EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics

Abstract The expanding scope and scale of next generation sequencing experiments in ecological plant epigenetics brings new challenges for computational analysis. Existing tools built for model data may not address the needs of users looking to apply these techniques to non-model species, particularly on a population or community level. Here we present a toolkit suitable for plant ecologists working with whole genome bisulfite sequencing; it includes pipelines for mapping, the calling of methylation values and differential methylation between groups, epigenome-wide association studies, and a novel implementation for both variant calling and discriminating between genetic and epigenetic variation.

[1]  N. Fernández-Pozo,et al.  The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline , 2021, Epigenomes.

[2]  P. Stadler,et al.  Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional bayesian approaches , 2021, BMC Genomics.

[3]  Donna M Bond,et al.  Estimating Global Methylation and Erasure Using Low-Coverage Whole-Genome Bisulfite Sequencing (WGBS ). , 2021, Methods in molecular biology.

[4]  Peter F. Stadler,et al.  Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis , 2020, bioRxiv.

[5]  Clemens Kreutz,et al.  A blind and independent benchmark study for detecting differentially methylated regions in plants , 2020, Bioinform..

[6]  Sven Nahnsen,et al.  The nf-core framework for community-curated bioinformatics pipelines , 2020, Nature Biotechnology.

[7]  Renan Valieris,et al.  Bioconda: sustainable and comprehensive software distribution for the life sciences , 2018, Nature Methods.

[8]  Vanessa Sochat,et al.  Singularity: Scientific containers for mobility of compute , 2017, PloS one.

[9]  Sonja J. Prohaska,et al.  Ecological plant epigenetics: Evidence from model and non-model species, and the way forward , 2017, bioRxiv.

[10]  Paolo Di Tommaso,et al.  Nextflow enables reproducible computational workflows , 2017, Nature Biotechnology.

[11]  Cheng Soon Ong,et al.  kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity , 2016, bioRxiv.

[12]  Chee Keong Kwoh,et al.  Gene, Environment and Methylation (GEM): a tool suite to efficiently navigate large scale epigenome wide association studies and integrate genotype and interaction between genotype and environment , 2016, BMC Bioinformatics.

[13]  Helene Kretzmer,et al.  metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data , 2016, Genome research.

[14]  Liqing Zhang,et al.  Objective and Comprehensive Evaluation of Bisulfite Short Read Mapping Tools , 2014, Adv. Bioinformatics.

[15]  Dirk Merkel,et al.  Docker: lightweight Linux containers for consistent development and deployment , 2014 .

[16]  Gabor T. Marth,et al.  Haplotype-based variant detection from short-read sequencing , 2012, 1207.3907.

[17]  P. Laird,et al.  Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data , 2012, Genome Biology.

[18]  M. Schatz,et al.  Current challenges in de novo plant genome sequencing and assembly , 2012, Genome Biology.

[19]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

[20]  I. Kovalchuk,et al.  Transgenerational response to stress in Arabidopsis thaliana , 2010, Plant signaling & behavior.

[21]  M. Pellegrini,et al.  Conservation and divergence of methylation patterning in plants and animals , 2010, Proceedings of the National Academy of Sciences.

[22]  M. Pigliucci,et al.  Experimental alteration of DNA methylation affects the phenotypic plasticity of ecologically relevant traits in Arabidopsis thaliana , 2010, Evolutionary Ecology.

[23]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[24]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[25]  S. Nelson,et al.  Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning , 2008, Nature.

[26]  L. E. McDonald,et al.  A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. , 1992, Proceedings of the National Academy of Sciences of the United States of America.