{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T19:15:13Z","timestamp":1778008513040,"version":"3.51.4"},"reference-count":74,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2021,11,1]],"date-time":"2021-11-01T00:00:00Z","timestamp":1635724800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia","doi-asserted-by":"publisher","award":["PTDC\/BIA-MIC\/31045\/2017"],"award-info":[{"award-number":["PTDC\/BIA-MIC\/31045\/2017"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia","doi-asserted-by":"publisher","award":["UIDB\/04293\/2020, UIDB\/04423\/2020 and UIDP\/04423\/2020"],"award-info":[{"award-number":["UIDB\/04293\/2020, UIDB\/04423\/2020 and UIDP\/04423\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia","doi-asserted-by":"publisher","award":["SFRH\/BD\/136357\/2018, CEECIND\/02968\/2017 and DL57\/2016\/CP1355\/CT0023"],"award-info":[{"award-number":["SFRH\/BD\/136357\/2018, CEECIND\/02968\/2017 and DL57\/2016\/CP1355\/CT0023"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Oceanic Observatory of Madeira","award":["M1420-01-0145-FEDER-000001"],"award-info":[{"award-number":["M1420-01-0145-FEDER-000001"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Marine Drugs"],"abstract":"<jats:p>The deep-sea constitutes a true unexplored frontier and a potential source of innovative drug scaffolds. Here, we present the genome sequence of two novel marine actinobacterial strains, MA3_2.13 and S07_1.15, isolated from deep-sea samples (sediments and sponge) and collected at Madeira archipelago (NE Atlantic Ocean; Portugal). The de novo assembly of both genomes was achieved using a hybrid strategy that combines short-reads (Illumina) and long-reads (PacBio) sequencing data. Phylogenetic analyses showed that strain MA3_2.13 is a new species of the Streptomyces genus, whereas strain S07_1.15 is closely related to the type strain of Streptomyces xinghaiensis. In silico analysis revealed that the total length of predicted biosynthetic gene clusters (BGCs) accounted for a high percentage of the MA3_2.13 genome, with several potential new metabolites identified. Strain S07_1.15 had, with a few exceptions, a predicted metabolic profile similar to S. xinghaiensis. In this work, we implemented a straightforward approach for generating high-quality genomes of new bacterial isolates and analyse in silico their potential to produce novel NPs. The inclusion of these in silico dereplication steps allows to minimize the rediscovery rates of traditional natural products screening methodologies and expedite the drug discovery process.<\/jats:p>","DOI":"10.3390\/md19110621","type":"journal-article","created":{"date-parts":[[2021,11,1]],"date-time":"2021-11-01T22:22:24Z","timestamp":1635805344000},"page":"621","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Complete Genome Sequence of Two Deep-Sea Streptomyces Isolates from Madeira Archipelago and Evaluation of Their Biosynthetic Potential"],"prefix":"10.3390","volume":"19","author":[{"given":"Pedro","family":"Albuquerque","sequence":"first","affiliation":[{"name":"i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal"},{"name":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal"}]},{"given":"In\u00eas","family":"Ribeiro","sequence":"additional","affiliation":[{"name":"CIIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos s\/n, 4450-208 Matosinhos, Portugal"},{"name":"ICBAS\u2014Instituto de Ci\u00eancias Biom\u00e9dicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal"}]},{"given":"Sofia","family":"Correia","sequence":"additional","affiliation":[{"name":"CIIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos s\/n, 4450-208 Matosinhos, Portugal"}]},{"given":"Ana Paula","family":"Mucha","sequence":"additional","affiliation":[{"name":"CIIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos s\/n, 4450-208 Matosinhos, Portugal"},{"name":"Departamento de Biologia, Faculdade de Ci\u00eancias, Universidade do Porto, Rua do Campo Alegre, Edif\u00edcio FC4, 4169-007 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4396-2122","authenticated-orcid":false,"given":"Paula","family":"Tamagnini","sequence":"additional","affiliation":[{"name":"i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal"},{"name":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal"},{"name":"Departamento de Biologia, Faculdade de Ci\u00eancias, Universidade do Porto, Rua do Campo Alegre, Edif\u00edcio FC4, 4169-007 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6335-2554","authenticated-orcid":false,"given":"Andreia","family":"Braga-Henriques","sequence":"additional","affiliation":[{"name":"OOM\u2014Oceanic Observatory of Madeira & MARE\u2014Marine and Environmental Sciences Centre, ARDITI\u2014Ag\u00eancia