Performance of Mapping Approaches for Whole-Genome Bisulfite Sequencing Data in Crop Plants

Grehl, Claudius; Wagner, M.; Lemnian, Ioana; Glaser, Bruno; Große, Ivo

doi:10.3389/fpls.2020.00176

Cited by 19 publications

(25 citation statements)

References 45 publications

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“…Concerning the skin microbiome, 85.89%, 85.35% and 54.9% of reads were mapped for RIMS-seq, DNA-seq and bisulfite-seq respectively. The low mapping rate for bisulfite-seq is a known challenge as the reduction of the alphabet to A, G, T generates ambiguous mapping ( 24 ).…”

Section: Resultsmentioning

confidence: 99%

Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes

Baum

Lin

Fomenkov

et al. 2021

Nucleic Acids Research

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DNA methylation is widespread amongst eukaryotes and prokaryotes to modulate gene expression and confer viral resistance. 5-Methylcytosine (m5C) methylation has been described in genomes of a large fraction of bacterial species as part of restriction-modification systems, each composed of a methyltransferase and cognate restriction enzyme. Methylases are site-specific and target sequences vary across organisms. High-throughput methods, such as bisulfite-sequencing can identify m5C at base resolution but require specialized library preparations and single molecule, real-time (SMRT) sequencing usually misses m5C. Here, we present a new method called RIMS-seq (rapid identification of methylase specificity) to simultaneously sequence bacterial genomes and determine m5C methylase specificities using a simple experimental protocol that closely resembles the DNA-seq protocol for Illumina. Importantly, the resulting sequencing quality is identical to DNA-seq, enabling RIMS-seq to substitute standard sequencing of bacterial genomes. Applied to bacteria and synthetic mixed communities, RIMS-seq reveals new methylase specificities, supporting routine study of m5C methylation while sequencing new genomes.

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Section: Resultsmentioning

confidence: 99%

Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes

Baum

Lin

Fomenkov

et al. 2021

Nucleic Acids Research

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show abstract

Section: Resultsmentioning

confidence: 99%

Rapid Identification of Methylase Specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes

Baum

Yu-Cheng-Lin

Fomenkov

et al. 2021

Preprint

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DNA methylation is widespread amongst eukaryotes and prokaryotes to modulate gene expression and confer viral resistance. 5-methylcytosine (m5C) methylation has been described in genomes of a large fraction of bacterial species as part of restriction-modification systems, each composed of a methyltransferase and cognate restriction enzyme. Methylases are site-specific and target sequences vary across organisms. High-throughput methods, such as bisulfite-sequencing can identify m5C at base resolution but require specialized library preparations and Single Molecule, Real-Time (SMRT) Sequencing usually misses m5C. Here, we present a new method called RIMS-seq (Rapid Identification of Methylase Specificity) to simultaneously sequence bacterial genomes and determine m5C methylase specificities using a simple experimental protocol that closely resembles the DNA-seq protocol for Illumina. Importantly, the resulting sequencing quality is identical to DNA-seq, enabling RIMS-seq to substitute standard sequencing of bacterial genomes. Applied to bacteria and synthetic mixed communities, RIMS-seq reveals new methylase specificities, supporting routine study of m5C methylation while sequencing new genomes.

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“…The second step was the alignment of the WGBS reads on the latest available genome sequence ( ) [ 3 ] by using BISMARK (version 0.16.3, [ 77 ] and Bowtie 2 tools (version 2.1.0; [ 78 ]). Due to sequenced genome quality (2090 scaffolds in version 2, N residues in intergenic sequences), BSMAP version 2.74 [ 79 , 80 ] was used to measure DNA methylation levels at each cytosine site on a reduced representation consisting on gene models (34,363) including 5 Kbp flanking regions. All data were processed in R [ 81 ].…”

Section: Materials and Methodsmentioning

confidence: 99%

Developmental Methylome of the Medicinal Plant Catharanthus roseus Unravels the Tissue-Specific Control of the Monoterpene Indole Alkaloid Pathway by DNA Methylation

Bernonville

Maury

Delaunay

et al. 2020

IJMS

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Catharanthus roseus produces a wide spectrum of monoterpene indole alkaloids (MIAs). MIA biosynthesis requires a tightly coordinated pathway involving more than 30 enzymatic steps that are spatio-temporally and environmentally regulated so that some MIAs specifically accumulate in restricted plant parts. The first regulatory layer involves a complex network of transcription factors from the basic Helix Loop Helix (bHLH) or AP2 families. In the present manuscript, we investigated whether an additional epigenetic layer could control the organ-, developmental- and environmental-specificity of MIA accumulation. We used Whole-Genome Bisulfite Sequencing (WGBS) together with RNA-seq to identify differentially methylated and expressed genes among nine samples reflecting different plant organs and experimental conditions. Tissue specific gene expression was associated with specific methylation signatures depending on cytosine contexts and gene parts. Some genes encoding key enzymatic steps from the MIA pathway were found to be simultaneously differentially expressed and methylated in agreement with the corresponding MIA accumulation. In addition, we found that transcription factors were strikingly concerned by DNA methylation variations. Altogether, our integrative analysis supports an epigenetic regulation of specialized metabolisms in plants and more likely targeting transcription factors which in turn may control the expression of enzyme-encoding genes.

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Performance of Mapping Approaches for Whole-Genome Bisulfite Sequencing Data in Crop Plants

Cited by 19 publications

References 45 publications

Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes

Rapid identification of methylase specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes

Rapid Identification of Methylase Specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes

Developmental Methylome of the Medicinal Plant Catharanthus roseus Unravels the Tissue-Specific Control of the Monoterpene Indole Alkaloid Pathway by DNA Methylation

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