**4. Conclusions**

In this work, we analyzed the genome of *Sphingopyxis lindanitolerans* WS5A3p derived from long-term pesticide-contaminated soil and capable of degrading xenobiotics. As predicted by its nucleotide sequence, WS5A3p degrades γ-HCH and may play an important role in the soil microbial community contaminated with this pesticide. This ability has been acquired by the process of horizontal gene transfer of *lin* genes. We also identified a new variant of LinA type-1 protein, namely LinA type-1a. This is the first well-documented communication of horizontal gene transfer of lindane degrading machinery to *Sphingopyxis* sp. Furthermore, a core protein set present in all sequenced representatives of this genus was described, as well as the unique protein sets identified for each genome, providing data for further investigations.

**Supplementary Materials:** The following are available online at http://www.mdpi.com/2073-4425/10/9/688/s1, Figure S1: γ-HCH degrading abilities of *Sphingopyxis lindanitolerans* WS5A3p, Figure S2: Accumulation plots of the *Sphingopyxis pangenome*, Figure S3: Correlation between minimal phylogenetic distance to the closest neighbour and number of unique protein clusters in the genome, Figure S4: Identification of enzymes potentially involved

in aromatic compound degradation, Figure S5: Organization of lin genes (blue) and IS6100 (green) identified on *Sphingopyxis lindanitolerans* WS5A3p plasmids, Table S1: General statistics of the *Sphingopyxis lindanitolerans* WS5A3p genome, Table S2: General information about 44 *Sphingopyxis* genomes used in this work, Table S3: Genome coordinates and locus tags of *lin* genes identified in WS5A3p genome sequence.

**Author Contributions:** L.L., A.S. conceived and directed the studies. DNA isolation, DNA libraries preparation, genome sequencing, and bioinformatics analysis were performed by M.A.K. with the support of L.L. The manuscript was written by M.A.K. and L.L., consulted and corrected by A.S., A.D. Funding for this work was provided by L.L. and A.D. All authors read and approved the final manuscript.

**Funding:** This work was supported by the European Union's European Regional Development Fund through the Innovative Economy Operational Program, 2007–2013 (project support agreemen<sup>t</sup> POIG.01.01.02-14-054/09-00).

**Conflicts of Interest:** The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
