Analyses of Methylomes Derived from Meso-American Common Bean (Phaseolus vulgaris L.) Using MeDIP-Seq and Whole Genome Sodium Bisulfite-Sequencing.

Mollee Crampton,Venkateswara R Sripathi,Venu Kalavacharla,Khwaja Hossain

doi:10.3389/fpls.2016.00447

Mollee Crampton, Venkateswara R Sripathi + Show 2 more

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https://doi.org/10.3389/fpls.2016.00447

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Abstract

Common bean (Phaseolus vulgaris L.) is economically important for its high protein, fiber, and micronutrient contents, with a relatively small genome size of ∼587 Mb. Common bean is genetically diverse with two major gene pools, Meso-American and Andean. The phenotypic variability within common bean is partly attributed to the genetic diversity and epigenetic changes that are largely influenced by environmental factors. It is well established that an important epigenetic regulator of gene expression is DNA methylation. Here, we present results generated from two high-throughput sequencing technologies, methylated DNA immunoprecipitation-sequencing (MeDIP-seq) and whole genome bisulfite-sequencing (BS-Seq). Our analyses revealed that this Meso-American common bean displays similar methylation patterns as other previously published plant methylomes, with CG ∼50%, CHG ∼30%, and CHH ∼2.7% methylation, however, these differ from the common bean reference methylome of Andean origin. We identified higher CG methylation levels in both promoter and genic regions than CHG and CHH contexts. Moreover, we found relatively higher CG methylation levels in genes than in promoters. Conversely, the CHG and CHH methylation levels were highest in promoters than in genes. This is the first genome-wide DNA methylation profiling study in a Meso-American common bean cultivar (“Sierra”) using NGS approaches. Our long-term goal is to generate genome-wide epigenomic maps in common bean focusing on chromatin accessibility, histone modifications, and DNA methylation.

Highlights

Common bean (Phaseolus vulgaris) is the most widely consumed legume, as it is high in protein, fiber, and essential nutrients, while low in glycemic index (Mitchell et al, 2009)
Though several regulatory mechanisms have been identified, DNA methylation, chromatin remodeling, histone acetylation, histone methylation, and gene silencing are of paramount importance
To understand the DNA methylation levels in the three contexts (CG, CHG, and CHH), we constructed two MeDIP-Seq libraries and one BS-Seq library using tissue collected from three sets of bean plants from the Meso-American common bean cultivar, Sierra, grown at three different times which were pooled and sequenced on the Illumina/HiSeq2500 platform

Summary

Introduction

Common bean (Phaseolus vulgaris) is the most widely consumed legume, as it is high in protein, fiber, and essential nutrients, while low in glycemic index (Mitchell et al, 2009). Common bean is consumed widely across the world due to its affordability and health benefits (Gepts et al, 2008). Food legumes such as common bean are an inherently rich source of vitamins and minerals, including B vitamins ( B1/thiamine and B9/folic acid), iron, zinc, calcium and magnesium (Akond et al, 2011; Beebe et al, 2013; Câmara et al, 2013; Petry et al, 2015). In order to effectively modulate genetic architecture and develop micronutrient-enriched crops, understanding the genes and their regulatory mechanisms involved in physiological processes is important. Though several regulatory mechanisms have been identified, DNA methylation, chromatin remodeling, histone acetylation, histone methylation, and gene silencing are of paramount importance

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