{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T22:31:54Z","timestamp":1778279514906,"version":"3.51.4"},"update-to":[{"DOI":"10.12688\/f1000research.158761.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,4,17]],"date-time":"2025-04-17T00:00:00Z","timestamp":1744848000000}}],"reference-count":76,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2025,4,17]],"date-time":"2025-04-17T00:00:00Z","timestamp":1744848000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns3:p>\n                    Background Bioremediation faces several compounds to recover oil spilled ecosystem. The BTEX (benzene, toluene, ethylbenzene, and xylene) are toxic hydrocarbons requiring efficient microbial degradation for bioremediation.\n                    <ns3:italic>Pseudomonas aeruginosa<\/ns3:italic>\n                    can degrade hydrocarbons through emulsification (\n                    <ns3:italic>rhl<\/ns3:italic>\n                    genes) and tolerance (\n                    <ns3:italic>mla<\/ns3:italic>\n                    genes). However, genomic organization of these systems in environmental\n                    <ns3:italic>P. aeruginosa<\/ns3:italic>\n                    strains remains unclear. This study aimed to investigate the\n                    <ns3:italic>rhl<\/ns3:italic>\n                    and\n                    <ns3:italic>mla<\/ns3:italic>\n                    systems in six strains isolated from hydrocarbon-contaminated sites in Peru. Methods Six\n                    <ns3:italic>Pseudomonas aeruginosa<\/ns3:italic>\n                    strains were evaluated in this study. Each strain were able to degrade hydrocarbon and tolerate heavy metals. DNA extraction, sequencing, and quality-controlled assembly, functional genome annotation was performed using BAKTA. Comparative analysis included high-quality\n                    <ns3:italic>Pseudomonas<\/ns3:italic>\n                    genomes from RefSeq, with ANI metrics. A phylogenetic tree was built from core gene alignment, revealed evolutionary connections and was visualized with iTOL. Results The assembled genomes ranged from 5.6 to 6.0 Mbp with ~66% GC content. All the strains were confirmed as\n                    <ns3:italic>P. aeruginosa<\/ns3:italic>\n                    by ANI; placing them within Clade 1 alongside environmental and clinical strains. Pangenome analysis identified 3,544 core genes and a diverse accessory genome. All strains had\n                    <ns3:italic>rhlABRI<\/ns3:italic>\n                    genes in a conserved 3\u2032-5\u2032 orientation. Most of them contained duplicated\n                    <ns3:italic>rhlB<\/ns3:italic>\n                    gene, except C1BHIC5 strain. However,\n                    <ns3:italic>rhlG<\/ns3:italic>\n                    varied in position and orientation, it was often near\n                    <ns3:italic>rhlC<\/ns3:italic>\n                    , with C1BHIC5 also displaying an exception in\n                    <ns3:italic>rhlG<\/ns3:italic>\n                    orientation.100% of strains presented\n                    <ns3:italic>mla<\/ns3:italic>\n                    system, associated with toluene tolerance, with two copies of\n                    <ns3:italic>mlaA<\/ns3:italic>\n                    ,\n                    <ns3:italic>mlaFEDC<\/ns3:italic>\n                    , and\n                    <ns3:italic>mlaEFD<\/ns3:italic>\n                    genes arranged with high synteny but variable orientations. In comparison to\n                    <ns3:italic>Pseudomonas putida<\/ns3:italic>\n                    , where\n                    <ns3:italic>mla<\/ns3:italic>\n                    genes are positioned between\n                    <ns3:italic>murA<\/ns3:italic>\n                    and\n                    <ns3:italic>ppcD<\/ns3:italic>\n                    with an additional toluene tolerance gene (\n                    <ns3:italic>ttg2D<\/ns3:italic>\n                    ). Conclusions In conclusion, the presence of the\n                    <ns3:italic>rhlABC<\/ns3:italic>\n                    genes and the BTEX tolerance genes in all of the analyzed strains allowed us to understand the great ability of\n                    <ns3:italic>P. aeruginosa<\/ns3:italic>\n                    to survive in polluted environments.