401
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Zhou X, Peris D, Kominek J, Kurtzman CP, Hittinger CT, Rokas A. In Silico Whole Genome Sequencer and Analyzer (iWGS): a Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies. G3 (BETHESDA, MD.) 2016; 6:3655-3662. [PMID: 27638685 PMCID: PMC5100864 DOI: 10.1534/g3.116.034249] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/08/2016] [Indexed: 11/18/2022]
Abstract
The availability of genomes across the tree of life is highly biased toward vertebrates, pathogens, human disease models, and organisms with relatively small and simple genomes. Recent progress in genomics has enabled the de novo decoding of the genome of virtually any organism, greatly expanding its potential for understanding the biology and evolution of the full spectrum of biodiversity. The increasing diversity of sequencing technologies, assays, and de novo assembly algorithms have augmented the complexity of de novo genome sequencing projects in nonmodel organisms. To reduce the costs and challenges in de novo genome sequencing projects and streamline their experimental design and analysis, we developed iWGS ( in silicoWhole Genome Sequencer and Analyzer), an automated pipeline for guiding the choice of appropriate sequencing strategy and assembly protocols. iWGS seamlessly integrates the four key steps of a de novo genome sequencing project: data generation (through simulation), data quality control, de novo assembly, and assembly evaluation and validation. The last three steps can also be applied to the analysis of real data. iWGS is designed to enable the user to have great flexibility in testing the range of experimental designs available for genome sequencing projects, and supports all major sequencing technologies and popular assembly tools. Three case studies illustrate how iWGS can guide the design of de novo genome sequencing projects, and evaluate the performance of a wide variety of user-specified sequencing strategies and assembly protocols on genomes of differing architectures. iWGS, along with a detailed documentation, is freely available at https://github.com/zhouxiaofan1983/iWGS.
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Affiliation(s)
- Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
| | - David Peris
- Laboratory of Genetics, Genome Center of Wisconsin, Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Wisconsin 53706
| | - Jacek Kominek
- Laboratory of Genetics, Genome Center of Wisconsin, Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Wisconsin 53706
| | - Cletus P Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, Illinois 61604
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Wisconsin 53706
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
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402
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Strassert JFH, Tikhonenkov DV, Pombert JF, Kolisko M, Tai V, Mylnikov AP, Keeling PJ. Moramonas marocensis gen. nov., sp. nov.: a jakobid flagellate isolated from desert soil with a bacteria-like, but bloated mitochondrial genome. Open Biol 2016; 6:150239. [PMID: 26887409 PMCID: PMC4772810 DOI: 10.1098/rsob.150239] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A new jakobid genus has been isolated from Moroccan desert soil. The cyst-forming protist Moramonas marocensis gen. nov., sp. nov. has two anteriorly inserted flagella of which one points to the posterior cell pole accompanying the ventral feeding groove and is equipped with a dorsal vane-a feature typical for the Jakobida. It further shows a flagellar root system consisting of singlet microtubular root, left root (R1), right root (R2) and typical fibres associated with R1 and R2. The affiliation of M. marocensis to the Jakobida was confirmed by molecular phylogenetic analyses of the SSU rRNA gene, five nuclear genes and 66 mitochondrial protein-coding genes. The mitochondrial genome has the high number of genes typical for jakobids, and bacterial features, such as the four-subunit RNA polymerase and Shine-Dalgarno sequences upstream of the coding regions of several genes. The M. marocensis mitochondrial genome encodes a similar number of genes as other jakobids, but is unique in its very large genome size (greater than 264 kbp), which is three to four times higher than that of any other jakobid species investigated yet. This increase seems to be due to a massive expansion in non-coding DNA, creating a bloated genome like those of plant mitochondria.
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Affiliation(s)
- Jürgen F H Strassert
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Denis V Tikhonenkov
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Region, Russia
| | | | - Martin Kolisko
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vera Tai
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander P Mylnikov
- Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Region, Russia
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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403
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Draft Genome Sequences of One Marine and One Clinical Vibrio parahaemolyticus Strain, Both Isolated in Sweden. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01196-16. [PMID: 27789643 PMCID: PMC5084867 DOI: 10.1128/genomea.01196-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Vibrio parahaemolyticus is the leading bacterial pathogen associated with seafood consumption. Here, we report the draft genome sequences of one marine and one clinical strain, both isolated in Sweden. These sequences will inform future comparative analysis of V. parahaemolyticus in northern Europe.
