Design and validation of a PCR screen for γ-butyrolactone-like regulatory systems in Streptomyces

• Main Author: Valentin Waschulin
• Format: Article in Journal/Newspaper
• Language: unknown
• Published: 2023
• Subjects: Antarctic; Antarc*
• Online Access: https://zenodo.org/record/8272490; https://doi.org/10.5281/zenodo.8272490

This archive contains data related to the article "Design and validation of a PCR screen for γ-butyrolactone-like regulatory systems in Streptomyces" in Access Microbiology. downloaded_genomes.txt: The list of the 2040 Streptomyces genomes downloaded by ncbi-genome-download and used in this analysis analysis_data_and_script.zip: cblaster output data search_ScbA_ScbR_600.txt - cblaster output file extracted_clusters_cblaster - gbk files of all clusters obtained using cblaster extract all_sequences.fasta - amino acid sequences of all proteins in the extracted clusters R markdown "Analysis script.rmd", which also contains some instructions for some bash operations using seqkit and grep intermediary files generated: ScbA_divergent_genes.txt - IDs of ScbA genes in divergent pair ScbR_divergent_genes.txt - IDs of ScbR genes in divergent pair ScbA_divergent.fasta - sequences of ScbA genes in divergent pair ScbR_divergent.fasta - sequences of ScbR genes in divergent pair ETxRx_containing_ScbA_list.txt - list of IDs of ScbA homologs containing ETxRx motif in divergent pair YFHx_containing_ScbR_list.txt - list of IDs of ScbR homologs containing YFHx motif in divergent pair ETxRx_containing_gbk_list.txt - list of extracted cluster genbank files containing ScbA homolog with ETxRx motif in divergent pair ETxRx_and_YFHx_containing_gbk_list.txt - list of extracted cluster genbank files containing ScbA homolog with ETxRx motif and ScbR homolog with YFHx motif in divergent pair, i.e. co-occurrence of motifs Sanger sequences (ending in .seq) of the PCR reactions The genomes of three newly sequenced Antarctic Streptomyces (illumina and nanopore hybrid assembly using unicycler).