DOI: 10.5061/dryad.g7t27
title: Data from: Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways

description: Background: Sphingobium spp. are efficient degraders of a wide range of
 chlorinated and aromatic hydrocarbons. In particular, strains which
 harbour the lin pathway genes mediating the degradation of
 hexachlorocyclohexane (HCH) isomers are of interest due to the widespread
 persistence of this contaminant. Here, we examined the evolution and
 diversification of the lin pathway under the selective pressure of HCH, by
 comparing the draft genomes of six newly-sequenced Sphingobium spp.
 (strains LL03, DS20, IP26, HDIPO4, P25 and RL3) isolated from HCH
 dumpsites, with three existing genomes (S. indicum B90A, S. japonicum
 UT26S and Sphingobium sp. SYK6). Results: Efficient HCH degraders
 phylogenetically clustered in a closely related group comprising of UT26S,
 B90A, HDIPO4 and IP26, where HDIPO4 and IP26 were classified as subspecies
 with ANI value &gt;98%. Less than 10% of the total gene content was
 shared among all nine strains, but among the eight HCH-associated strains,
 that is all except SYK6, the shared gene content jumped to nearly 25%.
 Genes associated with nitrogen stress response and two-component systems
 were found to be enriched. The strains also housed many xenobiotic
 degradation pathways other than HCH, despite the absence of these
 xenobiotics from isolation sources. Additionally, these strains, although
 non-motile, but posses flagellar assembly genes. While strains HDIPO4 and
 IP26 contained the complete set of lin genes, DS20 was entirely devoid of
 lin genes (except linKLMN) whereas, LL03, P25 and RL3 were identified as
 lin deficient strains, as they housed incomplete lin pathways. Further, in
 HDIPO4, linA was found as a hybrid of two natural variants i.e., linA1 and
 linA2 known for their different enantioselectivity. Conclusion: The
 bacteria isolated from HCH dumpsites provide a natural testing ground to
 study variations in the lin system and their effects on degradation
 efficacy. Further, the diversity in the lin gene sequences and copy
 number, their arrangement with respect to IS6100 and evidence for
 potential plasmid content elucidate possible evolutionary acquisition
 mechanisms for this pathway. This study further opens the horizon for
 selection of bacterial strains for inclusion in an HCH bioremediation
 consortium and suggests that HDIPO4, IP26 and B90A would be appropriate
 candidates for inclusion.
description: 16S rRNA gene sequences
 alignment16S rRNA gene sequences
 alignment for nine Sphingobium genomes under study16S9sphingos final
 uploaded.alnsingle copy genes
 final9genomes.fasta2single copy genes
 alignment of nine Sphingobium genomes under study. The amino acid
 sequences of 28 universally present single copy genes i.e., dnaA, frr,
 gyrB, infB, mnmA, nusA, pheS, rplB, rplC, rplM, rplS, rpoA, rpsB, rpsC,
 rpsH, rpsI, rpsJ, rpsS, trmD, tef, ychF, alaS, rplE, uvrC, lepA, rplI,
 rplP and rplD were used.tetra co-relation
 valuetetra co-relation value
 among the Sphingobium strains pairs.tetraallcorelationfinal.txtAverage Nucleotide Identity 9 GENOMESAverage Nucleotide Identity (ANI) pairwise comparison between nine Sphingobium spp.ANI9GENOMES.txt