Project description:The bacterial isolates of genus Rhodococcus are best known for their significant biodegradation abilities. Here, we report the data related to draft genome sequencing of Rhodococcus rhodochrous strain SPC17 isolated from sediments of Lonar Lake. The de novo assembly of 1598096 Illumina's paired-end sequencing reads resulted in 51 contigs for an overall genome assembly size of 4.98Mb. A total of 4546 genes were predicted using the National Center for Biotechnology Information- Prokaryotic Genome Annotation Pipeline (NCBI-PGAP). RAST server-based annotation of the Rhodococcus strain SPC17 genome resulted in a total of 295 subsystems with 25% subsystem coverage. The data on the draft genome shotgun project are accessible at NCBI-GenBank under the accession number WUUR00000000. Our data resource will facilitate further molecular and genomic studies of diverse hydrocarbon catabolizing genes present in Rhodococcus rhodochrous strain SPC17.
Project description:The accurate diagnosis of diseases caused by pathogenic bacteria requires a stable species classification. Rhodococcus fascians is the only documented member of its ill-defined genus that is capable of causing disease on a wide range of agriculturally important plants. Comparisons of genome sequences generated from isolates of Rhodococcus associated with diseased plants revealed a level of genetic diversity consistent with them representing multiple species. To test this, we generated a tree based on more than 1700 homologous sequences from plant-associated isolates of Rhodococcus, and obtained support from additional approaches that measure and cluster based on genome similarities. Results were consistent in supporting the definition of new Rhodococcus species within clades containing phytopathogenic members. We also used the genome sequences, along with other rhodococcal genome sequences to construct a molecular phylogenetic tree as a framework for resolving the Rhodococcus genus. Results indicated that Rhodococcus has the potential for having 20 species and also confirmed a need to revisit the taxonomic groupings within Rhodococcus.
Project description:BACKGROUND:Rhodococci are bacteria able to degrade a wide range of hydrocarbons, including the alkanes present in crude oil, due to alk genes in their genomes. FINDINGS:Genome sequencing of DNA from Rhodococcus erythropolis strain 4 (obtained from a deep-water bitumen mound) revealed four alk genes, and the predicted amino acid sequences coded by these genes were highly conserved, having sections up to 11 amino acid residues. CONCLUSIONS:Obtained four genes from Rhodococcus erythropolis were similar to corresponding genes from other bacteria collected from other environments, including marine sources. This indicated a large-scale horizontal alk gene transfer between bacteria from different subgenera.
Project description:Understanding how bacteria affect plant health is crucial for developing sustainable crop production systems. We coupled ecological sampling and genome sequencing to characterize the population genetic history of Rhodococcus and the distribution patterns of virulence plasmids in isolates from nurseries. Analysis of chromosome sequences shows that plants host multiple lineages of Rhodococcus, and suggested that these bacteria are transmitted due to independent introductions, reservoir populations, and point source outbreaks. We demonstrate that isolates lacking virulence genes promote beneficial plant growth, and that the acquisition of a virulence plasmid is sufficient to transition beneficial symbionts to phytopathogens. This evolutionary transition, along with the distribution patterns of plasmids, reveals the impact of horizontal gene transfer in rapidly generating new pathogenic lineages and provides an alternative explanation for pathogen transmission patterns. Results also uncovered a misdiagnosed epidemic that implicated beneficial Rhodococcus bacteria as pathogens of pistachio. The misdiagnosis perpetuated the unnecessary removal of trees and exacerbated economic losses.
Project description:The draft genome sequences of plant-associated Rhodococcus spp. from Tunisia are reported here. Two Rhodococcus fascians strains were obtained from almond rootstocks, and one Rhodococcus kroppenstedtii strain was obtained from a pistachio tree. The fourth Rhodococcus sp. strain was isolated from an ornamental plant.
Project description:Transcriptomics of Rhodococcus EP4 on ethylphenol, propylguiacol and succiate Overall design: rRNA-depleted mRNA from mid-log Rhodococcus EP4 on 1.0 mM ethylphenol, propylguiacol and succiate on 1 lane HiSeq4000 100bp-PE
Project description:Rhodococcus rhodochrous ATCC 17895 possesses an array of mono- and dioxygenases, as well as hydratases, which makes it an interesting organism for biocatalysis. R. rhodochrous is a Gram-positive aerobic bacterium with a rod-like morphology. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,869,887 bp long genome contains 6,609 protein-coding genes and 53 RNA genes. Based on small subunit rRNA analysis, the strain is more likely to be a strain of Rhodococcus erythropolis rather than Rhodococcus rhodochrous.
Project description:In this paper comparative genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 were performed. Rhodococcus sp. BCP1 was selected for its ability to grow on short-chain n-alkanes and R. opacus R7 was isolated for its ability to grow on naphthalene and on o-xylene. Results of genome comparison, including BCP1, R7, along with other Rhodococcus reference strains, showed that at least 30% of the genome of each strain presented unique sequences and only 50% of the predicted proteome was shared. To associate genomic features with metabolic capabilities of BCP1 and R7 strains, hundreds of different growth conditions were tested through Phenotype Microarray, by using Biolog plates and plates manually prepared with additional xenobiotic compounds. Around one-third of the surveyed carbon sources was utilized by both strains although R7 generally showed higher metabolic activity values compared to BCP1. Moreover, R7 showed broader range of nitrogen and sulphur sources. Phenotype Microarray data were combined with genomic analysis to genetically support the metabolic features of the two strains. The genome analysis allowed to identify some gene clusters involved in the metabolism of the main tested xenobiotic compounds. Results show that R7 contains multiple genes for the degradation of a large set of aromatic and PAHs compounds, while a lower variability in terms of genes predicted to be involved in aromatic degradation was found in BCP1. This genetic feature can be related to the strong genetic pressure exerted by the two different environment from which the two strains were isolated. According to this, in the BCP1 genome the smo gene cluster involved in the short-chain n-alkanes degradation, is included in one of the unique regions and it is not conserved in the Rhodococcus strains compared in this work. Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination processes.
Project description:We describe the first case of bloodstream infection caused by Rhodococcus erythropolis. The identification was performed using 16S rRNA sequencing. This case illustrates that non-equi Rhodococcus infections may be underdiagnosed due to difficulties in identification in the routine clinical microbiology laboratory.
Project description:Rhodococcus fascians, a phytopathogen that alters plant development, inflicts significant losses in plant production around the world. We report here the complete genome sequence of R. fascians D188, a well-characterized model isolate, and Rhodococcus species PBTS (pistachio bushy top syndrome) 1 and 2, which were shown to be responsible for a disease outbreak in pistachios.