Genomic Analysis of γ-Hexachlorocyclohexane-Degrading Sphingopyxis lindanitolerans WS5A3p Strain in the Context of the Pangenome of Sphingopyxis

Abstract

<i>Sphingopyxis</i> inhabit diverse environmental niches, including marine, freshwater, oceans, soil and anthropogenic sites. The genus includes 20 phylogenetically distinct, valid species, but only a few with a sequenced genome. In this work, we analyzed the nearly complete genome of the newly described species, <i>Sphingopyxis</i><i>lindanitolerans</i>, and compared it to the other available <i>Sphingopyxis</i> genomes. The genome included 4.3 Mbp in total and consists of a circular chromosome, and two putative plasmids. Among the identified set of <i>lin</i> genes responsible for γ-hexachlorocyclohexane pesticide degradation, we discovered a gene coding for a new isoform of the LinA protein. The significant potential of this species in the remediation of contaminated soil is also correlated with the fact that its genome encodes a higher number of enzymes potentially involved in aromatic compound degradation than for most other <i>S</i><i>p</i><i>hingopyxis</i> strains. Additional analysis of 44 <i>Sphingopyxis</i> representatives provides insights into the pangenome of <i>Sphingopyxis</i> and revealed a core of 734 protein clusters and between four and 1667 unique proteins per genome.