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404
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Draft Genome Sequence of Yarrowia lipolytica Strain A-101 Isolated from Polluted Soil in Poland. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01094-16. [PMID: 27795258 PMCID: PMC5054328 DOI: 10.1128/genomea.01094-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Yarrowia lipolytica is an early diverging species of the Saccharomycotina subphylum, which is recognized as a valuable host for many biotechnological applications exploiting its oleaginous capacities. The 20.5-Mb genome of the Polish Y. lipolytica strain A-101 will greatly help decipher the genetic basis of the regulation of its lipid metabolism.
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405
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Strepis N, Sánchez-Andrea I, van Gelder AH, van Kruistum H, Shapiro N, Kyrpides N, Göker M, Klenk HP, Schaap P, Stams AJM, Sousa DZ. Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses. Int J Syst Evol Microbiol 2016; 66:3957-3963. [DOI: 10.1099/ijsem.0.001294] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Nikolaos Strepis
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Laboratory of Systems and Synthetic Biology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Antonie H. van Gelder
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Henri van Kruistum
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Nicole Shapiro
- DOE Joint Genome Institute, 2800 Mitchell Drive 100, Walnut Creek, CA 94598, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, 2800 Mitchell Drive 100, Walnut Creek, CA 94598, USA
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
- School of Biology, Newcastle University, Ridley Building 2, Newcastle, NE1 7RU, UK
| | - Peter Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Diana Z. Sousa
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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406
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Rare Spontaneous Loss of Multiresistance Gene Carrying IncI/ST12 Plasmid in Escherichia coli in Pig Microbiota. Antimicrob Agents Chemother 2016; 60:6046-9. [PMID: 27480865 DOI: 10.1128/aac.00864-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/05/2016] [Indexed: 11/20/2022] Open
Abstract
Resistance to extended-spectrum cephalosporins (ESCs) is a matter of considerable concern for public health. Here, we studied the spontaneous loss of an extended-spectrum beta-lactamase (ESBL)-encoding plasmid from a rifampin-resistant Escherichia coli isolate orally inoculated into pigs under controlled conditions. Fecal samples were collected and cultured on rifampin-supplemented medium, and the resistance of the E. coli isolates to ESCs was studied by phenotypic tests, PCR detection of plasmid genes, and complete sequencing. The results showed that only 3 out of 353 rifampin-resistant E. coli isolates were ESC susceptible, and PCR and bioinformatics analysis confirmed the loss of the plasmid. These in vivo experiments indicate that the loss of an ESBL-encoding plasmid seems a rare event in gut microbiota.
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407
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Therkildsen NO, Palumbi SR. Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species. Mol Ecol Resour 2016; 17:194-208. [DOI: 10.1111/1755-0998.12593] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/27/2016] [Accepted: 07/02/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Nina Overgaard Therkildsen
- Hopkins Marine Station; Department of Biology; Stanford University; 120 Oceanview Blvd. Pacific Grove CA 93950 USA
| | - Stephen R. Palumbi
- Hopkins Marine Station; Department of Biology; Stanford University; 120 Oceanview Blvd. Pacific Grove CA 93950 USA
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408
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Draft Genome Sequence of Endophytic Bacterium Enterobacter asburiae PDA134, Isolated from Date Palm (Phoenix dactylifera L.) Roots. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00848-16. [PMID: 27540071 PMCID: PMC4991716 DOI: 10.1128/genomea.00848-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In this report, a draft of the Enterobacter asburiae strain PDA134 genome was sequenced. This bacterial strain was isolated from the root tissue of a date palm, where it has the ability to produce 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and indole-3-acetic acid (IAA) under salinity stress.