\n                  <\/ns3:p>","DOI":"10.12688\/f1000research.158761.2","type":"journal-article","created":{"date-parts":[[2025,4,17]],"date-time":"2025-04-17T11:10:07Z","timestamp":1744888207000},"page":"1519","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Comparative Genomics of Rhamnolipid Synthesis and Monoaromatic Hydrocarbon Tolerance Genes in Environmental Pseudomonas aeruginosa strains"],"prefix":"10.12688","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0333-7269","authenticated-orcid":false,"given":"ROGER A.","family":"PALOMINO HUARCAYA","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2770-1416","authenticated-orcid":false,"given":"Camila","family":"Castillo-Vilcahuaman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-6668-7832","authenticated-orcid":false,"given":"Sandro B.","family":"Martel-Torres","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fernando A.","family":"Merino Rafael","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Susana M.","family":"Guti\u00e9rrez Moreno","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"2560","published-online":{"date-parts":[[2025,4,17]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"287-308","DOI":"10.1007\/s00253-007-1018-5","article-title":"Bioremediation and monitoring of aromatic-polluted habitats.","volume":"76","author":"V Andreoni","year":"2007","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref2","article-title":"FastQC: A quality control tool for high throughput sequence data.","author":"S Andrews","year":"2010","journal-title":"Babraham Bioinformatics."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1007\/s11274-021-03093-4","article-title":"Biodegradation of binary mixtures of octane with benzene, toluene, ethylbenzene or xylene (BTEX): Insights on the potential of Burkholderia, Pseudomonas and Cupriavidus isolates.","volume":"37","author":"H Bacosa","year":"2021","journal-title":"World J. Microbiol. Biotechnol."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"455-465","DOI":"10.1002\/jctb.6820","article-title":"Assessment of degradation potential of Pseudomonas species in bioremediating soils contaminated with petroleum hydrocarbons.","volume":"97","author":"Z Baig","year":"2022","journal-title":"J. Chem. Technol. Biotechnol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"455-477","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing [Publisher: Mary Ann Liebert, Inc., publishers].","volume":"19","author":"A Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"550-563","DOI":"10.1080\/15287394.2019.1634380","article-title":"Environmental and biological monitoring of benzene, toluene, ethylbenzene and xylene (BTEX) exposure in residents living near gas stations.","volume":"82","author":"N Barros","year":"2019","journal-title":"J. Toxicol. Environ. Health A."},{"key":"ref73","doi-asserted-by":"publisher","first-page":"303-312","DOI":"10.1016\/B978-0-12-819025-8.00014-4","author":"G Bhattacharjee","year":"2020","journal-title":"Bioremediation of Pollutants."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"578-579","DOI":"10.1093\/bioinformatics\/btq683","article-title":"Scaffolding pre-assembled contigs using SSPACE.","volume":"27","author":"M Boetzer","year":"2011","journal-title":"Bioinformatics (Oxford, England)."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"R56","DOI":"10.1186\/gb-2012-13-6-r56","article-title":"Toward almost closed genomes with GapFiller.","volume":"13","author":"M Boetzer","year":"2012","journal-title":"Genome Biol."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"2114-2120","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for illumina sequence data.","volume":"30","author":"A Bolger","year":"2014","journal-title":"Bioinformatics."},{"key":"ref9","article-title":"reymonera\/pseudomonas_notebook: Pseudomonas-Notebook_v1.0 (v.1.0).","author":"C Castillo-Vilcahuaman","year":"2024a","journal-title":"Zenodo."},{"key":"ref10","article-title":"ANIm Percentage Identity Tabular Data (Version 1).","author":"C Castillo-Vilcahuaman","year":"2024b","journal-title":"figshare."},{"key":"ref11","doi-asserted-by":"publisher","DOI":"10.6084\/m9.figshare.27895629.v1","article-title":"Pangenome Presence-Absence Tables (Version 1).","author":"C Castillo-Vilcahuaman","year":"2024c","journal-title":"figshare."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"7741","DOI":"10.1038\/srep07","article-title":"Genomic and metabolic analysis of fluoranthene degradation pathway in Celeribacter indicus p73t.","volume":"5","author":"J Cao","year":"2015","journal-title":"Sci. Rep."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"289-304","DOI":"10.1007\/s00294-021-01225-9","article-title":"Genome-wide analysis reveals a rhamnolipid-dependent modulation of flagellar genes in Pseudomonas aeruginosa PAO1.","volume":"68","author":"M Castro","year":"2022","journal-title":"Curr. Genet."