The design and validation of a Dehalococcoides genus microarray and its application to two newly isolated Dehalococcoides strains for comparative genomics
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PROVIDER: PRJNA130891 | ENA |
REPOSITORIES: ENA
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Project description:The chlorinated ethene-respiring bacteria of the genus Dehalococcoides are important for bioremediation. A microarray targeting genes from all available sequenced genomes of the Dehalococcoides genus was designed with 4305 probe sets to target 98.6% of all genes from strains 195, CBDB1, BAV1, and VS. The microarrays were validated with genomic DNA (gDNA) of strains 195 and BAV1 and satisfactory analytical reproducibility, quantitative response and gene detection accuracy were obtained. These microarrays were applied to query the genomes of two recently isolated Dehalococcoides strains, ANAS1 and ANAS2. Strains ANAS1 and ANAS2 can both couple the reduction of TCE, cDCE and 1,1-DCE but not PCE and tDCE with growth while only strain ANAS2 couples VC reduction to growth. Analysis of the respective gDNA using the microarrays showed that the genomes of both strains are similar to each other and to strain 195, except for genes that are within the previously defined integrated elements (IEs) or high plasticity regions (HPRs). Similar results to the combined isolates were obtained when gDNA of ANAS, the enrichment culture from which the two Dehalococcoides isolates originated, was applied to the microarrays. The genome similarities, together with the distinct chlorinated ethene usage of strains ANAS1, ANAS2 and 195 demonstrate that closely phylogenetically related strains can be physiologically different. This incongruence between physiology and core genome phylogeny appears to be driven by the presence of distinct reductive dehalogenase (RDase)-encoding genes with characterized chlorinated ethene functions (pceA, tceA in strain 195; tceA in strain ANAS1; vcrA in strain ANAS2). Genes encoding central metabolic functions of strain 195 were all detected in strains ANAS1 and ANAS2, while interestingly, the tryptophan operon of these strains is similar to that of strain VS. Overall, the microarrays are a valuable high-throughput tool for comparative genomics of un-sequenced Dehalococcoides-containing samples. The genomic DNA (gDNA) of each culture was analyzed in triplicate. gDNA from strain 195 and strain BAV1 was used as positive control, while gDNA from Anaeromyxobacter dehalogenans strain 2CP-C served as negative control in validating the microarray. gDNA from the two newly isolated strains ANAS1 and ANAS2 as well as the enrichment culture (ANAS) where the two strains originated was also analyzed.
2011-08-17 | E-GEOD-23707 | biostudies-arrayexpress
Project description:The chlorinated ethene-respiring bacteria of the genus Dehalococcoides are important for bioremediation. A microarray targeting genes from all available sequenced genomes of the Dehalococcoides genus was designed with 4305 probe sets to target 98.6% of all genes from strains 195, CBDB1, BAV1, and VS. The microarrays were validated with genomic DNA (gDNA) of strains 195 and BAV1 and satisfactory analytical reproducibility, quantitative response and gene detection accuracy were obtained. These microarrays were applied to query the genomes of two recently isolated Dehalococcoides strains, ANAS1 and ANAS2. Strains ANAS1 and ANAS2 can both couple the reduction of TCE, cDCE and 1,1-DCE but not PCE and tDCE with growth while only strain ANAS2 couples VC reduction to growth. Analysis of the respective gDNA using the microarrays showed that the genomes of both strains are similar to each other and to strain 195, except for genes that are within the previously defined integrated elements (IEs) or high plasticity regions (HPRs). Similar results to the combined isolates were obtained when gDNA of ANAS, the enrichment culture from which the two Dehalococcoides isolates originated, was applied to the microarrays. The genome similarities, together with the distinct chlorinated ethene usage of strains ANAS1, ANAS2 and 195 demonstrate that closely phylogenetically related strains can be physiologically different. This incongruence between physiology and core genome phylogeny appears to be driven by the presence of distinct reductive dehalogenase (RDase)-encoding genes with characterized chlorinated ethene functions (pceA, tceA in strain 195; tceA in strain ANAS1; vcrA in strain ANAS2). Genes encoding central metabolic functions of strain 195 were all detected in strains ANAS1 and ANAS2, while interestingly, the tryptophan operon of these strains is similar to that of strain VS. Overall, the microarrays are a valuable high-throughput tool for comparative genomics of un-sequenced Dehalococcoides-containing samples.