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409
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van der Weide RH, Simonis M, Hermsen R, Toonen P, Cuppen E, de Ligt J. The Genomic Scrapheap Challenge; Extracting Relevant Data from Unmapped Whole Genome Sequencing Reads, Including Strain Specific Genomic Segments, in Rats. PLoS One 2016; 11:e0160036. [PMID: 27501045 PMCID: PMC4976967 DOI: 10.1371/journal.pone.0160036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/12/2016] [Indexed: 01/17/2023] Open
Abstract
Unmapped next-generation sequencing reads are typically ignored while they contain biologically relevant information. We systematically analyzed unmapped reads from whole genome sequencing of 33 inbred rat strains. High quality reads were selected and enriched for biologically relevant sequences; similarity-based analysis revealed clustering similar to previously reported phylogenetic trees. Our results demonstrate that on average 20% of all unmapped reads harbor sequences that can be used to improve reference genomes and generate hypotheses on potential genotype-phenotype relationships. Analysis pipelines would benefit from incorporating the described methods and reference genomes would benefit from inclusion of the genomic segments obtained through these efforts.
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Affiliation(s)
- Robin H. van der Weide
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, Utrecht, The Netherlands
- Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marieke Simonis
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Roel Hermsen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Pim Toonen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Edwin Cuppen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Joep de Ligt
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, Utrecht, The Netherlands
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410
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Torre S, Tattini M, Brunetti C, Guidi L, Gori A, Marzano C, Landi M, Sebastiani F. De Novo Assembly and Comparative Transcriptome Analyses of Red and Green Morphs of Sweet Basil Grown in Full Sunlight. PLoS One 2016; 11:e0160370. [PMID: 27483170 PMCID: PMC4970699 DOI: 10.1371/journal.pone.0160370] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/18/2016] [Indexed: 12/28/2022] Open
Abstract
Sweet basil (Ocimum basilicum), one of the most popular cultivated herbs worldwide, displays a number of varieties differing in several characteristics, such as the color of the leaves. The development of a reference transcriptome for sweet basil, and the analysis of differentially expressed genes in acyanic and cyanic cultivars exposed to natural sunlight irradiance, has interest from horticultural and biological point of views. There is still great uncertainty about the significance of anthocyanins in photoprotection, and how green and red morphs may perform when exposed to photo-inhibitory light, a condition plants face on daily and seasonal basis. We sequenced the leaf transcriptome of the green-leaved Tigullio (TIG) and the purple-leaved Red Rubin (RR) exposed to full sunlight over a four-week experimental period. We assembled and annotated 111,007 transcripts. A total of 5,468 and 5,969 potential SSRs were identified in TIG and RR, respectively, out of which 66 were polymorphic in silico. Comparative analysis of the two transcriptomes showed 2,372 differentially expressed genes (DEGs) clustered in 222 enriched Gene ontology terms. Green and red basil mostly differed for transcripts abundance of genes involved in secondary metabolism. While the biosynthesis of waxes was up-regulated in red basil, the biosynthesis of flavonols and carotenoids was up-regulated in green basil. Data from our study provides a comprehensive transcriptome survey, gene sequence resources and microsatellites that can be used for further investigations in sweet basil. The analysis of DEGs and their functional classification also offers new insights on the functional role of anthocyanins in photoprotection.
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Affiliation(s)
- Sara Torre
- Institute for Sustainable Plant Protection, Department of Biology, Agriculture and Food Sciences, The National Research Council of Italy, Sesto Fiorentino, Italy
| | - Massimiliano Tattini
- Institute for Sustainable Plant Protection, Department of Biology, Agriculture and Food Sciences, The National Research Council of Italy, Sesto Fiorentino, Italy
| | - Cecilia Brunetti
- Trees and Timber Institute, Department of Biology, Agriculture and Food Sciences, The National Research Council of Italy, Sesto Fiorentino, Italy
- Department of Agri-Food Production and Environmental Sciences, University of Florence, Sesto Fiorentino, Italy
| | - Lucia Guidi
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Antonella Gori
- Department of Agri-Food Production and Environmental Sciences, University of Florence, Sesto Fiorentino, Italy
| | - Cristina Marzano
- Department of Agri-Food Production and Environmental Sciences, University of Florence, Sesto Fiorentino, Italy
| | - Marco Landi
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Federico Sebastiani
- Institute for Sustainable Plant Protection, Department of Biology, Agriculture and Food Sciences, The National Research Council of Italy, Sesto Fiorentino, Italy
- * E-mail:
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411
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Draft Genome Sequence of Ustilago trichophora RK089, a Promising Malic Acid Producer. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00749-16. [PMID: 27469969 PMCID: PMC4966473 DOI: 10.1128/genomea.00749-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The basidiomycetous smut fungus Ustilago trichophora RK089 produces malate from glycerol. De novo genome sequencing revealed a 20.7-Mbp genome (301 gap-closed contigs, 246 scaffolds). A comparison to the genome of Ustilago maydis 521 revealed all essential genes for malate production from glycerol contributing to metabolic engineering for improving malate production.