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"36203-36214","DOI":"10.1007\/s11356-020-09650-y","article-title":"Degradation of BTEX mixture by a new Pseudomonas putida strain: Role of the quorum sensing in the modulation of the upper BTEX oxidative pathway.","volume":"27","author":"I Chicca","year":"2020","journal-title":"Environ. Sci. Pollut. Res."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"663-671","DOI":"10.1128\/AEM.02809-12","article-title":"Comparative genomic analysis and benzene, toluene, ethylbenzene, and o-, m-, and p-xylene (BTEX) degradation pathways of Pseudoxanthomonas spadix BD-a59 [Publisher: American Society for Microbiology].","volume":"79","author":"E Choi","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"e00532\u201320","DOI":"10.1128\/mBio.00532-20","article-title":"RhlR-regulated acyl-homoserine lactone quorum sensing in a cystic fibrosis isolate of Pseudomonas aeruginosa (S. C. Winans, Ed.).","volume":"11","author":"R Cruz","year":"2020","journal-title":"MBio."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"291-294","DOI":"10.1093\/molbev\/msz189","article-title":"ModelTest-NG: A new and scalable tool for the selection of DNA and protein evolutionary models.","volume":"37","author":"D Darriba","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref18","article-title":"Graph clustering by flow simulation [Accepted: 2001-02-13T10:26:00Z].","author":"S Dongen","year":"2000, May 29"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"e00749","DOI":"10.1128\/mbio.00749-15","article-title":"The Pseudomonas aeruginosa transcriptional landscape is shaped by environmental heterogeneity and genetic variation [Publisher: American Society for Microbiology].","volume":"6","author":"A D\u00f6tsch","year":"2015","journal-title":"MBio."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"109-120","DOI":"10.1093\/gbe\/evy259","article-title":"The Pseudomonas aeruginosa pangenome provides new insights on its population structure, horizontal gene transfer, and pathogenicity.","volume":"11","author":"L Freschi","year":"2019","journal-title":"Genome Biol. Evol."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"5224-5232","DOI":"10.1128\/jb.175.16.5224-5232.1993","article-title":"Gene components responsible for discrete sub-strate specificity in the metabolism of biphenyl (bph operon) and toluene (tod operon).","volume":"175","author":"K Furukawa","year":"1993","journal-title":"J. Bacteriol."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"25-34","DOI":"10.1099\/jmm.0.001116","article-title":"The third quorum-sensing system of Pseudomonas aeruginosa: Pseudomonas quinolone signal and the enigmatic PqsE protein.","volume":"69","author":"S Garc\u00eda-Reyes","year":"2020","journal-title":"J. Med. Microbiol."},{"key":"ref23","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.0136","article-title":"Current state of knowledge in microbial degradation of polycyclic aromatic hydrocarbons (PAHs): A review.","volume":"7","author":"D Ghosal","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref24","doi-asserted-by":"crossref","first-page":"35-44","DOI":"10.37761\/rsqp.v80i1.210","article-title":"Actividad emulsificante y de remoci\u00f3n de metales pesados del ramnol\u00edpido producido por Pseudomonas aeruginosa PB 25 [Publisher: Sociedad Qu\u00edmica del Per\u00fa Section: Revista de la Sociedad Qu\u00edmica del Per\u00fa].","volume":"80","author":"J Giraldo","year":"2014","journal-title":"Revista de la Sociedad Qu\u00edmica del Per\u00fa."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1186\/1471-2164-15-318","article-title":"Pseudomonas aeruginosa clinical and environmental isolates constitute a single population with high phenotypic diversity.","volume":"15","author":"M Grosso-Becerra","year":"2014","journal-title":"BMC Genomics."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"921-930","DOI":"10.1016\/j.apr.2018.12.020","article-title":"On the nature and health impacts of BTEX in a populated middle eastern city: Tehran, Iran.","volume":"10","author":"F Golkhorshidi","year":"2019","journal-title":"Atmos. Pollut. Res."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"1072-1075","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: Quality assessment tool for genome assemblies.","volume":"29","author":"A Gurevich","year":"2013","journal-title":"Bioinformatics (Oxford, England)."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"409-416","DOI":"10.1016\/j.molliq.2018.12.020","article-title":"The impact of selected polycyclic aromatic hydrocarbons (PAHs) on the morphology, stability and relaxation of ternary lipid monolayers imitating soil bacteria membrane.","volume":"276","author":"K H\u0105c-Wydro","year":"2019","journal-title":"J. Mol. Liq."