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Pipeline publication

[…] ne [HCH] isomers) variant genotype, isolated from a heavily contaminated (450 mg HCH/g of soil) HCH dumpsite., The disposal of hexachlorocylohexane (HCH) waste in the past has resulted in the pangenomic enrichment of various sphingomonad genotypes at HCH dumpsites (, ). In order to continue our efforts to sequence genomes of sphingomonads from the HCH dumpsite located near Lucknow, India (27°00′N and 81°09′E) (, ), we sequenced the genome of another sphingomonad strain, P25T (4.2 Mb)., The draft genome sequence of strain P25T was obtained by use of an Illumina Genome Analyzer II platform. The sequencing data (n = 3,882,670; 90 bp/read) were assembled into contigs (n = 181, >500 bp) using ABySS 1.3.3 () set at a k-mer size of 47. Contigs (N50, 45 kb) were further validated (paired-end criterion) using bwa-0.5.9 (). Glimmer-3.02 () was used to predict the protein-encoding genes, whereas tRNA and rRNA genes were identified using ARAGORN () and RNAmmer (), respectively. A total of 4,033 coding sequences (CDS), 70 pseudogenes, 54 tRNA genes, and 1 rRNA operon were observed, with an average G+C content of 64%. Validated (paired-end criterion) genome assembly was annotated using RAST version 4.0 () and the NCBI Prokaryotic Genomes Automatic Annotation pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html). Average nucleotide identity (ANI) () analysis revealed that Sphingobium japonicum UT26S (83.3%) (), Sphingobium indicum B90A (83.0%) (), and Sphingomonas sp. SKA58 (80.8%) are the closest phylogenetic neighbors of S. quisquiliarum P25T., The mechanisms of acquisition of lin genes in sphingomonads under HCH stress at these dumpsites are still not clearly understood (). The lin genes were first reported in S. japonicum UT26 () and subsequently from S. indicum B90A (). Many more sphingomonads have been isolated recently from the HCH dumpsite (, ) […]

Pipeline specifications

Software tools ABySS, BWA, Glimmer, ARAGORN, RNAmmer, RAST
Chemicals Hydrocarbons, Halogenated