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Whole-Genome Bisulfite Sequencing Reveals a Role for DNA Methylation in Variants from Callus Culture of Pineapple (Ananas comosus L.)

DNA methylation changes can occur in some loci during callus culture, resulting in somaclonal variations (SVs). In the present study, we applied whole genome bisulfite sequencing to analyze context-specific DNA methylation changes in the pineapple genome between the cutting seedings and 5 SV plants....

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Autores principales: Lin, Wenqiu, Xiao, Xi’ou, Zhang, Hongna, Li, Yunhe, Liu, Shenghui, Sun, Weisheng, Zhang, Xiumei, Wu, Qingsong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6895883/
https://www.ncbi.nlm.nih.gov/pubmed/31683898
http://dx.doi.org/10.3390/genes10110877
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author Lin, Wenqiu
Xiao, Xi’ou
Zhang, Hongna
Li, Yunhe
Liu, Shenghui
Sun, Weisheng
Zhang, Xiumei
Wu, Qingsong
author_facet Lin, Wenqiu
Xiao, Xi’ou
Zhang, Hongna
Li, Yunhe
Liu, Shenghui
Sun, Weisheng
Zhang, Xiumei
Wu, Qingsong
author_sort Lin, Wenqiu
collection PubMed
description DNA methylation changes can occur in some loci during callus culture, resulting in somaclonal variations (SVs). In the present study, we applied whole genome bisulfite sequencing to analyze context-specific DNA methylation changes in the pineapple genome between the cutting seedings and 5 SV plants. In general, SV plants exhibited methylation patterns analogous to those of cutting seedlings (CK). A total of 27.98% of the genomic cytosines of CK were methylcytosines, which was higher than that of 5 SV plants. Moreover, mCG and mCHG was hypermethylated, whereas mCHH was hypomethylated among the 5 SV plants genomic when compared with the CK. Most of the variation of DNA methylation was distributed in gene bodies, thus suggesting that phenotypic differences are probably perturbed by genes methylated from callus culture. In addition, the methylated genes were highly enriched for the Gene Ontology (GO) categories of binding and catalytic activity, cell part and organelle, cellular process, abiotic stimulus, and DNA modification. These results suggest that methylation mediates these pathways in the callus culture of pineapple. The results also suggested that the callus culture induced DNA methylation may result in the SV.
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spelling pubmed-68958832019-12-24 Whole-Genome Bisulfite Sequencing Reveals a Role for DNA Methylation in Variants from Callus Culture of Pineapple (Ananas comosus L.) Lin, Wenqiu Xiao, Xi’ou Zhang, Hongna Li, Yunhe Liu, Shenghui Sun, Weisheng Zhang, Xiumei Wu, Qingsong Genes (Basel) Article DNA methylation changes can occur in some loci during callus culture, resulting in somaclonal variations (SVs). In the present study, we applied whole genome bisulfite sequencing to analyze context-specific DNA methylation changes in the pineapple genome between the cutting seedings and 5 SV plants. In general, SV plants exhibited methylation patterns analogous to those of cutting seedlings (CK). A total of 27.98% of the genomic cytosines of CK were methylcytosines, which was higher than that of 5 SV plants. Moreover, mCG and mCHG was hypermethylated, whereas mCHH was hypomethylated among the 5 SV plants genomic when compared with the CK. Most of the variation of DNA methylation was distributed in gene bodies, thus suggesting that phenotypic differences are probably perturbed by genes methylated from callus culture. In addition, the methylated genes were highly enriched for the Gene Ontology (GO) categories of binding and catalytic activity, cell part and organelle, cellular process, abiotic stimulus, and DNA modification. These results suggest that methylation mediates these pathways in the callus culture of pineapple. The results also suggested that the callus culture induced DNA methylation may result in the SV. MDPI 2019-11-01 /pmc/articles/PMC6895883/ /pubmed/31683898 http://dx.doi.org/10.3390/genes10110877 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Lin, Wenqiu
Xiao, Xi’ou
Zhang, Hongna
Li, Yunhe
Liu, Shenghui
Sun, Weisheng
Zhang, Xiumei
Wu, Qingsong
Whole-Genome Bisulfite Sequencing Reveals a Role for DNA Methylation in Variants from Callus Culture of Pineapple (Ananas comosus L.)
title Whole-Genome Bisulfite Sequencing Reveals a Role for DNA Methylation in Variants from Callus Culture of Pineapple (Ananas comosus L.)
title_full Whole-Genome Bisulfite Sequencing Reveals a Role for DNA Methylation in Variants from Callus Culture of Pineapple (Ananas comosus L.)
title_fullStr Whole-Genome Bisulfite Sequencing Reveals a Role for DNA Methylation in Variants from Callus Culture of Pineapple (Ananas comosus L.)
title_full_unstemmed Whole-Genome Bisulfite Sequencing Reveals a Role for DNA Methylation in Variants from Callus Culture of Pineapple (Ananas comosus L.)
title_short Whole-Genome Bisulfite Sequencing Reveals a Role for DNA Methylation in Variants from Callus Culture of Pineapple (Ananas comosus L.)
title_sort whole-genome bisulfite sequencing reveals a role for dna methylation in variants from callus culture of pineapple (ananas comosus l.)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6895883/
https://www.ncbi.nlm.nih.gov/pubmed/31683898
http://dx.doi.org/10.3390/genes10110877
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