},{"key":"ref28","article-title":"gggenomes: A Grammar of Graphics for Comparative Genomics.","author":"T Hackl","year":"2024","journal-title":"R package version 1.0.1."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"81-89","DOI":"10.1007\/BF00281605","article-title":"Comparison of the nucleotide sequences of the meta-cleavage pathway genes of TOL plasmid pWW0 from Pseudomonas putida with other meta-cleavage genes suggests that both single and multiple nucleotide substitutions contribute to enzyme evolution.","volume":"239","author":"S Harayama","year":"1993","journal-title":"Mol. Gen. Genet. MGG."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"2595","DOI":"10.3389\/fmicb.2018.02595","article-title":"Genome sequence and metabolic analysis of a fluoranthene-degrading strain Pseudomonas aeruginosa DN1.","volume":"9","author":"C He","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"591-604","DOI":"10.1007\/s12223-022-00966-5","article-title":"Current research on simultaneous oxidation of aliphatic and aromatic hydrocarbons by bacteria of genus Pseudomonas.","volume":"67","author":"A Ivanova","year":"2022","journal-title":"Folia Microbiol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ani analysis of 90k prokaryotic genomes reveals clear species boundaries.","volume":"9","author":"C Jain","year":"2018","journal-title":"Nat. Commun."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"1145-1156","DOI":"10.1007\/s13213-016-1203-9","article-title":"Production of rhamnolipids with a high specificity by Pseudomonas aeruginosa m408 isolated from petroleum-contaminated soil using olive oil as sole carbon source [Number: 3 Publisher: BioMed Central].","volume":"66","author":"F Ji","year":"2016","journal-title":"Ann. Microbiol."},{"key":"ref77","doi-asserted-by":"publisher","first-page":"712","DOI":"10.3390\/pr10040712","article-title":"Synthetic biology: a new era in hydrocarbon bioremediation.","volume":"10","author":"V Jim\u00e9nez-D\u00edaz","year":"2022","journal-title":"Processes."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"6662-6666","DOI":"10.1128\/JB.183.22.6662-6666.2001","article-title":"The TOL plasmid pWW0 xylN gene product from Pseudomonas putida is involved in m- xylene uptake.","volume":"183","author":"Y Kasai","year":"2001","journal-title":"J. Bacteriol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"104132","DOI":"10.1016\/j.resmic.2023.104132","article-title":"Deficient Pseudomonas aeruginosa in MlaA\/VacJ outer membrane lipoprotein shows decrease in rhamnolipids secretion, motility, and biofilm formation, and increase in fluoroquinolones susceptibility and innate immune response.","volume":"174","author":"M Kaur","year":"2023","journal-title":"Res. Microbiol."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1186\/s12866-023-03138-8","article-title":"Maintenance of bacterial outer membrane lipid asymmetry: Insight into MlaA.","volume":"24","author":"M Kaur","year":"2024","journal-title":"BMC Microbiol."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"3577-3585","DOI":"10.1128\/AEM.67.8.3577-3585.2001","article-title":"Molecular cloning, nucleotide sequence, and expression of genes encoding a polycyclic aromatic ring dioxygenase from Mycobacterium sp. strain PYR-1.","volume":"67","author":"A Khan","year":"2001","journal-title":"Appl. Environ. Microbiol."},{"key":"ref38","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.7598955","article-title":"FelixKrueger\/TrimGalore: v0.6.10 - add default decompression path (0.6.10).","author":"F Krueger","year":"2023","journal-title":"Zenodo."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"1090-1107","DOI":"10.1080\/21505594.2020.1809327","article-title":"Surfactant phospholipids act as molecular switches for premature induction of quorum sensing-dependent virulence in Pseudomonas aeruginosa.","volume":"11","author":"Z Kuang","year":"2020","journal-title":"Virulence."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"xtad015","DOI":"10.1093\/femsmc\/xtad015","article-title":"Biotechnological potential of microbial biosurfactants, their significance, and diverse applications.","volume":"4","author":"R Kumari","year":"2023","journal-title":"FEMS Microbes."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"26-41","DOI":"10.1007\/s13238-014-0100-x","article-title":"The hierarchy quorum sensing network in Pseudomonas aeruginosa.","volume":"6","author":"J Lee","year":"2015","journal-title":"Protein Cell."