Regional para o Desenvolvimento da Investiga\u00e7\u00e3o Tecnologia e Inova\u00e7\u00e3o, Caminho da Penteada, 9020-105 Funchal, Portugal"},{"name":"Regional Directorate for Fisheries, Regional Secretariat for the Sea and Fisheries, Government of the Azores, Rua C\u00f4nsul Dabney\u2014Col\u00f3nia Alem\u00e3, 9900-014 Horta, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7181-0540","authenticated-orcid":false,"given":"Maria de F\u00e1tima","family":"Carvalho","sequence":"additional","affiliation":[{"name":"CIIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Avenida General Norton de Matos s\/n, 4450-208 Matosinhos, Portugal"},{"name":"ICBAS\u2014Instituto de Ci\u00eancias Biom\u00e9dicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6105-522X","authenticated-orcid":false,"given":"Marta V.","family":"Mendes","sequence":"additional","affiliation":[{"name":"i3S\u2014Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal"},{"name":"IBMC\u2014Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2021,11,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1007\/s11101-015-9448-7","article-title":"Dereplication strategies in natural product research: How many tools and methodologies behind the same concept?","volume":"16","author":"Hubert","year":"2017","journal-title":"Phytochem. Rev."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1007\/s10142-015-0433-4","article-title":"Insights from 20 years of bacterial genome sequencing","volume":"15","author":"Land","year":"2015","journal-title":"Funct. Integr. Genom."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Goh, K.M., Shahar, S., Chan, K.G., Chong, C.S., Amran, S.I., Sani, M.H., Zakaria, I.I., and Kahar, U.M. (2019). Current status and potential applications of underexplored prokaryotes. Microorganisms, 7.","DOI":"10.3390\/microorganisms7100468"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Doroghazi, J.R., and Metcalf, W.W. (2013). Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes. BMC Genom., 14.","DOI":"10.1186\/1471-2164-14-611"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2003","DOI":"10.1038\/s41598-020-58904-9","article-title":"Genome mining of biosynthetic and chemotherapeutic gene clusters in Streptomyces bacteria","volume":"10","author":"Belknap","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1007\/s10295-016-1815-x","article-title":"Gifted microbes for genome mining and natural product discovery","volume":"44","author":"Baltz","year":"2017","journal-title":"J. Ind. Microbiol. Biotechnol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1007\/s00253-007-0900-5","article-title":"Strategies to unravel the function of orphan biosynthesis pathways: Recent examples and future prospects","volume":"75","author":"Gross","year":"2007","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"6114","DOI":"10.1093\/nar\/gkz471","article-title":"Primary transcriptome and translatome analysis determines transcriptional and translational regulatory elements encoded in the Streptomyces clavuligerus genome","volume":"47","author":"Hwang","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Wick, R.R., Judd, L.M., Gorrie, C.L., and Holt, K.E. (2017). Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol., 13.","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.ygeno.2010.03.001","article-title":"Assembly algorithms for next-generation sequencing data","volume":"95","author":"Miller","year":"2010","journal-title":"Genomics"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"866","DOI":"10.1093\/bib\/bbx147","article-title":"Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data","volume":"20","author":"Jayakumar","year":"2019","journal-title":"Brief. Bioinform."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1016\/j.gpb.2015.08.002","article-title":"PacBio sequencing and its applications","volume":"13","author":"Rhoads","year":"2015","journal-title":"Genom. Proteom. Bioinform."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"128","DOI":"10.4172\/2469-9853.1000128","article-title":"Long read sequencing technology to solve complex genomic regions assembly in plants","volume":"3","author":"Bellec","year":"2016","journal-title":"Next Generat. Sequenc. Applic."},{"key":"ref_14","first-page":"e000294","article-title":"Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes","volume":"5","author":"Shaw","year":"2019","journal-title":"Microb. Genom."