DOI: 10.5061/dryad.t4624
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 mediate 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
 taxonomically clustered in a closly 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 but 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, the strains, while non-motile, each
 possessed flagellar assembly genes. While strains HDIPO4 and IP26
 contained the complete set of lin genes, DS20 was entirely devoid of lin
 genes (except linKLMN) and 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 having 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 efficiacy.
 Further, the diversity in the lin gene sequences and copy number, their
 arrangement with respect to IS6100, and evidence for potential plasmid
 content elucidates possible evolutionary acquisition mechanisms for this
 pathway. This study further opens the horizon for selection of bacterial
 for inclusion in an HCH bioremediation consortium, and suggests that
 HDIPO4, IP26 and B90A would be appropriate candidates for inclusion.
description: AUDA00000000Sphingobium chinhatense IP26ATDO00000000Sphingobium sp. HDIPO4AUWY00000000Sphingobium ummariense RL3ATHO00000000Sphingobium quisquilarium P25ATDP00000000Sphingobium lactosutens DS20ATIB00000000Sphingobium baderi LL0316S rRNA gene sequence of 9 SphingobiumAligned sequences of 16S rRNA gene of nine Sphingobium strains included in this comparative study16S9sphingos final uploaded.alnsingle copy genesSingle 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 are retrieved from these genomes, followed by their concatenation and alignment.tetraallcorelationfinalTetra scores were calculated for these nine Sphingobium genomes and these values were used to generate the matrix followed by its dendrogram construction.Average Nucleotide Identity score 9 GENOMESThis value for a genome was calculated in comparison with the another genome using Kostanditis ANI script. Then the matrix was generated, followed by its dendrogram construction.ANI9GENOMES.txt