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412
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Akogwu I, Wang N, Zhang C, Gong P. A comparative study of k-spectrum-based error correction methods for next-generation sequencing data analysis. Hum Genomics 2016; 10 Suppl 2:20. [PMID: 27461106 PMCID: PMC4965716 DOI: 10.1186/s40246-016-0068-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Innumerable opportunities for new genomic research have been stimulated by advancement in high-throughput next-generation sequencing (NGS). However, the pitfall of NGS data abundance is the complication of distinction between true biological variants and sequence error alterations during downstream analysis. Many error correction methods have been developed to correct erroneous NGS reads before further analysis, but independent evaluation of the impact of such dataset features as read length, genome size, and coverage depth on their performance is lacking. This comparative study aims to investigate the strength and weakness as well as limitations of some newest k-spectrum-based methods and to provide recommendations for users in selecting suitable methods with respect to specific NGS datasets. METHODS Six k-spectrum-based methods, i.e., Reptile, Musket, Bless, Bloocoo, Lighter, and Trowel, were compared using six simulated sets of paired-end Illumina sequencing data. These NGS datasets varied in coverage depth (10× to 120×), read length (36 to 100 bp), and genome size (4.6 to 143 MB). Error Correction Evaluation Toolkit (ECET) was employed to derive a suite of metrics (i.e., true positives, false positive, false negative, recall, precision, gain, and F-score) for assessing the correction quality of each method. RESULTS Results from computational experiments indicate that Musket had the best overall performance across the spectra of examined variants reflected in the six datasets. The lowest accuracy of Musket (F-score = 0.81) occurred to a dataset with a medium read length (56 bp), a medium coverage (50×), and a small-sized genome (5.4 MB). The other five methods underperformed (F-score < 0.80) and/or failed to process one or more datasets. CONCLUSIONS This study demonstrates that various factors such as coverage depth, read length, and genome size may influence performance of individual k-spectrum-based error correction methods. Thus, efforts have to be paid in choosing appropriate methods for error correction of specific NGS datasets. Based on our comparative study, we recommend Musket as the top choice because of its consistently superior performance across all six testing datasets. Further extensive studies are warranted to assess these methods using experimental datasets generated by NGS platforms (e.g., 454, SOLiD, and Ion Torrent) under more diversified parameter settings (k-mer values and edit distances) and to compare them against other non-k-spectrum-based classes of error correction methods.
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Affiliation(s)
- Isaac Akogwu
- School of Computing, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Nan Wang
- School of Computing, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Chaoyang Zhang
- School of Computing, University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Ping Gong
- Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS, 39180, USA.
