Dehalococcoides Genomes: Vinyl Chloride Respiration and Genomic Plasticity

Complete genome sequences of two Dehalococcoides strains, VS and BAV1, which respire the carcinogen vinyl chloride. The data includes comparative analysis with two previously sequenced genomes, revealing high plasticity regions containing genomic islands and up to 36 reductive dehalogenase genes per genome. The dataset was produced by Paul J. McMurdie of Stanford University.

Use Cases

• Study horizontal gene transfer mechanisms based on the distinct genomic islands containing vinyl chloride reductase genes vcrAB and bvcAB.
• Analyze niche adaptation in microbes based on the high number and variable location of reductive dehalogenase (rdhAB) genes.
• Investigate genome stability and plasticity based on the identified high plasticity regions (HPRs) near the origin of replication.
• Compare streamlined genome architecture across Dehalococcoides strains based on the syntenic core and strain-specific genes.

Strengths

• Includes the first complete genome sequences reported for microorganisms able to respire vinyl chloride.
• Comparative analysis covers four Dehalococcoides genomes, identifying up to 36 rdhAB genes in a single strain.
• Analysis identifies specific high plasticity regions (HPRs) containing 91 of 96 rdhAB genes and the majority of genomic islands.

Limitations

• Row count and file formats are unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• Last update date is unknown; freshness unverified.

Provenance

Source

paperswithcode

Collection Method

Genome sequencing and comparative genomic analysis.