Hiseq novaseq pe150 platform

Genomic DNA was extracted with the SDS method (Lim et al., 2016 (link)). Sequencing libraries were generated using NEBNext^® Ultra™ DNA Library Prep Kit for Illumina (NEB, United States) referring to the manufacturer’s recommendations. Purified libraries (AMPure XP system) were analyzed for size distribution by Agilent 2100 Bioanalyzer and quantified using real-time PCR. Library sequencing was performed with Illumina HiSeq/NovaSeq PE150 platform at the Beijing Allwegene Technology Co., Ltd. Quality filtered paired reads were assembled by the SPAdes (v3.13.0) (Bankevich et al., 2012 (link)) software into a number of scaffolds. Finally, scaffolds with larger than 500 bp were selected for subsequent analysis.

L. brevis and E. faecium were cultured in liquid MRS medium under anaerobic conditions at 37 °C for 2 d. Next, the bacteria were collected and the genomic DNAs were extracted by using a FastPure Bacteria DNA Isolation Mini Kit (Vazyme, Nanjing, China). The genomic DNAs were used for genome sequencing (Allwegene, Beijing, China). The DNA purity and integrity were analyzed by agarose gel electrophoresis and quantified by Qubit 2.0 fluorometer. Subsequently, sequencing libraries were constructed using the NEBNext Ultra DNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA), and were further sequenced using Illumina HiSeq/NovaSeq PE150 platform. Finally, all good-quality reads were assembled into longer scaffolds using SPAdes (v3.13.0) software, and scaffolds larger than 500 bp were selected for subsequent functional analysis.

ASFV DNA was extracted from infected BMDM using the SDS method. The harvested DNA was detected by agarose gel electrophoresis and quantified using the Qubit 2.0 fluorometer. Briefly, 1 μg of viral DNA was fragmented by sonication to a size of 350 bp, and DNA fragments were further ligated with the full-length adaptor and bar codes. The appropriate size range of the adapter-ligated library was collected and subjected to normalization of the library concentration. Sequencing libraries were generated using the NEBNext Ultra DNA library prep kit for Illumina (NEB, USA), following the manufacturer’s recommendations. The whole genome of ASFV-Δ9L/Δ7R was sequenced using the Illumina HiSeq/NovaSeq PE 150 platform at Allwegene Technology Co., Ltd. (Beijing). All good-quality paired reads were assembled using SPAdes (version 3.13.0). Finally, scaffolds with more than 500 bp were selected for subsequent analysis.