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413
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El-Metwally S, Zakaria M, Hamza T. LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads. Bioinformatics 2016; 32:3215-3223. [PMID: 27412092 DOI: 10.1093/bioinformatics/btw470] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 06/28/2016] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The deluge of current sequenced data has exceeded Moore's Law, more than doubling every 2 years since the next-generation sequencing (NGS) technologies were invented. Accordingly, we will able to generate more and more data with high speed at fixed cost, but lack the computational resources to store, process and analyze it. With error prone high throughput NGS reads and genomic repeats, the assembly graph contains massive amount of redundant nodes and branching edges. Most assembly pipelines require this large graph to reside in memory to start their workflows, which is intractable for mammalian genomes. Resource-efficient genome assemblers combine both the power of advanced computing techniques and innovative data structures to encode the assembly graph efficiently in a computer memory. RESULTS LightAssembler is a lightweight assembly algorithm designed to be executed on a desktop machine. It uses a pair of cache oblivious Bloom filters, one holding a uniform sample of [Formula: see text]-spaced sequenced [Formula: see text]-mers and the other holding [Formula: see text]-mers classified as likely correct, using a simple statistical test. LightAssembler contains a light implementation of the graph traversal and simplification modules that achieves comparable assembly accuracy and contiguity to other competing tools. Our method reduces the memory usage by [Formula: see text] compared to the resource-efficient assemblers using benchmark datasets from GAGE and Assemblathon projects. While LightAssembler can be considered as a gap-based sequence assembler, different gap sizes result in an almost constant assembly size and genome coverage. AVAILABILITY AND IMPLEMENTATION https://github.com/SaraEl-Metwally/LightAssembler CONTACT: sarah_almetwally4@mans.edu.egSupplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sara El-Metwally
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura 35516, Egypt
| | - Magdi Zakaria
- Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura 35516, Egypt
| | - Taher Hamza
- Department of Computer Science, Faculty of Computers and Information, Mansoura University, Mansoura 35516, Egypt
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414
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Abstract
Whole-genome sequencing of wild-derived rat species can provide novel genomic resources, which may help decipher the genetics underlying complex phenotypes. As a notorious pest, reservoir of human pathogens, and colonizer, the Asian house rat, Rattus tanezumi, is successfully adapted to its habitat. However, little is known regarding genetic variation in this species. In this study, we identified over 41,000,000 single-nucleotide polymorphisms, plus insertions and deletions, through whole-genome sequencing and bioinformatics analyses. Moreover, we identified over 12,000 structural variants, including 143 chromosomal inversions. Further functional analyses revealed several fixed nonsense mutations associated with infection and immunity-related adaptations, and a number of fixed missense mutations that may be related to anticoagulant resistance. A genome-wide scan for loci under selection identified various genes related to neural activity. Our whole-genome sequencing data provide a genomic resource for future genetic studies of the Asian house rat species and have the potential to facilitate understanding of the molecular adaptations of rats to their ecological niches.
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415
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Régnier M, Chassignet P. Accurate Prediction of the Statistics of Repetitions in Random Sequences: A Case Study in Archaea Genomes. Front Bioeng Biotechnol 2016; 4:35. [PMID: 27376057 PMCID: PMC4896921 DOI: 10.3389/fbioe.2016.00035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 04/08/2016] [Indexed: 11/15/2022] Open
Abstract
Repetitive patterns in genomic sequences have a great biological significance and also algorithmic implications. Analytic combinatorics allow to derive formula for the expected length of repetitions in a random sequence. Asymptotic results, which generalize previous works on a binary alphabet, are easily computable. Simulations on random sequences show their accuracy. As an application, the sample case of Archaea genomes illustrates how biological sequences may differ from random sequences.
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Affiliation(s)
- Mireille Régnier
- Inria, Palaiseau, France; LIX, Ecole Polytechnique, Palaiseau, France
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416
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Izuno A, Hatakeyama M, Nishiyama T, Tamaki I, Shimizu-Inatsugi R, Sasaki R, Shimizu KK, Isagi Y. Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations. JOURNAL OF PLANT RESEARCH 2016; 129:727-736. [PMID: 27052216 DOI: 10.1007/s10265-016-0822-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/15/2016] [Indexed: 06/05/2023]
Abstract
Whole genome sequences, which can be provided even for non-model organisms owing to high-throughput sequencers, are valuable in enhancing the understanding of adaptive evolution. Metrosideros polymorpha, a tree species endemic to the Hawaiian Islands, occupies a wide range of ecological habitats and shows remarkable polymorphism in phenotypes among/within populations. The biological functions of genetic variations observed within this species could provide significant insights into the adaptive radiation found in a single species. Here de novo assembled genome sequences of M. polymorpha are presented to reveal basic genomic parameters about this species and to develop our knowledge of ecological divergences. The assembly yielded 304-Mbp genome sequences, half of which were covered by 19 scaffolds with >5 Mbp, and contained 30 K protein-coding genes. Demographic history inferred from the genome-wide heterozygosity indicated that this species experienced a dramatic rise and fall in the effective population size, possibly owing to past geographic or climatic changes in the Hawaiian Islands. This M. polymorpha genome assembly represents a high-quality genome resource useful for future functional analyses of both intra- and interspecies genetic variations or comparative genomics.
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Affiliation(s)
- Ayako Izuno
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan.
