DNA methylation differences between stick insect ecotypes

Epigenetic mechanisms, such as DNA methylation, can influence gene regulation and affect phenotypic variation, raising the possibility that they contribute to ecological adaptation. To begin to address this issue requires high-resolution sequencing studies of natural populations to pinpoint epigenetic regions of potential ecological and evolutionary significance. However, such studies are still relatively uncommon, especially in insects, and are mainly restricted to a few model organisms. Here, we characterize patterns of DNA methylation for natural populations of Timema cristinae adapted to two host plant species (i.e., ecotypes). By integrating results from sequencing of whole transcriptomes, genomes, and methylomes, we investigate whether environmental, host, and genetic differences of these stick insects are associated with methylation levels of cytosine nucleotides in CpG context. We report an overall genome-wide methylation level for T. cristinae of ~14%, being enriched in gene bo..., Timema cristinae individuals from the selected populations were collected on the same date (25th April 2017) in the Californian spring using sweep nets, and kept in plastic containers at room temperature. Individuals were digitally photographed the following day under standard conditions, flash frozen using liquid nitrogen, and preserved at -80OC temperature. All procedures were performed to assure the methylation status was not considerably affected by variation in sampling conditions.Half of each specimen’s body (cut longitudinally) was used to isolate its genomic DNA using DNeasy Blood and Tissue Kits (Qiagen). We included non-methylated cl857 Sam7 Lambda phage DNA (Promega Corporation) a spike-in in each sample (1% of the final volume). We submitted genomic DNA of one T. cristinae sample (individual 17_0015, ‘NO_BS.WGBS’ sample) for BS-seq, and as a control for the BS-treatment (i.e., sequenced without sodium-bisulfite treatment). The sodium-bisulfite treatment and high-throughput s...,

2018Methylation_info_spreadsheet_standard.csv: Table with information regarding samples, locations, climatic information, and bisulfite conversion.

BSseq_pipeline: The series of scripts below were used in the pipeline to process bifulfite reads

1.1_parallel_trimmomatic.sh: Runs Trimmomatic to filter raw bisulfite reads
1.2_sampling24k.sh: Samples a number of reads to reduce batch effects on downstream analyses
1.3_bismark.mapping.to.phage.sh: Runs Bismark to map the bisulfite reads to the lambda phage (GenBank J02459)
1.4_bismark.maping.to.tcristinae.sh: Runs Bismark on unmapped reads to the phage to T. cristinae genome (v1.3c2)
1.5_parallel_bismark_methylation_extractor.sh: Runs Bismark function 'bismark_methylation_extractor' to call methylation into cytosine reports tables
1.6_remove.CT.GA.polymorphisms.pl: This script removes the SNPs listed on the file 'variants.raw.CT.GA.bial.noindel.qs20.cov0.whole.genomes.and.radseq.loci' and remove from the cytosine reports
variants.raw.CT...., # GENERAL INFORMATION

#### 1 .Title of Dataset: Data from: DNA methylation differences between stick insect ecotypes.

#### 2\. Author Information

##### Corresponding Investigator 1

Name: Dr. Clarissa F. de Carvalho
Institution: Universidade Federal de São Paulo (UNIFESP), São Paulo, SP 04021-001, Brazil
Email: [e-mail]

##### Corresponding Investigator 2

Name: Dr. Patrik Nosil
Institution: CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier 34293, France
Email: [e-mail]

##### Co-investigator 1

Name: Dr. Romain Villoutreix
Institution: CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier 34293, France

##### Co-investigator 2

Name: Pr. Zachariah Gompert
Institution: Department of Biology, Utah State University, Logan, UT 84321, USA

##### Co-investigator 3

Name: Pr. Jon Slate
Institution: School of Biosciences, University of Sheffield; Sheffield, S10 2TN, UK

#####...