Draft Genome Sequence of Sphingobium ummariense Strain RL-3, a Hexachlorocyclohexane-Degrading Bacterium

Abstract

Here, we report the draft genome sequence of the hexachlorocyclohexane (HCH)-degrading bacterium Sphingobium ummariense strain RL-3, which was isolated from the HCH dumpsite located in Lucknow, India (27°00′N and 81°09′E). The annotated draft genome sequence (4.75 Mb) of strain RL-3 consisted of 139 contigs, 4,645 coding sequences, and 65% G+C content.

GENOME ANNOUNCEMENT

Sphingobium ummariense strain RL-3 was isolated from the hexachlorocyclohexane (HCH) dumpsite created during the purification process of insecticidal γ-HCH isomer from technical HCH (1). The dumpsite is located at Ummari village in Lucknow, India (2). RL-3 has been documented to degrade all four major isomers of HCH, i.e., α-, β-, γ-, and δ-HCH, with a degradation rate comparable to that of Sphingobium indicum B90A, the representative avid degrader of HCH (3).

The genome of strain RL-3 was sequenced using Illumina HiSeq 2000 (2 kb paired-end library) and 454 GS FLX titanium platforms. The data were assembled (n = 4,706,077; 4.7 Mb) using ABySS assembler version 1.3.3 (4) set at a k-mer length of 57. The assembly generated 139 contigs (N₅₀ contigs, 363,277 bp), comprising 4,754,053 bp. The final assembly had 80-fold coverage, with the largest contig (GenBank accession number AUWY01000120) of 249,857 bp in size and mean G+C content of 65%.

The draft genome was annotated using RAST version 4.0 (5) and NCBI Prokaryotic Genome Annotation Pipeline (PGAP version 2.1; http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html). A total of 4,645 protein-coding sequences and 2,365 hypothetical proteins were predicted. Twelve rRNAs (4 each of 5S, 16S, and 23S), 56 tRNA genes, and 2 pseudogenes were predicted using PGAP.

Out of a battery of lin genes that degrade HCH isomers in sphingomonads (6), strain RL-3 was found to contain one copy each of linA, linB, and linX and three copies of linDER. Apart from housing the HCH-degradative lin genes, strain RL-3 also encodes a diverse array of proteins involved in the degradation of catechol, protocatechuate, and vanillate. Over 50 mobile genetic elements were identified, including IS6100, IS4, IS5, IS401, ISsp5, IS1247, ISSp1, and IS1412. RAST annotations revealed 399 subsystems. Sphingobium japonicum UT26S (score, 523), Sphingomonas sp. strain SKA58 (score, 484), and Sphingomonas wittichii RW1 (score, 424) were identified as the closest neighbors of strain RL-3. Four contigs (accession numbers AUWY01000011, AUWY01000023, AUWY01000029, and AUWY01000134) were assigned (i.e., BLASTN, e-10^-15) to the reference plasmid genotypes of the HCH degraders Sphingomonas sp. strain MM1 and Sphingobium japonicum UT26. All this clearly emphasized the role of horizontal gene transfer in shaping the genome of strain RL-3.

We now anticipate that combined analysis of our recent data on sphingomonad genomes (7–13) and metagenomes from the HCH dumpsite (14, 15) coupled with the genome sequence of strain RL-3 presented here may further help our ongoing efforts to elucidate the mechanism of acquisition and evolution of lin genes among sphingomonads under HCH pressure. The ability of strain RL-3 to degrade all the major HCH isomers, especially the recalcitrant β-HCH, and the presence of multiple copies of linDER as reported in this study further suggest the application of this strain in the development of a consortium for HCH bioremediation.

Nucleotide sequence accession numbers.

The genome sequence of Sphingobium ummariense RL-3 has been assigned the GenBank accession number AUWY00000000. The version described in this paper is version AUWY01000000.