PRJNA680461
Viral metagenomics unveiled extensive communications of viruses within giant pandas and their associated organisms in the same ecosystem
To investigate the virome of different types of samples of giant pandas and their associated organisms at Chengdu Research Base of Giant Panda Breeding, China, our study collected specimens from 2015 to 2020.The samples were collected by disposable materials and re-suspended in ten volumes of phosphate-buffered saline and vigorously vortexed for 5 min. The supernatant was then collected after centrifugation. 500 uL of supernatant was filtered through a 0.45-micron filter (Millipore) to remove eukaryotic- and bacterial cell-sized particles. The filtrate enriched in viral particles was treated with DNase and RNase to digest unprotected nucleic acid for 60 min. Remaining total nucleic acid was then isolated using QIAamp Viral RNA Mini Kit according to manufacturer's protocol. The libraries were then constructed using Nextera XT DNA Sample Preparation Kit (Illumina) and sequenced using the Illumina MiSeq or NovaSeq 6,000 with 250 bases paired ends with dual barcoding for each pool. For bioinformatics analysis, the generated 250 bp paired-end reads were debarcoded using vendor software from Illumina.