Identification of plasmidic sequences in draft genomes from Streptomyces and Micrococcus

Abstract

Plasmids are circular or linear extrachromosomal DNA molecules that replicate autonomously. The bacterial genome sequencing has generated a large number of "draft" genomes where the presence of plasmids is not detailed. However, there are several tools that allow predicting plasmid sequences based on raw sequencing data, and can contribute to the identification of new plasmids. This identification would bring new data to understand the diversity and evolution of plasmids, particularly in poorly studied genera.In this work we study genomes of two genera of Actinobacteria of sanitary and environmental importance: Streptomycesand Micrococcus. For each genome, contigs were generated by assembling reads obtained from the SRA-NCBI database. Four independent homology tools were used for the prediction of plasmids: PlasFlow, cBar, Recycler,and plasmidSPAdes. In addition, we face the predictions with the PLSDB online plasmid repository, which includes an extensive set of complete plasmids from the NCBI database, in order to check the presence of novel sequences.The assembled genomes turned out fragmented, in general. Even so, the prediction methods used were able to identify potentially plasmidic sequences. From 46 Streptomycesstrains analyzed, 446 sequences were predicted that would correspond to plasmids or fragments thereof, including 120 that would correspond to circular elements. These sequences on average had a length of 6385 bp and a GC content of 67.5%. On the other hand, 130 plasmidic sequences were identified in 9 strains of Micrococcus, of which 78 could correspond to circular plasmids. In this case, the sequences were on average 2909 bp in length with a GC content of 59.4%.This analysis allowed us to identify potentially plasmid sequences for the two genus of Actinobacteria studied, which sets a precedent with relevant data that can be validated in subsequent studies.