Hybrid Genome Assembly of sp. E602 and Bioinformatic Analysis Characterized a New Plasmid-Borne Operon Under Positive Selection.

Our previous study identified a new β-galactosidase in sp. E602. To further understand the lactose metabolism in this strain, genome assembly was conducted by using a strategy combining Illumina and PacBio sequencing technology. The whole genome of sp. E602 includes a 4.8 Mb chromosome and a 326 kb large plasmid. A total of 4,739 genes, including 4,543 protein-coding genes, 25 rRNAs, 82 tRNAs and 7 other ncRNAs genes were annotated. The plasmid was the largest one characterized in genus by far, and it contained a number of genes and pathways responsible for lactose metabolism and regulation. Moreover, a new plasmid-borne operon that lacked a typical β-galactoside transacetylase () gene was identified in the strain. Phylogenetic analysis showed that the genes and in the operon were under positive selection, indicating the adaptation of lactose metabolism to the environment in sp. E602. Our current study demonstrated that the hybrid genome assembly using Illumina and PacBio sequencing technologies, as well as the metabolic pathway analysis, provided a useful strategy for better understanding of the evolution of undiscovered microbial species or strains.