The Complete Genome Sequence and Structure of the Oleaginous Rhodococcus opacus Strain PD630 Through Nanopore Technology
Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic-ecollection
Typ dokumentu časopisecké články
PubMed
35252163
PubMed Central
PMC8892189
DOI
10.3389/fbioe.2021.810571
PII: 810571
Knihovny.cz E-zdroje
- Klíčová slova
- Rhodococcus genomics, Rhodococcus opacus PD630, Rhodococcus opacus plasmids, complete genome, lipid metabolism genes, nanopore sequencing, oleaginous bacteria, xenobiotic degradation genes,
- Publikační typ
- časopisecké články MeSH
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Alvarez H. M., Steinbüchel A. (2002). Triacylglycerols in Prokaryotic Microorganisms. Appl. Microbiol. Biot. 60, 367–376. 10.1007/s00253-002-1135-0 PubMed DOI
Alvarez H. M., Hernández M. A., Lanfranconi M. P., Silva R. A., Villalba M. S. (2021). Rhodococcus as Biofactories for Microbial Oil Production. Molecules 26, 4871. 10.3390/molecules26164871 PubMed DOI PMC
Alvarez H. M., Mayer F., Fabritius D., Steinbüchel A. (1996). Formation of Intracytoplasmic Lipid Inclusions by Rhodococcus opacus Strain PD630. Arch. Microbiol. 165, 377–386. 10.1007/s002030050341 PubMed DOI
Anthony W. E., Carr R. R., DeLorenzo D. M., Campbell T. P., Shang Z., Foston M., et al. (2019). Development of Rhodococcus opacus as a Chassis for Lignin Valorization and Bioproduction of High-Value Compounds. Biotechnol. Biofuels 12, 1–14. 10.1186/s13068-019-1535-3 PubMed DOI PMC
Aramaki T., Blanc-Mathieu R., Endo H., Ohkubo K., Kanehisa M., Goto S., et al. (2019). KofamKOALA: Kegg Ortholog Assignment Based on Profile HMM and Adaptive Score Threshold. Method. Biochem. Anal. 36, 2251–2252. 10.1093/bioinformatics/btz859 PubMed DOI PMC
Cappelletti M., Fedi S., Frascari D., Ohtake H., Turner R. J., Zannoni D. (2011). Analyses of Both the alkB Gene Transcriptional Start Site and alkB Promoter-Inducing Properties of Rhodococcus sp. Strain BCP1 Grown on N -alkanes. Appl. Environ. Microbiol. 77, 1619–1627. 10.1128/aem.01987-10 PubMed DOI PMC
Cappelletti M., Fedi S., Zampolli J., Di Canito A., D'Ursi P., Orro A., et al. (2016). Phenotype Microarray Analysis May Unravel Genetic Determinants of the Stress Response by Rhodococcus aetherivorans BCP1 and Rhodococcus opacus R7. Res. Microbiol. 167, 766–773. 10.1016/j.resmic.2016.06.008 PubMed DOI
Cappelletti M., Presentato A., Piacenza E., Firrincieli A., Turner R. J., Zannoni D. (2020). Biotechnology of Rhodococcus for the Production of Valuable Compounds. Appl. Microbiol. Biotechnol. 104, 8567–8594. 10.1007/s00253-020-10861-z PubMed DOI PMC
Cappelletti M., Zampolli J., Di Gennaro P., Zannoni D. (2019). “Genomics of Rhodococcus,” in Biology of Rhodococcus (Springer International Publishing; ), 23–60. 10.1007/978-3-030-11461-9_2 DOI
Chaumeil P.-A., Mussig A. J., Hugenholtz P., Parks D. H. (2019). GTDB-tk: A Toolkit to Classify Genomes with the Genome Taxonomy Database. Method. Biochem. Anal. 36, 1925–1927. 10.1093/bioinformatics/btz848 PubMed DOI PMC
Chen Y., Ding Y., Yang L., Yu J., Liu G., Wang X., et al. (2013). Integrated Omics Study Delineates the Dynamics of Lipid Droplets in Rhodococcus opacus PD630. Nucleic Acids Res. 42, 1052–1064. 10.1093/nar/gkt932 PubMed DOI PMC
de Carvalho C. C. C. R., Marques M. P. C., Hachicho N., Heipieper H. J. (2014). Rapid Adaptation of Rhodococcus erythropolis Cells to Salt Stress by Synthesizing Polyunsaturated Fatty Acids. Appl. Microbiol. Biotechnol. 98, 5599–5606. 10.1007/s00253-014-5549-2 PubMed DOI
DeLorenzo D. M., Rottinghaus A. G., Henson W. R., Moon T. S. (2018). Molecular Toolkit for Gene Expression Control and Genome Modification in Rhodococcus opacus PD630. ACS Synth. Biol. 7, 727–738. 10.1021/acssynbio.7b00416 PubMed DOI
Donini E., Firrincieli A., Cappelletti M. (2021). Systems Biology and Metabolic Engineering of Rhodococcus for Bioconversion and Biosynthesis Processes. Folia Microbiol. 66, 701–713. 10.1007/s12223-021-00892-y PubMed DOI PMC
Henson W. R., Campbell T., DeLorenzo D. M., Gao Y., Berla B., Kim S. J., et al. (2018). Multi-omic Elucidation of Aromatic Catabolism in Adaptively Evolved Rhodococcus opacus. Metab. Eng. 49, 69–83. 10.1016/j.ymben.2018.06.009 PubMed DOI
Holder J. W., Ulrich J. C., DeBono A. C., Godfrey P. A., Desjardins C. A., Zucker J., et al. (2011). Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development. Plos Genet. 7, e1002219. 10.1371/journal.pgen.1002219 PubMed DOI PMC
Hunt M., Silva N. D., Otto T. D., Parkhill J., Keane J. A., Harris S. R. (2015). Circlator: Automated Circularization of Genome Assemblies Using Long Sequencing Reads. Genome Biol. 16, 1–10. 10.1186/s13059-015-0849-0 PubMed DOI PMC
Janet D. (2014). Whole Genome Sequencing of Rhodococcus opacus PD630. Short Read Archive Available at: https://www.ncbi.nlm.nih.gov/sra/SRX875494 .