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1038\/s41598-018-36165-x","article-title":"Biodegradation of naphthalene, BTEX, and aliphatic hydrocarbons by Paraburkholderia aromaticivorans BN5 isolated from petroleum-contaminated soil [Publisher: Nature Publishing Group].","volume":"9","author":"Y Lee","year":"2019","journal-title":"Sci. Rep."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"W293-W296","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive tree of life (iTOL) v5: An online tool for phylogenetic tree display and annotation.","volume":"49","author":"I Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"488","DOI":"10.3390\/md20080488","article-title":"The molecular architecture of Pseudomonas aeruginosa quorum-sensing inhibitors [Number: 8 Publisher: Multidisciplinary Digital Publishing Institute].","volume":"20","author":"Q Li","year":"2022","journal-title":"Mar. Drugs."},{"key":"ref45","first-page":"130-144","article-title":"Microbial aspects of anaerobic BTEX degradation.","volume":"15","author":"B Lin","year":"2002","journal-title":"Biomed. Environ. Sci."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"307","DOI":"10.3390\/pr10020307","article-title":"Crude oil degradation by a novel strain Pseudomonas aeruginosa aqnu-1 isolated from an oil-contaminated lake wetland.","volume":"10","author":"H Liu","year":"2022","journal-title":"Processes."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"8124","DOI":"10.1038\/s41598-021-87487-2","article-title":"Genomic characterization of a polyvalent hydrocarbonoclastic bacterium Pseudomonas sp. strain BUN14 [Publisher: Nature Publishing Group].","volume":"11","author":"M Mahjoubi","year":"2021","journal-title":"Sci. Rep."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"860-870","DOI":"10.1016\/j.tibtech.2017.04.003","article-title":"Biotechnologies for marine oil spill cleanup: Indissoluble ties with microorganisms.","volume":"35","author":"F Mapelli","year":"2017","journal-title":"Trends Biotechnol."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"e00119-e00120","DOI":"10.1128\/mSphere.00119-20","article-title":"Molecular mechanisms of phosphate stress activation of Pseudomonas aeruginosa quorum sensing systems (C. D. Ellermeier, Ed.).","volume":"5","author":"X Meng","year":"2020","journal-title":"mSphere."},{"key":"ref78","doi-asserted-by":"publisher","first-page":"804234","DOI":"10.3389\/fbioe.2021.804234","article-title":"Synthetic biology approaches to hydrocarbon biosensors: a review.","volume":"9","author":"C Moratti","year":"2022","journal-title":"Front. Bioeng. Biotechnol."},{"key":"ref50","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.001265","article-title":"Frequency of quorum-sensing mutations in Pseudomonas aeruginosa strains isolated from different environments.","volume":"168","author":"K O\u2019Connor","year":"2022","journal-title":"Microbiology."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"333-339","DOI":"10.1099\/00207713-23-4-333","article-title":"Nucleic acid homologies in the genus Pseudomonas.","volume":"23","author":"N Palleroni","year":"1973","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"293-302","DOI":"10.15381\/rpb.v24i3.13902","article-title":"Presencia de genes rhlAB, rhlR y rhlC en Pseudomonas aeruginosa nativas sobreproductoras de ramnol\u00edpidos [Publisher: Universidad Nacional Mayor de San Marcos].","volume":"24","author":"R Palomino","year":"2017","journal-title":"Rev. Peru. Biol."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"1-73","DOI":"10.1016\/S0065- 2164(08)00401-2","article-title":"Diversity of microbial toluene degradation pathways.","volume":"64","author":"R Parales","year":"2008","journal-title":"Adv. Appl. Microbiol."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"1043-1055","DOI":"10.1101\/r.186072.114","article-title":"CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes [Company: Cold Spring Harbor Laboratory Press Distributor: Cold Spring Harbor Laboratory Press Institution: Cold Spring Harbor Laboratory Press Label: Cold Spring Harbor Laboratory Press Publisher: Cold Spring Harbor Lab].","volume":"25","author":"D Parks","year":"2015","journal-title":"Genome Res."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"12-24","DOI":"10.1039\/C5AY02550H","article-title":"Genomics and taxonomy in diagnostics for food security: Soft-rotting enterobacterial plant pathogens [Publisher: Royal Society of Chemistry].","volume":"8","author":"L Pritchard","year":"2016","journal-title":"Anal. Methods."