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Mounger JM, van Riemsdijk I, Boquete MT, Wagemaker CAM, Fatma S, Robertson MH, Voors SA, Oberstaller J, Gawehns F, Hanley TC, Grosse I, Verhoeven KJF, Sotka EE, Gehring CA, Hughes AR, Lewis DB, Schmid MW, Richards CL. Genetic and Epigenetic Differentiation Across Intertidal Gradients in the Foundation Plant Spartina alterniflora. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.868826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ecological genomics approaches have informed us about the structure of genetic diversity in natural populations that might underlie patterns in trait variation. However, we still know surprisingly little about the mechanisms that permit organisms to adapt to variable environmental conditions. The salt marsh foundation plant Spartina alterniflora exhibits a dramatic range in phenotype that is associated with a pronounced intertidal environmental gradient across a narrow spatial scale. Both genetic and non-genetic molecular mechanisms might underlie this phenotypic variation. To investigate both, we used epigenotyping-by-sequencing (epiGBS) to evaluate the make-up of natural populations across the intertidal environmental gradient. Based on recent findings, we expected that both DNA sequence and DNA methylation diversity would be explained by source population and habitat within populations. However, we predicted that epigenetic variation might be more strongly associated with habitat since similar epigenetic modifications could be rapidly elicited across different genetic backgrounds by similar environmental conditions. Overall, with PERMANOVA we found that population of origin explained a significant amount of the genetic (8.6%) and epigenetic (3.2%) variance. In addition, we found that a small but significant amount of genetic and epigenetic variance (<1%) was explained by habitat within populations. The interaction of population and habitat explained an additional 2.9% of the genetic variance and 1.4% of the epigenetic variance. By examining genetic and epigenetic variation within the same fragments (variation in close-cis), we found that population explained epigenetic variation in 9.2% of 8,960 tested loci, even after accounting for differences in the DNA sequence of the fragment. Habitat alone explained very little (<0.1%) of the variation in these close-cis comparisons, but the interaction of population and habitat explained 2.1% of the epigenetic variation in these loci. Using multiple matrix regression with randomization (MMRR) we found that phenotypic differences in natural populations were correlated with epigenetic and environmental differences even when accounting for genetic differences. Our results support the contention that sequence variation explains most of the variation in DNA methylation, but we have provided evidence that DNA methylation distinctly contributes to plant responses in natural populations.
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Gawehns F, Postuma M, Van Antro M, Nunn A, Sepers B, Fatma S, van Gurp TP, Wagemaker NCAM, Mateman AC, Milanovic-Ivanovic S, Grosse I, van Oers K, Vergeer P, Verhoeven KJF. epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing. Mol Ecol Resour 2022; 22:2087-2104. [PMID: 35178872 PMCID: PMC9311447 DOI: 10.1111/1755-0998.13597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/04/2022] [Accepted: 02/09/2022] [Indexed: 11/28/2022]
Abstract
Several reduced‐representation bisulfite sequencing methods have been developed in recent years to determine cytosine methylation de novo in nonmodel species. Here, we present epiGBS2, a laboratory protocol based on epiGBS with a revised and user‐friendly bioinformatics pipeline for a wide range of species with or without a reference genome. epiGBS2 is cost‐ and time‐efficient and the computational workflow is designed in a user‐friendly and reproducible manner. The library protocol allows a flexible choice of restriction enzymes and a double digest. The bioinformatics pipeline was integrated in the snakemake workflow management system, which makes the pipeline easy to execute and modular, and parameter settings for important computational steps flexible. We implemented bismark for alignment and methylation analysis and we preprocessed alignment files by double masking to enable single nucleotide polymorphism calling with freebayes (epifreebayes). The performance of several critical steps in epiGBS2 was evaluated against baseline data sets from Arabidopsis thaliana and great tit (Parus major), which confirmed its overall good performance. We provide a detailed description of the laboratory protocol and an extensive manual of the bioinformatics pipeline, which is publicly accessible on github (https://github.com/nioo‐knaw/epiGBS2) and zenodo (https://doi.org/10.5281/zenodo.4764652).
