DNA methylation analysis in plant gigagenomes: comparing two bisulfite sequencing techniques in Abies alba trees affected by dieback DOI Open Access
Isabel García-García, Belén Méndez‐Cea, Jose Luís Hórreo

et al.

Silvae genetica/Silvae Genetica, Journal Year: 2024, Volume and Issue: 73(1), P. 201 - 205

Published: Jan. 1, 2024

Abstract Phenotypic plasticity is a fundamental mechanism that enables plants to adapt shifting environmental conditions, such as those induced by climate change. Epigenetic modifications, notably DNA methylation, may play pivotal role in process. However, this field remains largely unstudied non-model organisms with large, complex genomes. Here, we focus on silver fir ( Abies alba ), more precisely natural population subjected stress, comparing the results obtained from two different bisulfite sequencing techniques study of epigenetic patterns its giga-genome. was extracted non-declining and declining A. individuals whole genome (WGBS) reduced representation (RRBS). General methylation levels each cytosine context (CpG, CHG CHH, where H stands for A, C, or T) were determined differentially methylated regions (DMRs) identified. WGBS sequenced higher amount cytosines, while RRBS had number CpG sites passing filtering conditions. Both showed high percentages contexts, but disagreed CHH sites, likely due having bias towards highly contexts. Differentially only identified using data could not be functionally annotated. In conclusion, successful assessment, neither nor produced desired outcome regarding identification DMRs. Thus, fragmented nature available reference genomes species large seems hinder attainment meaningful RRBS.

Language: Английский

DNA methylation analysis in plant gigagenomes: comparing two bisulfite sequencing techniques in Abies alba trees affected by dieback DOI Open Access
Isabel García-García, Belén Méndez‐Cea, Jose Luís Hórreo

et al.

Silvae genetica/Silvae Genetica, Journal Year: 2024, Volume and Issue: 73(1), P. 201 - 205

Published: Jan. 1, 2024

Abstract Phenotypic plasticity is a fundamental mechanism that enables plants to adapt shifting environmental conditions, such as those induced by climate change. Epigenetic modifications, notably DNA methylation, may play pivotal role in process. However, this field remains largely unstudied non-model organisms with large, complex genomes. Here, we focus on silver fir ( Abies alba ), more precisely natural population subjected stress, comparing the results obtained from two different bisulfite sequencing techniques study of epigenetic patterns its giga-genome. was extracted non-declining and declining A. individuals whole genome (WGBS) reduced representation (RRBS). General methylation levels each cytosine context (CpG, CHG CHH, where H stands for A, C, or T) were determined differentially methylated regions (DMRs) identified. WGBS sequenced higher amount cytosines, while RRBS had number CpG sites passing filtering conditions. Both showed high percentages contexts, but disagreed CHH sites, likely due having bias towards highly contexts. Differentially only identified using data could not be functionally annotated. In conclusion, successful assessment, neither nor produced desired outcome regarding identification DMRs. Thus, fragmented nature available reference genomes species large seems hinder attainment meaningful RRBS.

Language: Английский

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