Genome-wide identification of DCL, AGO and RDR gene families and their associated functional regulatory elements analyses in banana (Musa acuminata)
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) m...
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| description | 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. |
| doi_str_mv | 10.1371/journal.pone.0256873 |
| format | Article |
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Imran ; Sarkar, Md. Abdur Rauf ; Konak, Jesmin Naher ; Zohra, Fatema Tuz ; Shoyeb, Md ; Mondal, Samiran</creator><contributor>Ansari, Mahmood ur Rahman</contributor><creatorcontrib>Ahmed, Fee Faysal ; Hossen, Md. Imran ; Sarkar, Md. Abdur Rauf ; Konak, Jesmin Naher ; Zohra, Fatema Tuz ; Shoyeb, Md ; Mondal, Samiran ; Ansari, Mahmood ur Rahman</creatorcontrib><description>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.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0256873</identifier><identifier>PMID: 34473743</identifier><language>eng</language><publisher>San Francisco: Public Library of Science</publisher><subject>Analysis ; Banana ; Bananas ; Binding sites ; Bioinformatics ; Biology and life sciences ; Biosynthesis ; Cellular stress response ; Corn ; Crops ; DNA-directed RNA polymerase ; Epigenetics ; Flowers & plants ; Fruits ; Fungi ; Gene expression ; Gene families ; Gene regulation ; Gene silencing ; Genes ; Genetic aspects ; Genetic engineering ; Genetic transcription ; Genomes ; Homogeneity ; Mathematics ; Metabolic pathways ; MicroRNAs ; Musa acuminata ; Nucleotide sequence ; Ontology ; Phylogeny ; Post-transcription ; Proteins ; Regulatory sequences ; Research and Analysis Methods ; Ribonucleic acid ; RNA ; RNA polymerase ; RNA-directed RNA polymerase ; RNA-mediated interference ; Transcription factors</subject><ispartof>PloS one, 2021-09, Vol.16 (9), p.e0256873-e0256873</ispartof><rights>COPYRIGHT 2021 Public Library of Science</rights><rights>2021 Ahmed et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2021 Ahmed et al 2021 Ahmed et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c669t-9026b529f1546191aa0ba7ad463069b6bce15866be5aaae5bbb81700f96bb2763</citedby><cites>FETCH-LOGICAL-c669t-9026b529f1546191aa0ba7ad463069b6bce15866be5aaae5bbb81700f96bb2763</cites><orcidid>0000-0001-5692-6011</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8412350/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8412350/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793</link.rule.ids></links><search><contributor>Ansari, Mahmood ur Rahman</contributor><creatorcontrib>Ahmed, Fee Faysal</creatorcontrib><creatorcontrib>Hossen, Md. Imran</creatorcontrib><creatorcontrib>Sarkar, Md. Abdur Rauf</creatorcontrib><creatorcontrib>Konak, Jesmin Naher</creatorcontrib><creatorcontrib>Zohra, Fatema Tuz</creatorcontrib><creatorcontrib>Shoyeb, Md</creatorcontrib><creatorcontrib>Mondal, Samiran</creatorcontrib><title>Genome-wide identification of DCL, AGO and RDR gene families and their associated functional regulatory elements analyses in banana (Musa acuminata)</title><title>PloS one</title><description>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.</description><subject>Analysis</subject><subject>Banana</subject><subject>Bananas</subject><subject>Binding sites</subject><subject>Bioinformatics</subject><subject>Biology and life sciences</subject><subject>Biosynthesis</subject><subject>Cellular stress response</subject><subject>Corn</subject><subject>Crops</subject><subject>DNA-directed RNA polymerase</subject><subject>Epigenetics</subject><subject>Flowers & plants</subject><subject>Fruits</subject><subject>Fungi</subject><subject>Gene expression</subject><subject>Gene families</subject><subject>Gene regulation</subject><subject>Gene silencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic engineering</subject><subject>Genetic transcription</subject><subject>Genomes</subject><subject>Homogeneity</subject><subject>Mathematics</subject><subject>Metabolic pathways</subject><subject>MicroRNAs</subject><subject>Musa