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/s41597-020-0395-9","article-title":"Thirty complete Streptomyces genome sequences for mining novel secondary metabolite biosynthetic gene clusters","volume":"7","author":"Lee","year":"2020","journal-title":"Sci. Data"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Jagannathan, S.V., Manemann, E.M., Rowe, S.E., Callender, M.C., and Soto, W. (2021). Marine actinomycetes, new sources of biotechnological products. Mar. Drugs, 19.","DOI":"10.3390\/md19070365"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1007\/s00253-019-10227-0","article-title":"Exploration and genome mining of natural products from marine Streptomyces","volume":"104","author":"Yang","year":"2020","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"760","DOI":"10.3389\/fmicb.2017.00760","article-title":"Deep sea actinomycetes and their secondary metabolites","volume":"8","author":"Kamjam","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Wang, Y.N., Meng, L.H., and Wang, B.G. (2020). Progress in research on bioactive secondary metabolites from deep-sea derived microorganisms. Mar. Drugs, 18.","DOI":"10.3390\/md18120614"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"581","DOI":"10.3390\/md13010581","article-title":"Biosynthesis of akaeolide and lorneic acids and annotation of type I polyketide synthase gene clusters in the genome of Streptomyces sp. NPS554","volume":"13","author":"Zhou","year":"2015","journal-title":"Mar. Drugs"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"2870","DOI":"10.1099\/ijs.0.009878-0","article-title":"Streptomyces xinghaiensis sp. nov., isolated from marine sediment","volume":"59","author":"Zhao","year":"2009","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., Formsma, K., Gerdes, S., Glass, E.M., and Kubal, M. (2008). The RAST Server: Rapid annotations using subsystems technology. BMC Genom., 9.","DOI":"10.1186\/1471-2164-9-75"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"W81","DOI":"10.1093\/nar\/gkz310","article-title":"antiSMASH 5.0: Updates to the secondary metabolite genome mining pipeline","volume":"47","author":"Blin","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1007\/978-1-4939-9173-0_14","article-title":"BUSCO: Assessing genome assembly and annotation completeness","volume":"1962","author":"Seppey","year":"2019","journal-title":"Methods Mol. Biol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"W246","DOI":"10.1093\/nar\/gky425","article-title":"CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins","volume":"46","author":"Couvin","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3354\/ame01211","article-title":"Comparative actinomycete diversity in marine sediments","volume":"52","author":"Fenical","year":"2008","journal-title":"Aquatic. Microbial. Ecol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"W282","DOI":"10.1093\/nar\/gky467","article-title":"The Microbial Genomes Atlas (MiGA) webserver: Taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level","volume":"46","author":"Rodriguez","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"100803","DOI":"10.1016\/j.margen.2020.100803","article-title":"Complete genome sequence of Streptomyces sp. SCSIO 03032 isolated from Indian Ocean sediment, producing diverse bioactive natural products","volume":"55","author":"Ma","year":"2021","journal-title":"Mar. Genom."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"9549","DOI":"10.1007\/s00253-018-9337-2","article-title":"Genome mining of Streptomyces xinghaiensis NRRL B-24674(T) for the discovery of the gene cluster involved in anticomplement activities and detection of novel xiamycin analogs","volume":"102","author":"Chen","year":"2018","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"4162","DOI":"10.1093\/bioinformatics\/btz188","article-title":"GToTree: A user-friendly workflow for phylogenomics","volume":"35","author":"Lee","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1099\/ijsem.0.002516","article-title":"Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes","volume":"68","author":"Chun","year":"2018","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"19126","DOI":"10.1073\/pnas.0906412106","article-title":"Shifting the genomic gold standard for the prokaryotic species definition","volume":"106","author":"Richter","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Penn, K., and Jensen, P.R. (2012). Comparative genomics reveals evidence of marine adaptation in Salinispora species. BMC Genom., 13.","DOI":"10.1186\/1471-2164-13-86"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Ian, E., Malko, D.B., Sekurova, O.N., Bredholt, H., Ruckert, C., Borisova, M.E., Albersmeier, A., Kalinowski, J., Gelfand, M.S., and Zotchev, S.B. (2014). Genomics of sponge-associated Streptomyces spp. closely related to Streptomyces albus J1074: Insights into marine adaptation and secondary metabolite biosynthesis potential. