Genome Mining of <i>Pseudomonas</i> Species: Diversity and Evolution of Metabolic and Biosynthetic Potential
Microbial genome sequencing has uncovered a myriad of natural products (NPs) that have yet to be explored. Bacteria in the genus <i>Pseudomonas</i> serve as pathogens, plant growth promoters, and therapeutically, industrially, and environmentally important microorganisms. Though most spe...
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| Format: | Article |
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MDPI AG
2021-12-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/26/24/7524 |
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| author | Khorshed Alam Md. Mahmudul Islam Caiyun Li Sharmin Sultana Lin Zhong Qiyao Shen Guangle Yu Jinfang Hao Youming Zhang Ruijuan Li Aiying Li |
| author_facet | Khorshed Alam Md. Mahmudul Islam Caiyun Li Sharmin Sultana Lin Zhong Qiyao Shen Guangle Yu Jinfang Hao Youming Zhang Ruijuan Li Aiying Li |
| author_sort | Khorshed Alam |
| collection | DOAJ |
| description | Microbial genome sequencing has uncovered a myriad of natural products (NPs) that have yet to be explored. Bacteria in the genus <i>Pseudomonas</i> serve as pathogens, plant growth promoters, and therapeutically, industrially, and environmentally important microorganisms. Though most species of <i>Pseudomonas</i> have a large number of NP biosynthetic gene clusters (BGCs) in their genomes, it is difficult to link many of these BGCs with products under current laboratory conditions. In order to gain new insights into the diversity, distribution, and evolution of these BGCs in <i>Pseudomonas</i> for the discovery of unexplored NPs, we applied several bioinformatic programming approaches to characterize BGCs from <i>Pseudomonas</i> reference genome sequences available in public databases along with phylogenetic and genomic comparison. Our research revealed that most BGCs in the genomes of <i>Pseudomonas</i> species have a high diversity for NPs at the species and subspecies levels and built the correlation of species with BGC taxonomic ranges. These data will pave the way for the algorithmic detection of species- and subspecies-specific pathways for NP development. |
| first_indexed | 2024-03-10T03:29:45Z |
| format | Article |
| id | doaj.art-e22f23b3523e44d89995990470730d24 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T03:29:45Z |
| publishDate | 2021-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-e22f23b3523e44d89995990470730d242023-11-23T09:45:25ZengMDPI AGMolecules1420-30492021-12-012624752410.3390/molecules26247524Genome Mining of <i>Pseudomonas</i> Species: Diversity and Evolution of Metabolic and Biosynthetic PotentialKhorshed Alam0Md. Mahmudul Islam1Caiyun Li2Sharmin Sultana3Lin Zhong4Qiyao Shen5Guangle Yu6Jinfang Hao7Youming Zhang8Ruijuan Li9Aiying Li10Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, ChinaDepartment of Microbiology, Rajshahi Institute of Biosciences (RIB), University of Rajshahi, Rajshahi 6212, BangladeshHelmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, ChinaDepartment of Microbiology, University of Chittagong, Chittagong 4331, BangladeshHelmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, ChinaHelmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, ChinaHelmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, ChinaHelmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, ChinaHelmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, ChinaHelmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, ChinaHelmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, ChinaMicrobial genome sequencing has uncovered a myriad of natural products (NPs) that have yet to be explored. Bacteria in the genus <i>Pseudomonas</i> serve as pathogens, plant growth promoters, and therapeutically, industrially, and environmentally important microorganisms. Though most species of <i>Pseudomonas</i> have a large number of NP biosynthetic gene clusters (BGCs) in their genomes, it is difficult to link many of these BGCs with products under current laboratory conditions. In order to gain new insights into the diversity, distribution, and evolution of these BGCs in <i>Pseudomonas</i> for the discovery of unexplored NPs, we applied several bioinformatic programming approaches to characterize BGCs from <i>Pseudomonas</i> reference genome sequences available in public databases along with phylogenetic and genomic comparison. Our research revealed that most BGCs in the genomes of <i>Pseudomonas</i> species have a high diversity for NPs at the species and subspecies levels and built the correlation of species with BGC taxonomic ranges. These data will pave the way for the algorithmic detection of species- and subspecies-specific pathways for NP development.https://www.mdpi.com/1420-3049/26/24/7524<i>Pseudomonas</i>genome miningnatural productsbiosynthetic pathwaygene clustergenome comparison |
| spellingShingle | Khorshed Alam Md. Mahmudul Islam Caiyun Li Sharmin Sultana Lin Zhong Qiyao Shen Guangle Yu Jinfang Hao Youming Zhang Ruijuan Li Aiying Li Genome Mining of <i>Pseudomonas</i> Species: Diversity and Evolution of Metabolic and Biosynthetic Potential Molecules <i>Pseudomonas</i> genome mining natural products biosynthetic pathway gene cluster genome comparison |
| title | Genome Mining of <i>Pseudomonas</i> Species: Diversity and Evolution of Metabolic and Biosynthetic Potential |
| title_full | Genome Mining of <i>Pseudomonas</i> Species: Diversity and Evolution of Metabolic and Biosynthetic Potential |
| title_fullStr | Genome Mining of <i>Pseudomonas</i> Species: Diversity and Evolution of Metabolic and Biosynthetic Potential |
| title_full_unstemmed | Genome Mining of <i>Pseudomonas</i> Species: Diversity and Evolution of Metabolic and Biosynthetic Potential |
| title_short | Genome Mining of <i>Pseudomonas</i> Species: Diversity and Evolution of Metabolic and Biosynthetic Potential |
| title_sort | genome mining of i pseudomonas i species diversity and evolution of metabolic and biosynthetic potential |
| topic | <i>Pseudomonas</i> genome mining natural products biosynthetic pathway gene cluster genome comparison |
| url | https://www.mdpi.com/1420-3049/26/24/7524 |
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