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Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora

1
Department of Computer Science, Federal University of Technology-Parana, Cornelio Procopio 86300-000, Brazil
2
Group of Genomics and Transcriptomes in Plants, São Paulo State University, Rio Claro, Sao Paulo 13506-900, Brazil
3
Institut de Recherche pour le Développement (IRD), University Montpellier, 34394 Montpellier, France
*
Author to whom correspondence should be addressed.
Non-Coding RNA 2020, 6(3), 39; https://doi.org/10.3390/ncrna6030039
Received: 12 August 2020 / Revised: 2 September 2020 / Accepted: 8 September 2020 / Published: 11 September 2020
Coffea canephora grains 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 the C. canephora genome. This study aimed to provide a curated characterization of six ncRNA classes in the Coffea canephora genome. 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 the C. canephora genome. 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. View Full-Text
Keywords: coffee; plant ncRNAs; curated annotation; genome-wide; bioinformatics; in silico coffee; plant ncRNAs; curated annotation; genome-wide; bioinformatics; in silico
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MDPI and ACS Style

Lemos, S.M.C.; Fonçatti, L.F.C.; Guyot, R.; Paschoal, A.R.; Domingues, D.S. Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora. Non-Coding RNA 2020, 6, 39. https://doi.org/10.3390/ncrna6030039

AMA Style

Lemos SMC, Fonçatti LFC, Guyot R, Paschoal AR, Domingues DS. Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora. Non-Coding RNA. 2020; 6(3):39. https://doi.org/10.3390/ncrna6030039

Chicago/Turabian Style

Lemos, Samara M.C.; Fonçatti, Luiz F.C.; Guyot, Romain; Paschoal, Alexandre R.; Domingues, Douglas S. 2020. "Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora" Non-Coding RNA 6, no. 3: 39. https://doi.org/10.3390/ncrna6030039

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