Abstract
Here, we report the complete genome sequence of a γ-hexachlorocyclohexane (γ-HCH)-degrading bacterium, Sphingobium sp. strain MI1205. The genome of MI1205 consists of two chromosomes and four plasmids with sizes of 33 to 292 kb. All the lin genes for γ-HCH metabolism are dispersed on the four plasmids.
GENOME ANNOUNCEMENT
γ-Hexachlorocylohexane (γ-HCH; also called γ-BHC or lindane) is a chlorinated organic insecticide that has caused serious environmental problems due to its toxicity and long persistence in upland soils (1, 2). In this study, we determined the complete genome sequence of a γ-HCH-degrading bacterium, Sphingobium sp. strain MI1205, which was isolated from HCH-contaminated soil in Miyagi prefecture, Japan (3), and has been deposited in the Japan Collection of Microorganisms (JCM) under the accession number JCM 17233.
The MI1205 genome was sequenced using the 454 GS-FLX+ (Roche) system and the HiSeq 2000 (Illumina) mate-pair sequencing system, which was operated by Eurofins Genomics Inc., and 479,052 reads and 1,881,908 reads, respectively, were obtained. These reads were assembled using Newbler (Roche) to generate initial draft sequence data consisting of 16 scaffolds and 64 contigs. The finishing was facilitated using GenoFinisher and AceFileViewer (4). The complete genome sequence was annotated by the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP), and the resulting annotation was subjected to manual curation using the annotation support tool of GenomeMatcher (5). By referencing annotation data obtained from the Microbial Genome Annotation Pipeline (http://www.migap.org), we corrected the start codon positions and added several genes that were missing in the PGAAP annotation.
The MI1205 genome consists of two circular chromosomes, Chr1 (3,351,250 bp, 62.3% G+C, 3,278 open reading frames [ORFs]) and Chr2 (567,154 bp, 62.4% G+C, 516 ORFs), and four circular plasmids, pMI1 (292,135 bp, 62.8% G+C, 297 ORFs), pMI2 (287,488 bp, 62.5% G+C, 320 ORFs), pMI3 (88,374 bp, 61.0% G+C, 102 ORFs), and pMI4 (32,974 bp, 63.0% G+C, 45 ORFs). Two chromosomes carry two rRNA operons and 50 tRNA genes. The MI1205-specified linA, linB, linC, and linEb genes, and linRED and linGHIJ clusters for conversion of γ-HCH to metabolites in tricarboxylic acid (TCA) cycle (6) are almost identical to those from an archetypal γ-HCH-degrading strain, S. japonicum UT26 (7), and are dispersed on the four plasmids, pMI1 (linB, linC, linF, linEb, and linRED and linGHIJ clusters), pMI2 (linA and linRED cluster, whose linE is missing by frameshift), pMI3 (two copies of linB and linC), and pMI4 (linRED cluster). Localization of all the lin genes for γ-HCH metabolism on multiple plasmids was also observed in another γ-HCH-degrading strain, Sphingomonas sp. MM-1 (8, 9), but distribution patterns of the lin genes are different to each other.
Nucleotide sequence accession numbers.
Sequences with annotation information have been deposited in GenBank under accession numbers CP005188, CP005189, CP005190, CP005191, CP005192, and CP005193, for Chr1, Chr2, pMI1, pMI2, pMI3, and pMI4, respectively.
Footnotes
Citation Tabata M, Ohhata S, Nikawadori Y, Sato T, Kishida K, Ohtsubo Y, Tsuda M, Nagata Y. 2016. Complete genome sequence of a γ-hexachlorocyclohexane-degrading bacterium, Sphingobium sp. strain MI1205. Genome Announc 4(2):e00246-16. doi:10.1128/genomeA.00246-16.
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