Enzymatic Methyl sequencing of gills and mantle before and after POMS infection in Pacific oyster Magallana gigas GESTINOV 2021
Oyster Sampling and Production Five F1 oyster populations (#15) were produced from progenitors collected from four French oyster production basins in 2022, except population SC18 (#5), maintained under biosecure conditions since 2007. The F1 populations were grown for one year in tanks and fed phytoplankton, with exposure to POMS strictly controlled.  POMS Infection and Viral Suspension Two oyster populations (F14 and NSI) were used as donors to generate OsHV-1 Var viral suspensions. Donors were injected with the virus, then cohabited with 100 tagged recipient oysters from the five F1 populations. Infection progression was monitored every two hours, categorizing oysters as susceptible or resistant based on their ability to close their valves. Tissue samples were collected pre- and post-infection and stored for further analysis.  Survival and DNA Analysis Survival analysis of both donors and recipients was performed using Kaplan-Meier and Cox proportional hazard models. Genomic DNA was extracted from the gills and mantle, and the viral load of OsHV-1 Var was quantified using qPCR. DNA quality was assessed via nanodrop and Qubit measurements, followed by gel electrophoresis.  EM-seq and Bioinformatics Analysis EM-seq libraries were prepared and sequenced, with raw reads processed using FastQC, TrimGalore!, and Bismark for alignment and methylation calling. Differential methylation regions (DMRs) were identified using 'DSS' and assessed for overlap with gene body regions of the M. gigas genome. Conversion efficiency was checked with bacteriophage lambda spike-in controls.