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      Data on genome sequencing, assembly, annotation and genomic analysis of Rhodococcus rhodochrous strain SPC17 isolated from Lonar Lake

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          Abstract

          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.

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          The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse.

          Michael P McLeod, René L Warren, William W L Hsiao … (2006)
          Rhodococcus sp. RHA1 (RHA1) is a potent polychlorinated biphenyl-degrading soil actinomycete that catabolizes a wide range of compounds and represents a genus of considerable industrial interest. RHA1 has one of the largest bacterial genomes sequenced to date, comprising 9,702,737 bp (67% G+C) arranged in a linear chromosome and three linear plasmids. A targeted insertion methodology was developed to determine the telomeric sequences. RHA1's 9,145 predicted protein-encoding genes are exceptionally rich in oxygenases (203) and ligases (192). Many of the oxygenases occur in the numerous pathways predicted to degrade aromatic compounds (30) or steroids (4). RHA1 also contains 24 nonribosomal peptide synthase genes, six of which exceed 25 kbp, and seven polyketide synthase genes, providing evidence that rhodococci harbor an extensive secondary metabolism. Among sequenced genomes, RHA1 is most similar to those of nocardial and mycobacterial strains. The genome contains few recent gene duplications. Moreover, three different analyses indicate that RHA1 has acquired fewer genes by recent horizontal transfer than most bacteria characterized to date and far fewer than Burkholderia xenovorans LB400, whose genome size and catabolic versatility rival those of RHA1. RHA1 and LB400 thus appear to demonstrate that ecologically similar bacteria can evolve large genomes by different means. Overall, RHA1 appears to have evolved to simultaneously catabolize a diverse range of plant-derived compounds in an O(2)-rich environment. In addition to establishing RHA1 as an important model for studying actinomycete physiology, this study provides critical insights that facilitate the exploitation of these industrially important microorganisms.
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            Biodegradation potential of the genus Rhodococcus.

            Bronislava Uhnáková, Ludmila Martinkova, Jan Nesvera … (2008)
            A large number of aromatic compounds and organic nitriles, the two groups of compounds covered in this review, are intermediates, products, by-products or waste products of the chemical and pharmaceutical industries, agriculture and the processing of fossil fuels. The majority of these synthetic substances (xenobiotics) are toxic and their release and accumulation in the environment pose a serious threat to living organisms. Bioremediation using various bacterial strains of the genus Rhodococcus has proved to be a promising option for the clean-up of polluted sites. The large genomes of rhodococci, their redundant and versatile catabolic pathways, their ability to uptake and metabolize hydrophobic compounds, to form biofilms, to persist in adverse conditions and the availability of recently developed tools for genetic engineering in rhodococci make them suitable industrial microorganisms for biotransformations and the biodegradation of many organic compounds. The peripheral and central catabolic pathways in rhodococci are characterized for each type of aromatics (hydrocarbons, phenols, halogenated, nitroaromatic, and heterocyclic compounds) in this review. Pathways involved in the hydrolysis of nitrile pollutants (aliphatic nitriles, benzonitrile analogues) and the corresponding enzymes (nitrilase, nitrile hydratase) are described in detail. Examples of regulatory mechanisms for the expression of the catabolic genes are given. The strains that efficiently degrade the compounds in question are highlighted and examples of their use in biodegradation processes are presented.
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              Biodegradation and Rhodococcus--masters of catabolic versatility.

              Leonid Kulakov, Michael C. Allen, Oliver J Larkin (2005)
              The genus Rhodococcus is a very diverse group of bacteria that possesses the ability to degrade a large number of organic compounds, including some of the most difficult compounds with regard to recalcitrance and toxicity. They achieve this through their capacity to acquire a remarkable range of diverse catabolic genes and their robust cellular physiology. Rhodococcus appear to have adopted a strategy of hyper-recombination associated with a large genome. Notably, they harbour large linear plasmids that contribute to their catabolic diversity by acting as 'mass storage' for a large number of catabolic genes. In addition, there is increasing evidence that multiple pathways and gene homologues are present that further increase the catabolic versatility and efficiency of Rhodococcus.
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                Author and article information

                Contributors
                Satish Kumar
                Dhiraj Paul
                Yogesh Shouche
                Journal
                Journal ID (nlm-ta): Data Brief
                Journal ID (iso-abbrev): Data Brief
                Title: Data in Brief
                Publisher: Elsevier
                ISSN (Electronic): 2352-3409
                Publication date PMC-release: 26 February 2020
                Publication date Collection: April 2020
                Publication date (Electronic): 26 February 2020
                Volume: 29
                Electronic Location Identifier: 105336
                Affiliations
                [a ]National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, MH, India
                [b ]ICAR-National Institute of Abiotic Stress Management, Baramati, Pune, MH, India
                [c ]Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore, 575018, Karnataka, India
                Author notes
                [∗ ]Corresponding author. National Centre for Microbial resource, National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, 411007, Maharashtra State, India. satish.kumar10@ 123456icar.gov.in
                [∗∗ ]Corresponding author. National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, 411007, Maharashtra State, India. dhiraj.paul@ 123456nccs.res.in
                [∗∗∗ ]Corresponding author. National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, 411007, Maharashtra State, India. yogesh@ 123456nccs.res.in
                [1]

                Both the authors contributed equally to this work.

                Article
                Publisher ID: S2352-3409(20)30230-4 Publisher ID: 105336
                DOI: 10.1016/j.dib.2020.105336
                PMC ID: 7058525
                PubMed ID: 32154356
                SO-VID: ab9db6f5-c43d-4666-9602-a34486b41a3f
                Copyright © © 2020 The Authors
                License:

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 27 January 2020
                Date revision received : 17 February 2020
                Date accepted : 18 February 2020
                Categories
                Subject: Genetics, Genomics and Molecular Biology

                Keywords: rhodococcus,soda lake,draft genome sequence,biodegradation,hydrocarbon
                Data availability:
                Keywords: rhodococcus, soda lake, draft genome sequence, biodegradation, hydrocarbon

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