Sequence quality and alignment
We assessed the quality of the sequences using FastQC
(Andrews 2010), trimming of adaptors and
low-quality reads was done using the RRBS default parameters (function:
–rrbs) in TrimGalore! (Krueger 2016).
Reads were aligned to the Kryptolebias marmoratus reference
genome (NCBI ASM164957v1) (Rhee et
al. 2017) prior to in-silico bisulphite conversion using Bismark
v0.17.0 (Krueger & Andrews 2011), which
was also used to perform cytosine methylation calls. We only considered
methylation within CpG context for the downstream analysis
(Feng et al. 2010) and included
CpGs with a minimum coverage of ≥10 reads in each sample across the 30
individuals sequenced. Individuals were grouped into generations
(parents/offspring) and environments (own/parental) (Table S2). Mapped
reads were processed and compared using the R package methylKit v. 1. 10
(Akalin et al. 2012). All analyses
were conducted on a local server running NEBC Bio-Linux 8.