Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/153775
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dc.contributor.authorCervantes-Pérez, Sergio Alanen_US
dc.contributor.authorYong-Villalobos, Leninen_US
dc.contributor.authorFlorez-Zapata, Nathalia M. V.en_US
dc.contributor.authorOropeza-Aburto, Aracelien_US
dc.contributor.authorRico-Reséndiz, Félixen_US
dc.contributor.authorAmasende-Morales, Itzelen_US
dc.contributor.authorLan, Tianyingen_US
dc.contributor.authorMartínez, Octavioen_US
dc.contributor.authorVielle-Calzada, Jean Philippeen_US
dc.contributor.authorAlbert, Victor A.en_US
dc.contributor.authorHerrera-Estrella, Luisen_US
dc.date.accessioned2021-12-27T06:59:23Z-
dc.date.available2021-12-27T06:59:23Z-
dc.date.issued2021-
dc.identifier.citationCervantes-Pérez, S. A., Yong-Villalobos, L., Florez-Zapata, N. M. V., Oropeza-Aburto, A., Rico-Reséndiz, F., Amasende-Morales, I., Lan, T., Martínez, O., Vielle-Calzada, J. P., Albert, V. A. & Herrera-Estrella, L. (2021). Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba. Scientific Reports, 11(1), 15725-. https://dx.doi.org/10.1038/s41598-021-95054-yen_US
dc.identifier.issn2045-2322en_US
dc.identifier.urihttps://hdl.handle.net/10356/153775-
dc.description.abstractThe most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide DNA methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding RNAs and the impact on DNA methylation in small plant genomes with reduced noncoding regions. Because of the small length of intergenic regions in the compact genome of the carnivorous plant Utricularia gibba, we investigated its repertoire of noncoding RNA and DNA methylation landscape. Here, we report that, compared to other angiosperms, U. gibba has an unusual distribution of small RNAs and reduced global DNA methylation levels. DNA methylation was determined using a novel strategy based on long-read DNA sequencing with the Pacific Bioscience platform and confirmed by whole-genome bisulfite sequencing. Moreover, some key genes involved in the RdDM pathway may not represented by compensatory paralogs or comprise truncated proteins, for example, U. gibba DICER-LIKE 3 (DCL3), encoding a DICER endonuclease that produces 24-nt small-interfering RNAs, has lost key domains required for complete function. Our results unveil that a truncated DCL3 correlates with a decreased proportion of 24-nt small-interfering RNAs, low DNA methylation levels, and developmental abnormalities during female gametogenesis in U. gibba. Alterations in female gametogenesis are reminiscent of RdDM mutant phenotypes in Arabidopsis thaliana. It would be interesting to further study the biological implications of the DCL3 truncation in U. gibba, as it could represent an initial step in the evolution of RdDM pathway in compact genomes.en_US
dc.language.isoenen_US
dc.relation.ispartofScientific Reportsen_US
dc.rights© 2021 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.en_US
dc.subjectScience::Biological sciencesen_US
dc.titleAtypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibbaen_US
dc.typeJournal Articleen
dc.contributor.schoolSchool of Biological Sciencesen_US
dc.identifier.doi10.1038/s41598-021-95054-y-
dc.description.versionPublished versionen_US
dc.identifier.pmid34344949-
dc.identifier.scopus2-s2.0-85111992283-
dc.identifier.issue1en_US
dc.identifier.volume11en_US
dc.identifier.spage15725en_US
dc.subject.keywordsTransposable Elementsen_US
dc.subject.keywordsNoncoding Transcriptionen_US
dc.description.acknowledgementThe authors thank G. Alejo-Jacuinde, B. Pérez-Sánchez and Q. Ortiz-Vasquez for help collecting plants and fowering specimens. Special thanks to R. Purbojati and S. Schuster for providing us the PacBio raw sequencing data. We thank J. Cervantes-Luevano for informatic support, Luis Delaye for evolutionary analysis advice and Koribinian Schneeberger for provided us syntenic dataset generating by SyRI. Authors acknowledge Dr. T. Markow for critical review of this manuscript. S.A.C.-P., I.A.-M. and F.R.-R are the recipients of a graduate scholarship from Conacyt. Tis work was supported in part by a Senior Scholar grant from the Howard Hughes Medical Institute and a Basic Science grant from CONACytT Mexico to L.H.-E.en_US
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