AUTHOR=Xia Yu , Wei Zhi-Yuan , He Rui , Li Jia-Huan , Wang Zhi-Xin , Huo Jun-Da , Chen Jian-Huan 

TITLE=Hybrid de novo Genome Assembly of Erwinia sp. E602 and Bioinformatic Analysis Characterized a New Plasmid-Borne lac Operon Under Positive Selection

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.783195

DOI=10.3389/fmicb.2021.783195

ISSN=1664-302X

ABSTRACT=<p>Our previous study identified a new β-galactosidase in <italic>Erwinia</italic> sp. E602. To further understand the lactose metabolism in this strain, <italic>de novo</italic> genome assembly was conducted by using a strategy combining Illumina and PacBio sequencing technology. The whole genome of <italic>Erwinia</italic> 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 <italic>Erwinia</italic> by far, and it contained a number of genes and pathways responsible for lactose metabolism and regulation. Moreover, a new plasmid-borne <italic>lac</italic> operon that lacked a typical β-galactoside transacetylase (<italic>lacA</italic>) gene was identified in the strain. Phylogenetic analysis showed that the genes <italic>lacY</italic> and <italic>lacZ</italic> in the operon were under positive selection, indicating the adaptation of lactose metabolism to the environment in <italic>Erwinia</italic> sp. E602. Our current study demonstrated that the hybrid <italic>de novo</italic> 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.</p>