Genome Sequence of Novosphingobium lindaniclasticum LE124T, Isolated from a Hexachlorocyclohexane Dumpsite

Novosphingobium lindaniclasticum LE124T is a hexachlorocyclohexane (HCH)-degrading bacterium isolated from a high-dosage-point HCH dumpsite (450 mg HCH/g soil) located in Lucknow, India (27°00′N and 81°09′E). Here, we present the annotated draft genome sequence of strain LE124T, which has an estimated size of 4.86 Mb and is comprised of 4,566 coding sequences.

degrade and/or assimilate a wide range of xenobiotic compounds, including mono-and polycyclic aromatic compounds, chlorinated compounds, and pesticides (1). Members of this taxon are also known to be efficient degraders of hexachlorocyclohexane (HCH) isomers (1)(2)(3). In conformity with our primary objective, i.e., to elucidate the pangenomic variations across HCH-degrading genotypes, we have already sequenced two sphingomonads (4,5). Both of their genomes represent species belonging to the genus Sphingobium (4,5). We have sequenced the genome of yet another sphingomonad, belonging to the genus Novosphingobium, i.e., N. lindaniclasticum strain LE124 T , isolated from an HCH dumpsite (6).
The HCH-degrading lin genes (13,14) were found scattered throughout the draft genome assembly. A single copy of linA (dehydrochlorinase) was represented in the sequenced genome. Additionally, linH, linK, linL, linM, and two copies of linG were also present. In contrast to Sphingobium indicum B90A (4), linB (haloalkane dehalogenase) and linDER were absent from the genome of strain LE124 T ; this was also confirmed by PCR amplification. We have recently reported that HCH selection pressure is responsible for bringing lin genes through horizontal gene transfer (HGT) into sphingomonads (15), and these findings reflect that strain LE124 T has yet to acquire these genes through HGT.
Interestingly, the draft genome of strain LE124 T also showed the presence of a benzoate-degrading gene cluster with the presence of 4-hydroxybenzoate 3-monooxygenase, benzoate transporter proteins, and genes for the chloroaromatic catechol branch of the ␤-ketoadipate pathway. Additionally, genes encoding ortho-halobenzoate 1,2-dioxygenase alpha-and beta-intracellular serine protease (ISP) protein (ohbA, ohbB), known to be involved in xenobiotic and benzoate degradation, were also found. The genetic compendium required to resolve the intergenus-level genetic divergence of the lin genes and degradation pathway can be analyzed by doing comparative analyses of genomes of sphingomonads that have now been sequenced.
Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. ATHL00000000. The version described in this paper is version ATHL01000000.

ACKNOWLEDGMENTS
The work was supported by grants from the Department of Biotechnology (DBT), Government of India, under project no. BT/PR3301/BCE/8/875/ 11, the University of Delhi/Department of Science and Technology Promotion of University Research and Scientific Excellence du DST-PURSE grant and the National Bureau of Agriculturally Important Microorganisms (NBAIM) AMASS/2006 -07/NBAIM/CIR, and the All India Network Project Soil Biodiversity-Biofertilizer (ICAR). A.S., N.N., N.S., and R.K. gratefully acknowledge the University Grants Commission (UGC) and the Council for Scientific and Industrial Research (CSIR), New Delhi, for providing research fellowships. This paper was finalized during the renewed visit under the Alexander von Humbolt fellowship (at the University of Freiburg, Germany) awarded to R.L.