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Functional Genomics Center Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-0934, Japan
| | - Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu, 501-3714, Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Ryuta Sasaki
- Organization of Frontier Science and Innovation, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
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417
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Spence RJ, Noune C, Hauxwell C. Complete Genome Sequences of Four Isolates of Plutella xylostella Granulovirus. GENOME ANNOUNCEMENTS 2016; 4:e00633-16. [PMID: 27365355 PMCID: PMC4929518 DOI: 10.1128/genomea.00633-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 05/17/2016] [Indexed: 11/23/2022]
Abstract
Granuloviruses are widespread pathogens of Plutella xylostella L. (diamondback moth) and potential biopesticides for control of this global insect pest. We report the complete genomes of four Plutella xylostella granulovirus isolates from China, Malaysia, and Taiwan exhibiting pairs of noncoding, homologous repeat regions with significant sequence variation but equivalent length.
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Affiliation(s)
- Robert J Spence
- Queensland University of Technology (QUT), Brisbane, Australia
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418
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Complete Genome Sequence of Mycobacterium chelonae Type Strain CCUG 47445, a Rapidly Growing Species of Nontuberculous Mycobacteria. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00550-16. [PMID: 27284158 PMCID: PMC4901242 DOI: 10.1128/genomea.00550-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mycobacterium chelonae strains are ubiquitous rapidly growing mycobacteria associated with skin and soft tissue infections, cellulitis, abscesses, osteomyelitis, catheter infections, disseminated diseases, and postsurgical infections after implants with prostheses, transplants, and even hemodialysis procedures. Here, we report the complete genome sequence of M. chelonae type strain CCUG 47445.
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419
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Wingfield BD, Ambler JM, Coetzee MP, de Beer ZW, Duong TA, Joubert F, Hammerbacher A, McTaggart AR, Naidoo K, Nguyen HD, Ponomareva E, Santana QS, Seifert KA, Steenkamp ET, Trollip C, van der Nest MA, Visagie CM, Wilken PM, Wingfield MJ, Yilmaz N. IMA Genome-F 6: Draft genome sequences of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica and Penicillium freii DAOMC 242723. IMA Fungus 2016; 7:217-27. [PMID: 27433447 PMCID: PMC4941685 DOI: 10.5598/imafungus.2016.07.01.11] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/15/2016] [Indexed: 10/25/2022] Open
Abstract
The genomes of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica, and Penicillium freii DAOMC 242723 are presented in this genome announcement. These six genomes are from plant pathogens and otherwise economically important fungal species. The genome sizes range from 21 Mb in the case of Ceratocystiopsis minuta to 58 Mb for the basidiomycete Armillaria fuscipes. These genomes include the first reports of genomes for the genus Endoconidiophora. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these pathogens cause disease.
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Affiliation(s)
- Brenda D. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Jon M. Ambler
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Martin P.A. Coetzee
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Z. Wilhelm de Beer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Tuan A. Duong
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Fourie Joubert
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry and Genomics Research Institute, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Almuth Hammerbacher
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Alistair R. McTaggart
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Kershney Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Hai D.T. Nguyen
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
- Department of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, Ontario, K1N6N5, Canada
| | - Ekaterina Ponomareva
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Quentin S. Santana
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Keith A. Seifert
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Emma T. Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Conrad Trollip
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Magriet A. van der Nest
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Cobus M. Visagie
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - P. Markus Wilken
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Michael J. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Neriman Yilmaz
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
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420
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Agaba M, Ishengoma E, Miller WC, McGrath BC, Hudson CN, Bedoya Reina OC, Ratan A, Burhans R, Chikhi R, Medvedev P, Praul CA, Wu-Cavener L, Wood B, Robertson H, Penfold L, Cavener DR. Giraffe genome sequence reveals clues to its unique morphology and physiology. Nat Commun 2016; 7:11519. [PMID: 27187213 PMCID: PMC4873664 DOI: 10.1038/ncomms11519] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 04/01/2016] [Indexed: 11/12/2022] Open
Abstract
The origins of giraffe's imposing stature and associated cardiovascular adaptations are unknown. Okapi, which lacks these unique features, is giraffe's closest relative and provides a useful comparison, to identify genetic variation underlying giraffe's long neck and cardiovascular system. The genomes of giraffe and okapi were sequenced, and through comparative analyses genes and pathways were identified that exhibit unique genetic changes and likely contribute to giraffe's unique features. Some of these genes are in the HOX, NOTCH and FGF signalling pathways, which regulate both skeletal and cardiovascular development, suggesting that giraffe's stature and cardiovascular adaptations evolved in parallel through changes in a small number of genes. Mitochondrial metabolism and volatile fatty acids transport genes are also evolutionarily diverged in giraffe and may be related to its unusual diet that includes toxic plants. Unexpectedly, substantial evolutionary changes have occurred in giraffe and okapi in double-strand break repair and centrosome functions. Giraffe's unique anatomy and physiology include its stature and associated cardiovascular adaptation. Here, Douglas Cavener and colleagues provide de novo genome assemblies of giraffe and its closest relative okapi and provide comparative analyses to infer insights into evolution and adaptation.