Kim H. M., Chae T. U., Choi S. Y., Kim W. J., Lee S. Y. (2019). Engineering of an Oleaginous Bacterium for the Production of Fatty Acids and Fuels. Nat. Chem. Biol. 15, 721–729. 10.1038/s41589-019-0295-5 PubMed DOI
Koren S., Walenz B. P., Berlin K., Miller J. R., Bergman N. H., Phillippy A. M. (2017). Canu: Scalable and Accurate Long-Read Assembly via Adaptive K-Mer Weighting and Repeat Separation. Genome Res. 27, 722–736. 10.1101/gr.215087.116 PubMed DOI PMC
Laver T., Harrison J., O’Neill P. A., Moore K., Farbos A., Paszkiewicz K., et al. (2015). Assessing the Performance of the Oxford Nanopore Technologies MinION. Biomol. Detect. Quantification 3, 1–8. 10.1016/j.bdq.2015.02.001 PubMed DOI PMC
Li W., O’Neill K. R., Haft D. H., DiCuccio M., Chetvernin V., Badretdin A., et al. (2020). RefSeq: Expanding the Prokaryotic Genome Annotation Pipeline Reach with Protein Family Model Curation. Nucleic Acids Res. 49, D1020–D1028. 10.1093/nar/gkaa1105 PubMed DOI PMC
Liang Y., Yu H. (2021). Genetic Toolkits for Engineering Rhodococcus Species with Versatile Applications. Biotechnol. Adv. 49, 107748. 10.1016/j.biotechadv.2021.107748 PubMed DOI
Manni M., Berkeley M. R., Seppey M., Simão F. A., Zdobnov E. M. (2021). BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol. Biol. Evol. 38, 4647–4654. 10.1093/molbev/msab199 PubMed DOI PMC
Minkin I., Patel A., Kolmogorov M., Vyahhi N., Pham S. (2013). Sibelia: A Scalable and Comprehensive Synteny Block Generation Tool for Closely Related Microbial Genomes. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 8126 LNBI, 215–229. 10.1007/978-3-642-40453-5_17 DOI
Monnahan P. J., Michno J. M., O'Connor C., Brohammer A. B., Springer N. M., McGaugh S. E., et al. (2020). Using Multiple Reference Genomes to Identify and Resolve Annotation Inconsistencies. BMC 21. 10.1186/s12864-020-6696-8 PubMed DOI PMC
Orro A., Cappelletti M., D’Ursi P., Milanesi L., Di Canito A., Zampolli J., et al. (2015). Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance. PLoS ONE 10, e0139467. 10.1371/journal.pone.0139467 PubMed DOI PMC
Pátek M., Grulich M., Nešvera J. (2021). Stress Response in Rhodococcus Strains. Biotechnol. Adv. 53, 107698. 10.1016/j.biotechadv.2021.107698 PubMed DOI
Sohn J.-i., Nam J.-W. (2016). The Present and Future of de Novo Whole-Genome. Brief Bioinform 19, bbw096. 10.1093/bib/bbw096 PubMed DOI
Walker B. J., Abeel T., Shea T., Priest M., Abouelliel A., Sakthikumar S., et al. (2014). Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE 9, e112963. 10.1371/journal.pone.0112963 PubMed DOI PMC
Wetzel J., Kingsford C., Pop M. (2011). Assessing the Benefits of Using Mate-Pairs to Resolve Repeats in De Novo Short-Read Prokaryotic Assemblies. BMC Bioinformatics 12, 1–14. 10.1186/1471-2105-12-95 PubMed DOI PMC
Wick R. R., Holt K. E. (2021). Benchmarking of Long-Read Assemblers for Prokaryote Whole Genome Sequencing. F1000Res 8, 2138. 10.12688/f1000research.21782.4 PubMed DOI PMC
Yoneda A., Henson W. R., Goldner N. K., Park K. J., Forsberg K. J., Kim S. J., et al. (2016). Comparative Transcriptomics Elucidates Adaptive Phenol Tolerance and Utilization in Lipid-accumulating Rhodococcus opacus PD630. Nucleic Acids Res. 44, 2240–2254. 10.1093/nar/gkw055 PubMed DOI PMC
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