Ning; Muhammad, Tayeb; Liang, Yan

doi:10.3390/ijms19041038

Cited by 59 publications

(45 citation statements)

References 81 publications

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“…32 genes in rice [14], 28 genes in maize [39] and tomato [33], 38 genes in foxtail millet [40], 22 genes in grapevine [41] and pepper [42] and 20 genes in cucumber [43]. Recently 23 genes in Barley (Hordeum vulgare L.) [44], 36 genes in sugarcane (Saccharum spontaneum) [45] and 25 genes in sweet orange (Citrus sinensis) [46] belonging to DCL, AGO and RDR genes have been identified and characterized.…”

Section: Plos Onementioning

confidence: 99%

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

et al. 2020

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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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Section: Plos Onementioning

confidence: 99%

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

et al. 2020

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“…In general, these reports show the presence of 4 classes of DCLs, with more than one member for each class. Seven DCLs have been identified in the tomato Solanum lycopersicum [36], eight in rice [37], five in maize [38], five in poplar [12, 39], four in grapevine [40], eight in Brassica napus [41], three in Archis duranensis , and four in chickpea, pigeonpea, A. ipaensis [42] and four in pepper [43]. Thus far, cotton DCLs have only been identified in the G .…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification of the Dicer-like family in cotton and analysis of the DCL expression modulation in response to biotic stress in two contrasting commercial cultivars

et al. 2019

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BackgroundDicer-like proteins (DCLs) are essential players in RNA-silencing mechanisms, acting in gene regulation via miRNAs and in antiviral protection in plants and have also been associated to other biotic and abiotic stresses. To the best of our knowledge, despite being identified in some crops, cotton DCLs haven’t been characterized until now. In this work, we characterized the DCLs of three cotton species and analyzed their expression profiles during biotic stress.ResultsAs main results, 11 DCLs in the allotetraploid cotton Gossypium hirsutum, 7 and 6 in the diploid G. arboreum and G. raimondii, were identified, respectively. Among some DCLs duplications observed in these genomes, the presence of an extra DCL3 in the three cotton species were detected, which haven’t been found in others eudicots. All the DCL types identified by in silico analysis in the allotetraploid cotton genome were able to generate transcripts, as observed by gene expression analysis in distinct tissues. Based on the importance of DCLs for plant defense against virus, responses of cotton DCLs to virus infection and/or herbivore attack using two commercial cotton cultivars (cv.), one susceptible (FM966) and another resistant (DO) to polerovirus CLRDV infection, were analyzed. Both cvs. Responded differently to virus infection. At the inoculation site, the resistant cv. showed strong induction of DCL2a and b, while the susceptible cv. showed a down-regulation of these genes, wherever DCL4 expression was highly induced. A time course of DCL expression in aerial parts far from inoculation site along infection showed that DCL2b and DCL4 were repressed 24 h after infection in the susceptible cotton. As CLRDV is aphid-transmitted, herbivore attack was also checked. Opposite expression pattern of DCL2a and b and DCL4 was observed for R and S cottons, showing that aphid feeding alone may induce DCL modulation.ConclusionsAlmost all the DCLs of the allotetraploide G. hirsutum cotton were found in their relative diploids. Duplications of DCL2 and DCL3 were found in the three species. All four classes of DCL responded to aphid attack and virus infection in G. hirsutum. DCLs initial responses against the virus itself and/or herbivore attack may be contributing towards virus resistance.

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“…In general, these reports show the presence of 4 classes of DCLs, with more than one member for each class. Seven DCLs have been identified in the tomato Solanum lycopersicum [36], eight in rice [37], five in maize [38], five in poplar [12,39], four in grapevine [40], eight in Brassica napus [41], three in Archis duranensis, and four in chickpea, pigeonpea, A. ipaensis [42] and four in pepper [43]. Thus far, cotton DCLs have only been identified in the G. raimondii genome [44], but they have not been investigated by comparative evolutionary and expression analyses in cotton species.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification of the Dicer-like family in cotton and analysis of the DCL expression modulation in response to biotic stress in two contrasting commercial cultivars

Moura

Fausto

Fanelli

et al. 2019

Preprint

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Background Dicer-like proteins (DCLs) are fundamental players in RNA-silencing mechanisms acting in gene regulation via miRNAs and in antiviral protection in plants, in addition to being related to other biotic and abiotic stresses. Despite be identified in some crops, cotton DCLs weren't characterized until now. Here we characterize the DCLs of three cotton species and analyzed their expression profiles during biotic stress. Results We identified 11 DCLs in the allotetraploid cotton Gossypium hirsutum and 7 and 6 in the diploid G. arboreum and G. raimondii, respectively. Among some DCL duplication observed in these genomes, we observe the presence of an extra DCL3 in the three cotton species, not found in others eudicots until now. All the DCL types identified by in silico analysis in the allotetraploid cotton genome were able to generate transcripts, as observed by gene expression analysis in distinct tissues. Based on the importance of DCLs for plant virus defense, responses of cotton DCLs to virus infection and/or herbivore attack using two commercial cotton cultivars (cv.), one susceptible (Fibermax 966) and another resistant (Delta Opal) to polerovirus CLRDV infection were analyzed. Both cvs. responded differently to virus infection. At the initial stages, 24dpi, the resistant cv. showed strong induction of DCL2a and b, while the susceptible cv. showed a down-regulation of these genes, wherever DCL4 expression was highly induced. Herbivore attack did not induce contrasting profiles between cotton DCLs transcripts in either cotton cv. Conclusions The allotetraploide cotton G. hirsutum has almost all DCLs found in their diploid relative and duplication of DCL2 and DCL3 were found in the three species. All the four classes of DCL respond to aphid attack and virus infection in G. hirsutum, however, remarkable differences in DCL initial responses against the virus itself may be responsible for the virus susceptible and/or resistant phenotype of the contrasting cotton cv. studied.

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Genome-Wide Analysis of DCL, AGO, and RDR Gene Families in Pepper (Capsicum Annuum L.)

Cited by 59 publications

References 81 publications

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

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

Genome-wide identification of the Dicer-like family in cotton and analysis of the DCL expression modulation in response to biotic stress in two contrasting commercial cultivars

Genome-wide identification of the Dicer-like family in cotton and analysis of the DCL expression modulation in response to biotic stress in two contrasting commercial cultivars

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