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Affiliation(s)
- Fleur Gawehns
- Netherlands Institute of Ecology (NIOO-KNAW), Bioinformatics Unit, Wageningen, the Netherlands
| | - Maarten Postuma
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, the Netherlands.,Wageningen University & Research (WUR), Plant Ecology and Nature Conservation Group, Wageningen, the Netherlands
| | - Morgane Van Antro
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, the Netherlands
| | - Adam Nunn
- ecSeq Bioinformatics GmbH, Leipzig, Germany.,Universität Leipzig, Institut für Informatik, Leipzig, Germany
| | - Bernice Sepers
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Animal Ecology, Wageningen, the Netherlands.,Wageningen University & Research (WUR), Behavioural Ecology Group, Wageningen, the Netherlands
| | - Samar Fatma
- Martin Luther University Halle-Wittenberg, Institute of Computer Science, Halle, Germany
| | - Thomas P van Gurp
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, the Netherlands
| | | | - A Christa Mateman
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Animal Ecology, Wageningen, the Netherlands
| | - Slavica Milanovic-Ivanovic
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, the Netherlands
| | - Ivo Grosse
- Martin Luther University Halle-Wittenberg, Institute of Computer Science, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Kees van Oers
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Animal Ecology, Wageningen, the Netherlands.,Wageningen University & Research (WUR), Behavioural Ecology Group, Wageningen, the Netherlands
| | - Philippine Vergeer
- Wageningen University & Research (WUR), Plant Ecology and Nature Conservation Group, Wageningen, the Netherlands
| | - Koen J F Verhoeven
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, the Netherlands
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McNew SM, Boquete MT, Espinoza‐Ulloa S, Andres JA, Wagemaker NCAM, Knutie SA, Richards CL, Clayton DH. Epigenetic effects of parasites and pesticides on captive and wild nestling birds. Ecol Evol 2021; 11:7713-7729. [PMID: 34188846 PMCID: PMC8216931 DOI: 10.1002/ece3.7606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
Anthropogenic changes to the environment challenge animal populations to adapt to new conditions and unique threats. While the study of adaptation has focused on genetic variation, epigenetic mechanisms may also be important. DNA methylation is sensitive to environmental stressors, such as parasites and pesticides, which may affect gene expression and phenotype. We studied the effects of an invasive ectoparasite, Philornis downsi, on DNA methylation of Galápagos mockingbirds (Mimus parvulus). We used the insecticide permethrin to manipulate P. downsi presence in nests of free-living mockingbirds and tested for effects of parasitism on nestling mockingbirds using epiGBS, a reduced-representation bisulfite sequencing (RRBS) approach. To distinguish the confounding effects of insecticide exposure, we conducted a matching experiment exposing captive nestling zebra finches (Taeniopygia guttata) to permethrin. We used zebra finches because they were the closest model organism to mockingbirds that we could breed in controlled conditions. We identified a limited number of differentially methylated cytosines (DMCs) in parasitized versus nonparasitized mockingbirds, but the number was not more than expected by chance. In contrast, we saw clear effects of permethrin on methylation in captive zebra finches. DMCs in zebra finches paralleled documented effects of permethrin exposure on vertebrate cellular signaling and endocrine function. Our results from captive birds indicate a role for epigenetic processes in mediating sublethal nontarget effects of pyrethroid exposure in vertebrates. Environmental conditions in the field were more variable than the laboratory, which may have made effects of both parasitism and permethrin harder to detect in mockingbirds. RRBS approaches such as epiGBS may be a cost-effective way to characterize genome-wide methylation profiles. However, our results indicate that ecological epigenetic studies in natural populations should consider the number of cytosines interrogated and the depth of sequencing in order to have adequate power to detect small and variable effects.