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Affiliation(s)
- Morris Agaba
- School of Life Sciences and Bioengineering, African Institute of Science and Technology, Arusha 4222, Tanzania.,Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi GPO00100, Kenya.,Center for Genomics and Bioinformatics, Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Edson Ishengoma
- School of Life Sciences and Bioengineering, African Institute of Science and Technology, Arusha 4222, Tanzania
| | - Webb C Miller
- Center for Genomics and Bioinformatics, Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Barbara C McGrath
- Center for Genomics and Bioinformatics, Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Chelsea N Hudson
- Center for Genomics and Bioinformatics, Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Oscar C Bedoya Reina
- Center for Genomics and Bioinformatics, Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.,MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Aakrosh Ratan
- Center for Genomics and Bioinformatics, Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Center for Public Health Genomics, Department of Computer Science, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Rico Burhans
- Center for Genomics and Bioinformatics, Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Rayan Chikhi
- Center for Genomics and Bioinformatics, Department of Computer Science and Engineering, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Paul Medvedev
- Center for Genomics and Bioinformatics, Department of Computer Science and Engineering, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Craig A Praul
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Lan Wu-Cavener
- Center for Genomics and Bioinformatics, Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Brendan Wood
- Center for Genomics and Bioinformatics, Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | | | | | - Douglas R Cavener
- School of Life Sciences and Bioengineering, African Institute of Science and Technology, Arusha 4222, Tanzania.,Center for Genomics and Bioinformatics, Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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421
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Schilthuizen M, Santos Pimenta LP, Lammers Y, Steenbergen PJ, Flohil M, Beveridge NGP, van Duijn PT, Meulblok MM, Sosef N, van de Ven R, Werring R, Beentjes KK, Meijer K, Vos RA, Vrieling K, Gravendeel B, Choi Y, Verpoorte R, Smit C, Beukeboom LW. Incorporation of an invasive plant into a native insect herbivore food web. PeerJ 2016; 4:e1954. [PMID: 27190702 PMCID: PMC4867706 DOI: 10.7717/peerj.1954] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/30/2016] [Indexed: 11/23/2022] Open
Abstract
The integration of invasive species into native food webs represent multifarious dynamics of ecological and evolutionary processes. We document incorporation of Prunus serotina (black cherry) into native insect food webs. We find that P. serotina harbours a herbivore community less dense but more diverse than its native relative, P. padus (bird cherry), with similar proportions of specialists and generalists. While herbivory on P. padus remained stable over the past century, that on P. serotina gradually doubled. We show that P. serotina may have evolved changes in investment in cyanogenic glycosides compared with its native range. In the leaf beetle Gonioctena quinquepunctata, recently shifted from native Sorbus aucuparia to P. serotina, we find divergent host preferences on Sorbus- versus Prunus-derived populations, and weak host-specific differentiation among 380 individuals genotyped for 119 SNP loci. We conclude that evolutionary processes may generate a specialized herbivore community on an invasive plant, allowing prognoses of reduced invasiveness over time. On the basis of the results presented here, we would like to caution that manual control might have the adverse effect of a slowing down of processes of adaptation, and a delay in the decline of the invasive character of P. serotina.
