@entity2555 ( @entity2556 ) are ubiquitous environmental pollutants and microbial biodegradation is an important means of remediation of @entity2556 -contaminated soil. @entity17497 Cs1-4 (formerly @entity68336 ) was isolated by using @entity11966 as the sole @entity505 source from @entity2556 contaminated soil in Wisconsin. Its full genome sequence was determined to gain insights into a mechanisms underlying biodegradation of @entity2556 . Three genomic libraries were constructed and sequenced: an Illumina GAii shotgun library (916,416,493 reads), a 454 Titanium standard library (770,171 reads) and one paired-end 454 library (average insert size of 8 kb, 508,092 reads). The initial assembly contained 40 contigs in two scaffolds. The 454 Titanium standard data and the 454 paired end data were assembled together and the consensus sequences were computationally shredded into 2 kb overlapping shreds. Illumina sequencing data was assembled, and the consensus sequence was computationally shredded into 1.5 kb overlapping shreds. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks. A total of 182 additional reactions were needed to close gaps and to raise the quality of the finished sequence. The final assembly is based on 253.3 Mb of 454 draft data (averaging 38.4 X coverage) and 590.2 Mb of Illumina draft data (averaging 89.4 X coverage). The genome of strain Cs1-4 consists of a single circular chromosome of 6,685,842 bp (66.7 %G+C) containing 6,028 predicted genes; 5,931 of these genes were protein-encoding and 4,425 gene products were assigned to a putative function. Genes encoding @entity11966 degradation were localized to a 232 kb genomic island (termed the phn island), which contained near its 3' end a @entity19725 -like integrase, an enzyme often associated with chromosomal integration of mobile genetic elements. Other biodegradation pathways reconstructed from the genome sequence included: @entity10555 (by the @entity6625 pathway), @entity8886 , @entity1670 (by the maleamate pathway) and the pesticides Dicamba and Fenitrothion. Determination of the complete genome sequence of @entity17497 Cs1-4 has provided new insights the microbial mechanisms of @entity2556 biodegradation that may shape the process in the environment.

Complete genome sequence of the XXXX -degrading soil bacterium @entity17497 Cs1-4.

@entity68336 :: ('742013', 'Species') :: ['Delftia sp. Cs1-4'] @entity2555 :: ('MESH:D011084', 'Chemical') :: ['Polycyclic aromatic hydrocarbons'] @entity8886 :: ('MESH:D020058', 'Chemical') :: ['styrene'] @entity17497 :: ('80866', 'Species') :: ['Delftia acidovorans', 'D. acidovorans'] @entity1670 :: ('MESH:D009525', 'Chemical') :: ['nicotinic acid'] @entity19725 :: ('10680', 'Species') :: ['bacteriophage P4'] @entity2556 :: ('CHEBI:33848', 'Chemical') :: ['PAH'] @entity505 :: ('MESH:D002244', 'Chemical') :: ['carbon'] @entity6625 :: ('MESH:D000105', 'Chemical') :: ['acetyl-CoA'] @entity10555 :: ('MESH:D001565', 'Chemical') :: ['benzoate'] @entity11966 :: ('MESH:C031181', 'Chemical') :: ['phenanthrene']
@entity11966 :: (MESH:C031181,Chemical) :: ['phenanthrene']