},{"key":"ref56","article-title":"Evaluaci\u00f3n de la capacidad degradativa sobre benceno y tolueno de cepas nativas de Pseudomonas aeruginosa aisladas de ambientes contaminadas con petr\u00f3leo.","author":"C Querebal\u00fa Garc\u00eda","year":"2020"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"287-331","DOI":"10.1146\/annurev.micro.52.1.287","article-title":"development of hybrid strains for the mineralization of chloroaromatics by patchwork assembly.","volume":"52","author":"W Reineke","year":"1998","journal-title":"Ann. Rev. Microbiol."},{"key":"ref58","first-page":"11","article-title":"Degradaci\u00f3n de n-alcanos por Pseudomonas aeruginosa MGP-1 [Publisher: USB. Universidad Sim\u00f3n Bol\u00edvar Section: Investigaci\u00f3n Universitaria Multidisciplinaria: Revista de Investigaci\u00f3n de la Universidad Sim\u00f3n Bol\u00edvar].","volume":"7","author":"R Salgado Brito","year":"2008","journal-title":"Investigaci\u00f3n Universitaria Multidisciplinaria: Revista de Investigaci\u00f3n de la Universidad Sim\u00f3n Bol\u00edvar."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"000685","DOI":"10.1099\/mgen.0.000685","article-title":"Bakta: Rapid and standardized annotation of bacterial genomes via alignment-free sequence identification [Publisher: Microbiology Society].","volume":"7","author":"O Schwengers","year":"2021","journal-title":"Microbial Genomics."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"84-92","DOI":"10.1007\/s40726-019-00113-8","article-title":"Biological degradation of polycyclic aromatic compounds (PAHs) in soil: A current perspective.","volume":"5","author":"E Shahsavari","year":"2019","journal-title":"Curr. Pollut. Rep."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"11527-11535","DOI":"10.1021\/acs.est.5b03197","article-title":"Distribution, elimination, and rearrangement of cyclic volatile methylsiloxanes in oil-contaminated soil of the Shengli oilfield, China.","volume":"49","author":"Y Shi","year":"2015","journal-title":"Environ. Sci. Technol."},{"key":"ref62","doi-asserted-by":"publisher","first-page":"3210-3212","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs.","volume":"31","author":"F Sim\u00e3o","year":"2015","journal-title":"Bioinformatics."},{"key":"ref71","article-title":"MinCED.","author":"C Skennerton","year":"2021","journal-title":"Github."},{"key":"ref68","doi-asserted-by":"publisher","first-page":"1312-1313","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies.","volume":"30","author":"A Stamatakis","year":"2014","journal-title":"Bioinformatics."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"247-258","DOI":"10.15381\/rpb.v22i2.11359","article-title":"Optimizacion y modificacion del metodo para la deteccion de ramnolipidos.","volume":"22","author":"T Tabuchi","year":"2015","journal-title":"Revista Peruana de Biologia."},{"key":"ref63","article-title":"Evaluaci\u00f3n de la capacidad hidrocarbonocl\u00e1stica de un consorcio formulado con bacterias aisladas de canchas de tratamiento de tierra contaminada con petr\u00f3leo.","author":"P Ter\u00e1n Morales","year":"2020"},{"key":"ref64","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1186\/s13059-020-02090-4","article-title":"Producing polished prokaryotic pangenomes with the panaroo pipeline.","volume":"21","author":"G Tonkin-Hill","year":"2020","journal-title":"Genome Biol."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"1679-1686","DOI":"10.1099\/mic.0.28605-0","article-title":"Mutation analysis of the Pseudomonas aeruginosa mvfR and pqsABCDE gene promoters demonstrates complex quorum-sensing circuitry.","volume":"152","author":"G Xiao","year":"2006","journal-title":"Microbiology."},{"key":"ref70","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.00519","article-title":"Integrated Comparative Genomic Analysis and Phenotypic Profiling of Pseudomonas aeruginosa Isolates From Crude Oil.","volume":"11","author":"A Xu","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"1-16","DOI":"10.1038\/s42003-021-01968-8","article-title":"The Pseudomonas aeruginosa substrate-binding protein ttg2d functions as a general glycerophospho- lipid transporter across the periplasm [Publisher: Nature Publishing Group].","volume":"4","author":"D Yero","year":"2021","journal-title":"Commun. Biol."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"14940-14946","DOI":"10.1016\/S0021-9258(18)63793-7","article-title":"Toluene degradation by Pseudomonas putida f1: Nucleotide sequence of the todC1c2bade genes and their expression in Escherichia coli [Publisher: Elsevier].","volume":"264","author":"G Zylstra","year":"1989","journal-title":"J. Biol. 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