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0096719"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1713","DOI":"10.3389\/fmicb.2019.01713","article-title":"Comparative genomics of marine sponge-derived Streptomyces spp. isolates SM17 and SM18 with their closest terrestrial relatives provides novel insights into environmental niche adaptations and secondary metabolite biosynthesis potential","volume":"10","author":"Almeida","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1016\/j.cell.2014.06.034","article-title":"Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters","volume":"158","author":"Cimermancic","year":"2014","journal-title":"Cell"},{"key":"ref_37","first-page":"D454","article-title":"MIBiG 2.0: A repository for biosynthetic gene clusters of known function","volume":"48","author":"Kautsar","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"105252","DOI":"10.1016\/j.micpath.2021.105252","article-title":"Genome mining of biosynthetic gene clusters intended for secondary metabolites conservation in actinobacteria","volume":"161","author":"Arulprakasam","year":"2021","journal-title":"Microb. Pathog."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1021\/acs.orglett.9b00208","article-title":"Genome mining of Streptomyces atratus SCSIO ZH16: Discovery of atratumycin and identification of its biosynthetic gene cluster","volume":"21","author":"Sun","year":"2019","journal-title":"Org. Lett."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Yang, Z., Wei, X., He, J., Sun, C., Ju, J., and Ma, J. (2019). Characterization of the noncanonical regulatory and transporter genes in atratumycin biosynthesis and production in a heterologous host. Mar. Drugs, 17.","DOI":"10.3390\/md17100560"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1002\/cbic.201800762","article-title":"Identifying the biosynthetic gene cluster for triacsins with an N-hydroxytriazene moiety","volume":"20","author":"Twigg","year":"2019","journal-title":"ChemBioChem"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"2172","DOI":"10.1002\/cbic.201500407","article-title":"The cremeomycin biosynthetic gene cluster encodes a pathway for diazo formation","volume":"16","author":"Waldman","year":"2015","journal-title":"ChemBioChem"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"9083","DOI":"10.1021\/jacs.8b05354","article-title":"Discovery of unprecedented hydrazine-forming machinery in bacteria","volume":"140","author":"Matsuda","year":"2018","journal-title":"J. Am. Chem. Soc."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1906","DOI":"10.1093\/gbe\/evw125","article-title":"Phylogenomic analysis of natural products biosynthetic gene clusters allows discovery of arseno-organic metabolites in model Streptomycetes","volume":"8","author":"Kopp","year":"2016","journal-title":"Genome Biol. Evol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"8449","DOI":"10.1073\/pnas.1917664117","article-title":"Unraveling the iterative type I polyketide synthases hidden in Streptomyces","volume":"117","author":"Wang","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"4840","DOI":"10.1002\/anie.201402078","article-title":"Mechanistic insights into polycycle formation by reductive cyclization in ikarugamycin biosynthesis","volume":"53","author":"Zhang","year":"2014","journal-title":"Angew. Chem. Int. Ed. Engl."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"6258","DOI":"10.1073\/pnas.1019077108","article-title":"Identification of a bioactive 51-membered macrolide complex by activation of a silent polyketide synthase in Streptomyces ambofaciens","volume":"108","author":"Laureti","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"4828","DOI":"10.1039\/C4OB00970C","article-title":"Fluoroacetate biosynthesis from the marine-derived bacterium Streptomyces xinghaiensis NRRL B-24674","volume":"12","author":"Huang","year":"2014","journal-title":"Org. Biomol. Chem."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1039\/b415087m","article-title":"Fluorometabolite biosynthesis and the fluorinase from Streptomyces cattleya","volume":"21","author":"Deng","year":"2004","journal-title":"Nat. Prod. Rep."