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Classification of the plant-associated lifestyle of Pseudomonas strains using genome properties and machine learning. Sci Rep 2022; 12:10857. [PMID: 35760985 PMCID: PMC9237127 DOI: 10.1038/s41598-022-14913-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 06/15/2022] [Indexed: 12/30/2022] Open
Abstract
The rhizosphere, the region of soil surrounding roots of plants, is colonized by a unique population of Plant Growth Promoting Rhizobacteria (PGPR). Many important PGPR as well as plant pathogens belong to the genus Pseudomonas. There is, however, uncertainty on the divide between beneficial and pathogenic strains as previously thought to be signifying genomic features have limited power to separate these strains. Here we used the Genome properties (GP) common biological pathways annotation system and Machine Learning (ML) to establish the relationship between the genome wide GP composition and the plant-associated lifestyle of 91 Pseudomonas strains isolated from the rhizosphere and the phyllosphere representing both plant-associated phenotypes. GP enrichment analysis, Random Forest model fitting and feature selection revealed 28 discriminating features. A test set of 75 new strains confirmed the importance of the selected features for classification. The results suggest that GP annotations provide a promising computational tool to better classify the plant-associated lifestyle.
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Draft Genome Sequences of Three Isolates of Golubevia sp. Basidiomycete Fungi Isolated from Powdery Mildew Pustules. Microbiol Resour Announc 2020; 9:9/23/e00473-20. [PMID: 32499356 PMCID: PMC7272565 DOI: 10.1128/mra.00473-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The genomes of three Golubevia isolates (BC0812, BC0850, and BC0902) that have been shown to reduce conidiation of Blumeria graminis f. sp. tritici were sequenced using a dual-platform approach. The assembled genomes will help to elucidate the molecular mechanisms underlying the biocontrol effect of this understudied group. The genomes of three Golubevia isolates (BC0812, BC0850, and BC0902) that have been shown to reduce conidiation of Blumeria graminis f. sp. tritici were sequenced using a dual-platform approach. The assembled genomes will help to elucidate the molecular mechanisms underlying the biocontrol effect of this understudied group.
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Warris S, Schijlen E, van de Geest H, Vegesna R, Hesselink T, Te Lintel Hekkert B, Sanchez Perez G, Medvedev P, Makova KD, de Ridder D. Correcting palindromes in long reads after whole-genome amplification. BMC Genomics 2018; 19:798. [PMID: 30400848 PMCID: PMC6218980 DOI: 10.1186/s12864-018-5164-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/15/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Next-generation sequencing requires sufficient DNA to be available. If limited, whole-genome amplification is applied to generate additional amounts of DNA. Such amplification often results in many chimeric DNA fragments, in particular artificial palindromic sequences, which limit the usefulness of long sequencing reads. RESULTS Here, we present Pacasus, a tool for correcting such errors. Two datasets show that it markedly improves read mapping and de novo assembly, yielding results similar to these that would be obtained with non-amplified DNA. CONCLUSIONS With Pacasus long-read technologies become available for sequencing targets with very small amounts of DNA, such as single cells or even single chromosomes.
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Affiliation(s)
- Sven Warris
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands.
| | - Elio Schijlen
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Henri van de Geest
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands.,Present address Genetwister Technologies BV, Wageningen, The Netherlands
| | - Rahulsimham Vegesna
- Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Computation, Bioinformatics, Statistics Graduate Training Program, Pennsylvania State University, University Park, State College, PA, 16802, USA.,The Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Thamara Hesselink
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Bas Te Lintel Hekkert
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands
| | - Gabino Sanchez Perez
- Applied Bioinformatics, Wageningen University and Research, Wageningen, The Netherlands.,Present address Genetwister Technologies BV, Wageningen, The Netherlands
| | - Paul Medvedev
- The Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Department of Computer Science and Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA.,The Center for Medical Genomics, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Kateryna D Makova
- The Center for Medical Genomics, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Department of Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands
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