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Affiliation(s)
- Sabrina M. McNew
- School of Biological SciencesUniversity of UtahSalt Lake CityUTUSA
- Cornell Lab of OrnithologyCornell UniversityIthacaNYUSA
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
| | - M. Teresa Boquete
- Department of Integrative BiologyUniversity of South FloridaTampaFLUSA
- Department of Evolutionary EcologyEstación Biológica de DoñanaCSICSevillaSpain
| | - Sebastian Espinoza‐Ulloa
- Department of BiologyUniversity of SaskatchewanSaskatoonSKCanada
- Facultad de MedicinaPontifica Universidad Católica del EcuadorQuitoEcuador
| | - Jose A. Andres
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
- Department of BiologyUniversity of SaskatchewanSaskatoonSKCanada
| | | | - Sarah A. Knutie
- School of Biological SciencesUniversity of UtahSalt Lake CityUTUSA
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsCTUSA
- Institute for Systems GenomicsUniversity of ConnecticutStorrsCTUSA
| | | | - Dale H. Clayton
- School of Biological SciencesUniversity of UtahSalt Lake CityUTUSA
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Werner O, Prudencio ÁS, de la Cruz-Martínez E, Nieto-Lugilde M, Martínez-Gómez P, Ros RM. A Cost Reduced Variant of Epi-Genotyping by Sequencing for Studying DNA Methylation in Non-model Organisms. FRONTIERS IN PLANT SCIENCE 2020; 11:694. [PMID: 32547585 PMCID: PMC7270828 DOI: 10.3389/fpls.2020.00694] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 05/01/2020] [Indexed: 05/27/2023]
Abstract
Reference-free reduced representation bisulfite sequencing uses enzymatic digestion for reducing genome complexity and allows detection of markers to study DNA methylation of a high number of individuals in natural populations of non-model organisms. Current methods like epiGBS enquire the use of a higher number of methylated DNA oligos with a significant cost (especially for small labs and first pilot studies). In this paper, we present a modification of this epiGBS protocol that requires the use of only one hemimethylated P2 (common) adapter, which is combined with unmethylated barcoded adapters. The unmethylated cytosines of one chain of the barcoded adapter are replaced by methylated cytosines using nick translation with methylated cytosines in dNTP solution. The basic version of our technique uses only one restriction enzyme, and as a result, genomic fragments are integrated into two orientations with respect to the adapter sequences. Comparing the sequences of two chain orientations makes it possible to reconstruct the original sequence before bisulfite treatment with the help of standard software and newly developed software written in C and described here. We provide a proof of concept via data obtained from almond (Prunus dulcis). Example data and a detailed description of the complete software pipeline starting from the raw reads up until the final differentially methylated cytosines are given in Supplementary Material making this technique accessible to non-expert computer users. The adapter design showed in this paper should allow the use of a two restriction enzyme approach with minor changes in software parameters.
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Affiliation(s)
- Olaf Werner
- Laboratory of Molecular Systematics, Phylogeography and Conservation in Bryophytes, Department of Plant Biology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - Ángela S. Prudencio
- Laboratory of Fruit Tree Breeding, Department of Plant Breeding, CEBAS-CSIC, Murcia, Spain
| | - Elena de la Cruz-Martínez
- Laboratory of Molecular Systematics, Phylogeography and Conservation in Bryophytes, Department of Plant Biology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - Marta Nieto-Lugilde
- Laboratory of Molecular Systematics, Phylogeography and Conservation in Bryophytes, Department of Plant Biology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - Pedro Martínez-Gómez
- Laboratory of Fruit Tree Breeding, Department of Plant Breeding, CEBAS-CSIC, Murcia, Spain
| | - Rosa M. Ros
- Laboratory of Molecular Systematics, Phylogeography and Conservation in Bryophytes, Department of Plant Biology, Faculty of Biology, University of Murcia, Murcia, Spain
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