Genome Analysis of Oxytetracycline Production in Streptomyces rimosus

Project Overview

Welcome to the Genome Analysis project focused on uncovering the genetic mechanisms underlying oxytetracycline production in Streptomyces rimosus. The objective of the project is to conduct a comprehensive analysis of the S. rimosus genome to gain insights into the pathways and regulatory elements involved in antibiotic hyperproduction.

Objectives

1. Genome Assembly:

   • Perform de novo assembly of long Nanopore sequencing reads.
   • Refine the assembly using short Illumina reads to improve accuracy and completeness.

2. Transcriptomics and Differential Expression Analysis:

   • Conduct transcriptomic analysis to compare gene expression profiles between the hyperproducer S. rimosus strain and the wild-type strain.
   • Perform differential expression analysis to identify genes and pathways associated with antibiotic hyperproduction.

3. Genome Annotation and Synteny Evaluation:

   • Annotate the assembled genome to identify protein-coding genes, non-coding RNAs, and other functional elements.
   • Evaluate synteny with the wild-type genome to assess structural conservation and identify genomic variations.

4. Candidate Gene Identification:

   • Identify candidate genes and pathways potentially involved in oxytetracycline biosynthesis and regulation.

5. Documentation:

   • Document findings, methodologies, and analysis workflows for future reference and reproducibility.