Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.3390/ncrna6030039 http://hdl.handle.net/11449/208869 |
Resumo: | Coffea canephoragrains are highly traded commodities worldwide. Non-coding RNAs (ncRNAs) are transcriptional products involved in genome regulation, environmental responses, and plant development. There is not an extensive genome-wide analysis that uncovers the ncRNA portion of theC. canephoragenome. This study aimed to provide a curated characterization of six ncRNA classes in theCoffea canephoragenome. For this purpose, we employed a combination of similarity-based and structural-based computational approaches with stringent curation. Candidate ncRNA loci had expression evidence analyzed using sRNA-seq libraries. We identified 7455 ncRNA loci (6976 with transcriptional evidence) in theC. canephoragenome. This comprised of total 115 snRNAs, 1031 snoRNAs, 92 miRNA precursors, 602 tRNAs, 72 rRNAs, and 5064 lncRNAs. For miRNAs, we identified 159 putative high-confidence targets. This study was the most extensive genomic catalog of curated ncRNAs in the Coffea genus. This data might help elaborating more robust hypotheses in future comparative genomic studies as well as gene regulation and genome dynamics, helping to understand the molecular basis of domestication, environmental adaptation, resistance to pests and diseases, and coffee productivity. |
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Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephoracoffeeplant ncRNAscurated annotationgenome-widebioinformaticsin silicoCoffea canephoragrains are highly traded commodities worldwide. Non-coding RNAs (ncRNAs) are transcriptional products involved in genome regulation, environmental responses, and plant development. There is not an extensive genome-wide analysis that uncovers the ncRNA portion of theC. canephoragenome. This study aimed to provide a curated characterization of six ncRNA classes in theCoffea canephoragenome. For this purpose, we employed a combination of similarity-based and structural-based computational approaches with stringent curation. Candidate ncRNA loci had expression evidence analyzed using sRNA-seq libraries. We identified 7455 ncRNA loci (6976 with transcriptional evidence) in theC. canephoragenome. This comprised of total 115 snRNAs, 1031 snoRNAs, 92 miRNA precursors, 602 tRNAs, 72 rRNAs, and 5064 lncRNAs. For miRNAs, we identified 159 putative high-confidence targets. This study was the most extensive genomic catalog of curated ncRNAs in the Coffea genus. This data might help elaborating more robust hypotheses in future comparative genomic studies as well as gene regulation and genome dynamics, helping to understand the molecular basis of domestication, environmental adaptation, resistance to pests and diseases, and coffee productivity.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Univ Tecnol Fed Parana, Dept Comp Sci, BR-86300000 Cornelio Procopio, BrazilSao Paulo State Univ, Grp Genom & Transcriptomes Plants, BR-13506900 Rio Claro, SP, BrazilUniv Montpellier, Inst Rech Dev IRD, F-34394 Montpellier, FranceSao Paulo State Univ, Grp Genom & Transcriptomes Plants, BR-13506900 Rio Claro, SP, BrazilCAPES: 001MdpiUniv Tecnol Fed ParanaUniversidade Estadual Paulista (Unesp)Univ MontpellierLemos, Samara M. C. [UNESP]Foncatti, Luiz F. C.Guyot, RomainPaschoal, Alexandre R.Domingues, Douglas S. [UNESP]2021-06-25T11:23:13Z2021-06-25T11:23:13Z2020-09-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article15http://dx.doi.org/10.3390/ncrna6030039Non-coding Rna. Basel: Mdpi, v. 6, n. 3, 15 p., 2020.http://hdl.handle.net/11449/20886910.3390/ncrna6030039WOS:000578912600001Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengNon-coding Rnainfo:eu-repo/semantics/openAccess2021-10-23T19:23:15Zoai:repositorio.unesp.br:11449/208869Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462021-10-23T19:23:15Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora |
title |
Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora |
spellingShingle |
Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora Lemos, Samara M. C. [UNESP] coffee plant ncRNAs curated annotation genome-wide bioinformatics in silico |
title_short |
Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora |
title_full |
Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora |
title_fullStr |
Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora |
title_full_unstemmed |
Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora |
title_sort |
Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora |
author |
Lemos, Samara M. C. [UNESP] |
author_facet |
Lemos, Samara M. C. [UNESP] Foncatti, Luiz F. C. Guyot, Romain Paschoal, Alexandre R. Domingues, Douglas S. [UNESP] |
author_role |
author |
author2 |
Foncatti, Luiz F. C. Guyot, Romain Paschoal, Alexandre R. Domingues, Douglas S. [UNESP] |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
Univ Tecnol Fed Parana Universidade Estadual Paulista (Unesp) Univ Montpellier |
dc.contributor.author.fl_str_mv |
Lemos, Samara M. C. [UNESP] Foncatti, Luiz F. C. Guyot, Romain Paschoal, Alexandre R. Domingues, Douglas S. [UNESP] |
dc.subject.por.fl_str_mv |
coffee plant ncRNAs curated annotation genome-wide bioinformatics in silico |
topic |
coffee plant ncRNAs curated annotation genome-wide bioinformatics in silico |
description |
Coffea canephoragrains are highly traded commodities worldwide. Non-coding RNAs (ncRNAs) are transcriptional products involved in genome regulation, environmental responses, and plant development. There is not an extensive genome-wide analysis that uncovers the ncRNA portion of theC. canephoragenome. This study aimed to provide a curated characterization of six ncRNA classes in theCoffea canephoragenome. For this purpose, we employed a combination of similarity-based and structural-based computational approaches with stringent curation. Candidate ncRNA loci had expression evidence analyzed using sRNA-seq libraries. We identified 7455 ncRNA loci (6976 with transcriptional evidence) in theC. canephoragenome. This comprised of total 115 snRNAs, 1031 snoRNAs, 92 miRNA precursors, 602 tRNAs, 72 rRNAs, and 5064 lncRNAs. For miRNAs, we identified 159 putative high-confidence targets. This study was the most extensive genomic catalog of curated ncRNAs in the Coffea genus. This data might help elaborating more robust hypotheses in future comparative genomic studies as well as gene regulation and genome dynamics, helping to understand the molecular basis of domestication, environmental adaptation, resistance to pests and diseases, and coffee productivity. |
publishDate |
2020 |
dc.date.none.fl_str_mv |
2020-09-01 2021-06-25T11:23:13Z 2021-06-25T11:23:13Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.3390/ncrna6030039 Non-coding Rna. Basel: Mdpi, v. 6, n. 3, 15 p., 2020. http://hdl.handle.net/11449/208869 10.3390/ncrna6030039 WOS:000578912600001 |
url |
http://dx.doi.org/10.3390/ncrna6030039 http://hdl.handle.net/11449/208869 |
identifier_str_mv |
Non-coding Rna. Basel: Mdpi, v. 6, n. 3, 15 p., 2020. 10.3390/ncrna6030039 WOS:000578912600001 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Non-coding Rna |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
15 |
dc.publisher.none.fl_str_mv |
Mdpi |
publisher.none.fl_str_mv |
Mdpi |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1803046237567451136 |