Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba

Abstract The 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...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Sergio Alan Cervantes-Pérez, Lenin Yong-Villalobos, Nathalia M. V. Florez-Zapata, Araceli Oropeza-Aburto, Félix Rico-Reséndiz, Itzel Amasende-Morales, Tianying Lan, Octavio Martínez, Jean Philippe Vielle-Calzada, Victor A. Albert, Luis Herrera-Estrella
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/93464d22550e4bb09bd87baba028fe91
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:93464d22550e4bb09bd87baba028fe91
record_format	dspace
spelling	oai:doaj.org-article:93464d22550e4bb09bd87baba028fe912021-12-02T17:06:31ZAtypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba10.1038/s41598-021-95054-y2045-2322https://doaj.org/article/93464d22550e4bb09bd87baba028fe912021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-95054-yhttps://doaj.org/toc/2045-2322Abstract The 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.Sergio Alan Cervantes-PérezLenin Yong-VillalobosNathalia M. V. Florez-ZapataAraceli Oropeza-AburtoFélix Rico-ReséndizItzel Amasende-MoralesTianying LanOctavio MartínezJean Philippe Vielle-CalzadaVictor A. AlbertLuis Herrera-EstrellaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sergio Alan Cervantes-Pérez Lenin Yong-Villalobos Nathalia M. V. Florez-Zapata Araceli Oropeza-Aburto Félix Rico-Reséndiz Itzel Amasende-Morales Tianying Lan Octavio Martínez Jean Philippe Vielle-Calzada Victor A. Albert Luis Herrera-Estrella Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba
description	Abstract The 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.
format	article
author	Sergio Alan Cervantes-Pérez Lenin Yong-Villalobos Nathalia M. V. Florez-Zapata Araceli Oropeza-Aburto Félix Rico-Reséndiz Itzel Amasende-Morales Tianying Lan Octavio Martínez Jean Philippe Vielle-Calzada Victor A. Albert Luis Herrera-Estrella
author_facet	Sergio Alan Cervantes-Pérez Lenin Yong-Villalobos Nathalia M. V. Florez-Zapata Araceli Oropeza-Aburto Félix Rico-Reséndiz Itzel Amasende-Morales Tianying Lan Octavio Martínez Jean Philippe Vielle-Calzada Victor A. Albert Luis Herrera-Estrella
author_sort	Sergio Alan Cervantes-Pérez
title	Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba
title_short	Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba
title_full	Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba
title_fullStr	Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba
title_full_unstemmed	Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba
title_sort	atypical dna methylation, srna-size distribution, and female gametogenesis in utricularia gibba
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/93464d22550e4bb09bd87baba028fe91
work_keys_str_mv	AT sergioalancervantesperez atypicaldnamethylationsrnasizedistributionandfemalegametogenesisinutriculariagibba AT leninyongvillalobos atypicaldnamethylationsrnasizedistributionandfemalegametogenesisinutriculariagibba AT nathaliamvflorezzapata atypicaldnamethylationsrnasizedistributionandfemalegametogenesisinutriculariagibba AT aracelioropezaaburto atypicaldnamethylationsrnasizedistributionandfemalegametogenesisinutriculariagibba AT felixricoresendiz atypicaldnamethylationsrnasizedistributionandfemalegametogenesisinutriculariagibba AT itzelamasendemorales atypicaldnamethylationsrnasizedistributionandfemalegametogenesisinutriculariagibba AT tianyinglan atypicaldnamethylationsrnasizedistributionandfemalegametogenesisinutriculariagibba AT octaviomartinez atypicaldnamethylationsrnasizedistributionandfemalegametogenesisinutriculariagibba AT jeanphilippeviellecalzada atypicaldnamethylationsrnasizedistributionandfemalegametogenesisinutriculariagibba AT victoraalbert atypicaldnamethylationsrnasizedistributionandfemalegametogenesisinutriculariagibba AT luisherreraestrella atypicaldnamethylationsrnasizedistributionandfemalegametogenesisinutriculariagibba
_version_	1718381567835897856

Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba

Ejemplares similares