Episonic 2000 sonication system

The retinas were dissected in PBS and suspended in 120 μL of RIPA buffer (per retina) containing proteinase inhibitor cocktail (Bimake, Shanghai, China, #B14002), protein phosphatase inhibitor A (Beyotime, Shanghai, China, #P1082) and protein phosphatase inhibitor C (Beyotime, Shanghai, China, #P1092). The total proteins were extracted sonication using an EpiSonic 2000 Sonication System (EPIGENTEK, Farmingdale, NY, USA) (Amplitude: 40%, 10 s on and 10 s off for 7 min in total). For Western blot (WB) analysis, it was performed as described previously with some modifications [14 (link)]. For each WB, 30–50 μg of total protein was used. The protein was separated by 12% SDS-PAGE and transferred to the PVDF membrane. The membrane was blocked by 5% milk in TBST for 1 h. After washing with TBST, the membrane was incubated with primary antibodies γH2Ax (Santa Cruz, Dallas, Texas, USA, sc-517348, 1:1000 dilution) and GAPDH (Proteintech, Rosemont, IL, USA, #60004-1-Ig, 1:2000 dilution). The secondary antibody was diluted in TBST (1:3000 dilution). After washing with TBST, enhanced chemiluminescence (ECL) detection was performed by using the Ultra sensitive ECL Chemiluminescence Kit (NCM Biotech, Suzhou, China, #P10300) according to the manufacturer’s specifications. The exposure and development of PVDF membrane were performed using Tanon 5200 (Tanon, Shanghai, China).

The extracted DNA from 51 P. larvae isolates from the SI dataset was quantified using the Qubit 1 × dsDNA High-Sensitivity Assay Kit with the Qubit 3.0 fluorometer (both Thermo Fisher Scientific) and subjected to agarose gel electrophoresis to confirm its integrity. DNA was fragmented using the EpiSonic 2000 Sonication System (EpiGentek) and DNA libraries were constructed using the NEBNext Ultra DNA Sample Prep Master Mix Kit (NEB). The paired-end (2 × 150 bp) sequencing was performed on the NovaSeq 6000 System (Illumina) to a minimum coverage of 200 ×.

The retinas were dissected in PBS and suspended in 150 μl of RIPA (per retina) containing proteinase inhibitor cocktail and protein phosphatase inhibitor as described before [26 (link)]. The total proteins were extracted sonication using an EpiSonic 2000 Sonication System (EPIGENTEK, Farmingdale, NY, USA) (Amplitude: 40%, 5 s on and 5 s off for 5 min in total). For WB analysis, 25–50 μg of total protein was used. The uncropped WB images are shown in Additional file 2: Fig. S2.