An Effective Preprocessing Method for High-Quality Pan-Genome Analysis of Bacillus subtilis and Escherichia coli

Bacillus subtilis and Escherichia coli, as widely used microbial species, are of great significance in studying microbial community relationships, adaptive evolution in various niches, engineering cell factories that produce specific products, and designing genome reduction. The pan-genome analysis is an effective method for studying the characteristics and functions of genes among and within species. Many research directions and conclusions usually depend on accurate gene identification and reliable pan-genome results. However, there currently lack enough studies showing how to achieve high-quality pan-genome results between or within certain species. This chapter will take Bacillus subtilis as an example to introduce a stepwise manner for improving the quality of the pan-genome by gradually removing confounding strains step-by-step, and ultimately obtaining a reliable high-quality pan-genome landscape of Bacillus subtilis, which could be used as a quality control protocol in pan-genome analysis pipeline. Finally, we suggest further improving the pan-genome analysis results of Escherichia coli to prove the feasibility and credibility of the quality control protocol for obtaining high-quality pan-genome landscape.