Henri van Kruistum presented at the Nanopore Community Meeting 2021 on “Allele-specific DNA methylation in the live-bearing fish Poeciliopsis gracilis.” Kruistum is a Ph.D. student at Wageningen University in the Netherlands. They are working on the Poecillidae live-bearing fishes. There are sever species and on the genomic level there is interest in learning about the sex-specific evolution and if it causes genomic imprinting. They extracted DNA from four individuals of Poecillopsis gracillis: the male parent, female parent, male offspring, and female offspring. They extracted DNA from muscle/fin using the QIAGEN Genomic-tip kit and then used the Circulomics SRE kit to select for HMW DNA. They sequenced on a single PromethION flow cell using the rapid barcoding kit (SQK-RBK004). The yield was 80 Gb of data which is about 20-30x coverage per individual. They then searched for allele-specific methylation. Next, the searched for regions with significant methylation, for example. Kruistum presented evidence of allele-specific methylation. They applied the test to all four individuals, finding from 1,499 to 9,949 regions with evidence for allele-specific methylation. Imprinting seems to happen in a subset of sites. They applied a set of rules to test the “intralocus sexual conflict hypothesis.” They found 184 genes that show “crosswise methylation in their vicinity.” They concluded that nanopore sequencing can be used to detect allele-specific methylation with high accuracy. They found allele-specific methylation is widespread in this fish. Interestingly, the genes around loci with evidence for crosswise methylation seem to code for brain-associated proteins!