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Wang, P., Wang, D., Zhang, R., Wang, Y., Kong, F., Fu, P., and Zhu, W. (2020). Novel macrolactams from a deep-sea-derived Streptomyces species. Mar. Drugs, 19.","DOI":"10.3390\/md19010013"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"2075","DOI":"10.1099\/mic.0.000386","article-title":"Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters","volume":"162","author":"Schorn","year":"2016","journal-title":"Microbiology"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1548","DOI":"10.1016\/j.csbj.2020.06.024","article-title":"Mini review: Genome mining approaches for the identification of secondary metabolite biosynthetic gene clusters in Streptomyces","volume":"18","author":"Lee","year":"2020","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Thrash, A., Hoffmann, F., and Perkins, A. (2020). Toward a more holistic method of genome assembly assessment. BMC Bioinform., 21.","DOI":"10.1186\/s12859-020-3382-4"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1038\/nrmicro1236","article-title":"Opinion: Re-evaluating prokaryotic species","volume":"3","author":"Gevers","year":"2005","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"10973","DOI":"10.1038\/s41598-019-47406-y","article-title":"The genome sequence of Streptomyces rochei 7434AN4, which carries a linear chromosome and three characteristic linear plasmids","volume":"9","author":"Nindita","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1038\/ismej.2010.103","article-title":"Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913","volume":"5","author":"Qin","year":"2011","journal-title":"ISME J."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1128\/jb.173.2.697-703.1991","article-title":"16S ribosomal DNA amplification for phylogenetic study","volume":"173","author":"Weisburg","year":"1991","journal-title":"J. Bacteriol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"6614","DOI":"10.1093\/nar\/gkw569","article-title":"NCBI prokaryotic genome annotation pipeline","volume":"44","author":"Tatusova","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"W448","DOI":"10.1093\/nar\/gkt391","article-title":"BAGEL3: Automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides","volume":"41","author":"Kok","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"W80","DOI":"10.1093\/nar\/gkx408","article-title":"RiPPMiner: A bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links","volume":"45","author":"Agrawal","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"W362","DOI":"10.1093\/nar\/gkr323","article-title":"NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity","volume":"39","author":"Rottig","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"2115","DOI":"10.1093\/molbev\/msx148","article-title":"Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper","volume":"34","author":"Forslund","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"eggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses","volume":"47","author":"Szklarczyk","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"W30","DOI":"10.1093\/nar\/gkx343","article-title":"IslandViewer 4: Expanded prediction of genomic islands for larger-scale datasets","volume":"45","author":"Bertelli","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: A better, faster version of the PHAST phage search tool","volume":"44","author":"Arndt","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"W185","DOI":"10.1093\/nar\/gkab341","article-title":"EDGAR3.0: Comparative genomics and phylogenomics on a scalable infrastructure","volume":"49","author":"Dieckmann","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"D633","DOI":"10.1093\/nar\/gkt1244","article-title":"Ribosomal Database Project: Data and tools for high throughput rRNA analysis","volume":"42","author":"Cole","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Jolley, K.A., and Maiden, M.C. (2010). BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics, 11.","DOI":"10.1186\/1471-2105-11-595"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1093\/dnares\/dsq026","article-title":"Genome sequence of Kitasatospora setae NBRC 14216T: An evolutionary snapshot of the family Streptomycetaceae","volume":"17","author":"Ichikawa","year":"2010","journal-title":"DNA Res."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1039\/C5AY02550H","article-title":"Genomics and taxonomy in diagnostics for food security: Soft-rotting enterobacterial plant pathogens","volume":"8","author":"Pritchard","year":"2016","journal-title":"Anal. Methods"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1529","DOI":"10.1128\/JCM.02981-13","article-title":"Benchmarking of methods for genomic taxonomy","volume":"52","author":"Larsen","year":"2014","journal-title":"J. Clin. Microbiol."}],"container-title":["Marine Drugs"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1660-3397\/19\/11\/621\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T07:24:15Z","timestamp":1760167455000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1660-3397\/19\/11\/621"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11,1]]},"references-count":74,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2021,11]]}},"alternative-id":["md19110621"],"URL":"https:\/\/doi.org\/10.3390\/md19110621","relation":{},"ISSN":["1660-3397"],"issn-type":[{"value":"1660-3397","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,11,1]]}}}