2011-08-18 | GSE23707 | GEO
Project description:The genomes of three newly isolated Dehalococcoides strains (11a, 11a5 and MB) were compared against known genomes in the Dehalococcoides genus via a microarray targeting four sequenced Dehalococcoides strains (195, CBDB1, BAV1, and VS). All three strains exhibit different dechlorination patterns, with strains 11a dechlorinating TCE to ethene, 11a5 dechlorinating TCE to VC and MB dechlorinating PCE only to isomers of DCE. Hybridization of their respective genomic DNA to the microarrays showed that the genomes of strains 11a and 11a5 show great similarity to each other and to strains CBDB1 and BAV1 of the Pinellas subgroup, while strain MB shows strong genome similarity to members of the Cornell subgroup. All genes within the respective subgroups that were not detected by microarray are within the respective high plasticity regions or integrated elements of the sequenced strains. A large number of reductive dehalogenase (RDase)-encoding genes are present within each genome, and the presence of the vcrA and tceA genes in strains 11a and 11a5 respectively, and the absence of any of the four functionally-characterized chlorinated ethene RDases (pceA, tceA, vcrA, bvcA) within strain MB appear to dictate chlorinated ethene usages regardless of the respective core genome phylogeny of the three strains. Considering the current data set together with previous comparative genomics results from application of the Dehalococcoides genus microarray to two other un-sequenced strains, the observed incongruence between the core genome phylogeny and chlorinated ethene usage of Dehalococcoides strains is likely driven by horizontal gene transfer of functional RDases. The other genomic features that are repeatedly observed in the microarray analyses of all five un-sequenced Dehalococcoides strains as well as the environmental implications on this work are presented in this study. The genomic DNA (gDNA) of each culture was analyzed in triplicate. gDNA from the two newly isolated Dehalococcoides strains 11a and 11a5 were analyzed.
2013-03-01 | E-GEOD-27611 | biostudies-arrayexpress
Project description:This research focuses on the design, manufacturing and validation of a new Agrobacterium tumefaciens C58 whole-genome tiling microarray platform for novel RNA transcript discovery. A whole-genome tiling microarray allows both annotated genes as well as previously unknown RNA transcripts to be detected and quantified at once. The Agrobacterium tumefaciens C58 genome is re-acquired with next-generation sequencing and then used to design the tilinlg microarray with the thermodynamic analysis program Picky. Validations are performed by subjecting Agrobacterium tumefaciens C58 under various growth conditions and then using the tling microarrays to verify expected gene expression patterns.
2014-09-25 | GSE61737 | GEO
Project description:This research focuses on the design, manufacturing and validation of a new E. coli whole-genome tiling micraorray platform for novel RNA transcript discovery. A whole-genome tiling microarray allows both annotated genes as well as previously unknown RNA transcripts to be detected and quantified at once. The E. coli MG1655 genome is re-acquired with next-generation sequencing and then used to design the tiling microarray with the thermodynamic analysis program Picky. Validations are performed by subjecting E. coli under various growth conditions and then using the tiling microarrays to verify expected gene expression patterns.
2014-09-25 | GSE61736 | GEO
Project description:Bacteria of the group “Dehalococcoides” display the ability to respire recalcitrant chlorinated organic compounds in laboratory and field site applications. Though reductive dehalogenases (RDases) have been shown to directly catalyze dechlorination reactions, the respiratory pathways and function of most genome-encoded RDases in Dehalococcoides strains remain incompletely described. In order to broaden the understanding of the biological organization of “Dehalococcoides”, this study monitored the trancriptomic response of “Dehalococcoides ethenogenes” stain 195 through microarray technology. Batch versus continuously fed cultures were examined and compared. When similarly respiring (~120 μeeq PCE/(L-hr)) batch and pseudo steady-state cultures were contrasted, the reductive dehalogenases (RDases) DET1545 and DET0180 were up-regulated in the PSS system indicating their activity at lower overall electron acceptor concentration.
2018-10-13 | GSE25499 | GEO
Project description:Dehalococcoides mccartyi IBARAKI
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Project description:Dehalococcoides mccartyi Raw sequence reads
| PRJNA843443 | ENA
Project description:Dehalococcoides mccartyi Genome sequencing and assembly
| PRJNA428836 | ENA
Project description:Dehalococcoides mccartyi Transcriptome of three strains
| PRJNA231971 | ENA