acuminata</subject><subject>Nucleotide sequence</subject><subject>Ontology</subject><subject>Phylogeny</subject><subject>Post-transcription</subject><subject>Proteins</subject><subject>Regulatory sequences</subject><subject>Research and Analysis Methods</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA polymerase</subject><subject>RNA-directed RNA polymerase</subject><subject>RNA-mediated interference</subject><subject>Transcription factors</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk2-r0zAUxoso3uvVbyAYEORecDNtmrR9I4xdnYPJYP55G07a0y0jTWbTqvsefmDTbcqd3BdS0qanv_OcnoecKHoe03HMsvjN1vWtBTPeOYtjmnCRZ-xBdBkXLBmJhLKHd_YX0RPvt5RylgvxOLpgaZqxLGWX0a8ZWtfg6IeukIRlO13rEjrtLHE1uZ0uXpPJbEnAVmR1uyJrtEhqaLTR6A_RboO6JeC9KzV0WJG6t-WQD4a0uO4NdK7dEzTYBPUhB8zeh2RtiQovFsj1x94DgbJvtIUObp5Gj2owHp-dnlfRl_fvPk8_jBbL2Xw6WYxKIYpuVNBEKJ4UdcxTERcxAFWQQZUKRkWhhCox5qFhhRwAkCul8jijtC6EUkkm2FX04qi7M87Lk6FeDl7ynFOaB2J-JCoHW7lrdQPtXjrQ8hBw7VpC2-nSoKwVQMKhzsI9LbiAUINDDlWWJGmWxEHr7alarxqsyuBGC-ZM9PyL1Ru5dt9lnsYJ4zQIXJ8EWvetR9_JRvsSjQGLrj_8d8GyXLCh1st_0Pu7O1FrCA1oW7tQtxxE5URkKc0Lzoay43uocFXY6DKcvlqH-FnCzVlCYDr82a2h917OP63-n11-PWdf3WE3CKbbeGf64bD5czA9gmXrvG-x_mtyTOUwPH_ckMPwyNPwsN-SPwsy</recordid><startdate>20210902</startdate><enddate>20210902</enddate><creator>Ahmed, Fee Faysal</creator><creator>Hossen, Md. 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Imran</au><au>Sarkar, Md. Abdur Rauf</au><au>Konak, Jesmin Naher</au><au>Zohra, Fatema Tuz</au><au>Shoyeb, Md</au><au>Mondal, Samiran</au><au>Ansari, Mahmood ur Rahman</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide identification of DCL, AGO and RDR gene families and their associated functional regulatory elements analyses in banana (Musa acuminata)</atitle><jtitle>PloS one</jtitle><date>2021-09-02</date><risdate>2021</risdate><volume>16</volume><issue>9</issue><spage>e0256873</spage><epage>e0256873</epage><pages>e0256873-e0256873</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>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.</abstract><cop>San Francisco</cop><pub>Public Library of Science</pub><pmid>34473743</pmid><doi>10.1371/journal.pone.0256873</doi><tpages>e0256873</tpages><orcidid>https://orcid.org/0000-0001-5692-6011</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | PloS one, 2021-09, Vol.16 (9), p.e0256873-e0256873 |
| issn | 1932-6203 1932-6203 |
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| source | DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Analysis Banana Bananas Binding sites Bioinformatics Biology and life sciences Biosynthesis Cellular stress response Corn Crops DNA-directed RNA polymerase Epigenetics Flowers & plants Fruits Fungi Gene expression Gene families Gene regulation Gene silencing Genes Genetic aspects Genetic engineering Genetic transcription Genomes Homogeneity Mathematics Metabolic pathways MicroRNAs Musa acuminata Nucleotide sequence Ontology Phylogeny Post-transcription Proteins Regulatory sequences Research and Analysis Methods Ribonucleic acid RNA RNA polymerase RNA-directed RNA polymerase RNA-mediated interference Transcription factors |
| title | Genome-wide identification of DCL, AGO and RDR gene families and their associated functional regulatory elements analyses in banana (Musa acuminata) |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-19T16%3A26%3A03IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genome-wide%20identification%20of%20DCL,%20AGO%20and%20RDR%20gene%20families%20and%20their%20associated%20functional%20regulatory%20elements%20analyses%20in%20banana%20(Musa%20acuminata)&rft.jtitle=PloS%20one&rft.au=Ahmed,%20Fee%20Faysal&rft.date=2021-09-02&rft.volume=16&rft.issue=9&rft.spage=e0256873&rft.epage=e0256873&rft.pages=e0256873-e0256873&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0256873&rft_dat=%3Cgale_plos_%3EA674089530%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2568585008&rft_id=info:pmid/34473743&rft_galeid=A674089530&rft_doaj_id=oai_doaj_org_article_fbaa25af7a254956abb25a8ad7224721&rfr_iscdi=true |