Multidimensional insights into the biodiversity of Streptomyces in soils of China: a preliminary study
Description
Processed genomes data of 136 Streptomyces isolates in this study: The genomes of these strains isolated from 19 locations across 14 provinces in China, were assembled by Unicycler v0.5.0 from quality-filtered Illumina next-generation sequencing data.
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We collected soil samples from 19 sites across China, covering a distance of over 2000 km in both north-south and east-west directions. Initially, 1 gram of soil was diluted in sterilized Ultrapure water at a ratio of 1:10 (w/v) and vigorously mixed for 10 minutes at room temperature. Following a 7-minute heating step in a 65°C water bath, the soil extract was further diluted at ratios of 1:10^3 or 1:10^4 (v/v) in sterilized Ultrapure water. Then, The soil extract was plated onto Marine Agar 2216E solid medium supplemented with 20 mg/liter Nalidixic acid. Marine Agar 2216E medium consists of 1 g yeast extract, 5 g peptone, 0.01 g FePO4, 15 g agar, and 1 L of filtered artificial seawater. Plates were then incubated at 28°C for 4 days and single actinomycete colonies were selected from the plates. Subsequently, we incubated the cells with lysozyme (1.5μL in 25μL) at 37°C overnight, to degrade cell walls. We then extracted high-quality genomic DNA using the MasterPure™ Complete DNA & RNA Purification Kit. For the isolated Streptomyces, we prepared whole-genome libraries with the Vazyme TruePrep DNA Library Prep Kit V2 (Vazyme, Cat. No.: TD501-01) for Illumina, following a recent miniaturized protocol developed by our lab. Illumina PE150 sequencing was done at Berry Genomics, Beijing, and Novogene, Beijing. Finally, for the 136 isolates with genomes successfully sequenced , we filtered raw reads with fastp v0.23.4 for quality control, and subsequently performed assembly using Unicycler v0.5.0.