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Affiliation(s)
- Menno Schilthuizen
- Endless Forms group, Naturalis Biodiversity Center, Leiden, the Netherlands; Institute for Biology Leiden, Leiden University, Leiden, the Netherlands; Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
| | - Lúcia P Santos Pimenta
- Institute for Biology Leiden, Leiden University, Leiden, the Netherlands; Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Youri Lammers
- Endless Forms group, Naturalis Biodiversity Center , Leiden , the Netherlands
| | | | | | - Nils G P Beveridge
- Endless Forms group, Naturalis Biodiversity Center, Leiden, the Netherlands; Institute for Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Pieter T van Duijn
- Endless Forms group, Naturalis Biodiversity Center, Leiden, the Netherlands; University of Applied Sciences Leiden, Leiden, the Netherlands
| | - Marjolein M Meulblok
- Endless Forms group, Naturalis Biodiversity Center, Leiden, the Netherlands; University of Applied Sciences Leiden, Leiden, the Netherlands
| | - Nils Sosef
- Endless Forms group, Naturalis Biodiversity Center, Leiden, the Netherlands; University of Applied Sciences Leiden, Leiden, the Netherlands
| | - Robin van de Ven
- Endless Forms group, Naturalis Biodiversity Center, Leiden, the Netherlands; University of Applied Sciences Leiden, Leiden, the Netherlands
| | - Ralf Werring
- Endless Forms group, Naturalis Biodiversity Center, Leiden, the Netherlands; University of Applied Sciences Leiden, Leiden, the Netherlands
| | - Kevin K Beentjes
- Biodiversity Discovery group, Naturalis Biodiversity Center , Leiden , the Netherlands
| | - Kim Meijer
- Groningen Institute for Evolutionary Life Sciences, University of Groningen , Groningen , the Netherlands
| | - Rutger A Vos
- Endless Forms group, Naturalis Biodiversity Center, Leiden, the Netherlands; IBED, University of Amsterdam, Amsterdam, the Netherlands
| | - Klaas Vrieling
- Institute for Biology Leiden, Leiden University , Leiden , the Netherlands
| | - Barbara Gravendeel
- Endless Forms group, Naturalis Biodiversity Center, Leiden, the Netherlands; Institute for Biology Leiden, Leiden University, Leiden, the Netherlands; University of Applied Sciences Leiden, Leiden, the Netherlands
| | - Young Choi
- Institute for Biology Leiden, Leiden University, Leiden, the Netherlands; Natural Products Laboratory, Leiden University, Leiden, the Netherlands
| | - Robert Verpoorte
- Institute for Biology Leiden, Leiden University , Leiden , the Netherlands
| | - Chris Smit
- Groningen Institute for Evolutionary Life Sciences, University of Groningen , Groningen , the Netherlands
| | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen , Groningen , the Netherlands
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422
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Zhong Z, Norvienyeku J, Chen M, Bao J, Lin L, Chen L, Lin Y, Wu X, Cai Z, Zhang Q, Lin X, Hong Y, Huang J, Xu L, Zhang H, Chen L, Tang W, Zheng H, Chen X, Wang Y, Lian B, Zhang L, Tang H, Lu G, Ebbole DJ, Wang B, Wang Z. Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species. Sci Rep 2016; 6:25591. [PMID: 27151494 PMCID: PMC4858695 DOI: 10.1038/srep25591] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/20/2016] [Indexed: 02/07/2023] Open
Abstract
One major threat to global food security that requires immediate attention, is the increasing incidence of host shift and host expansion in growing number of pathogenic fungi and emergence of new pathogens. The threat is more alarming because, yield quality and quantity improvement efforts are encouraging the cultivation of uniform plants with low genetic diversity that are increasingly susceptible to emerging pathogens. However, the influence of host genome differentiation on pathogen genome differentiation and its contribution to emergence and adaptability is still obscure. Here, we compared genome sequence of 6 isolates of Magnaporthe species obtained from three different host plants. We demonstrated the evolutionary relationship between Magnaporthe species and the influence of host differentiation on pathogens. Phylogenetic analysis showed that evolution of pathogen directly corresponds with host divergence, suggesting that host-pathogen interaction has led to co-evolution. Furthermore, we identified an asymmetric selection pressure on Magnaporthe species. Oryza sativa-infecting isolates showed higher directional selection from host and subsequently tends to lower the genetic diversity in its genome. We concluded that, frequent gene loss or gain, new transposon acquisition and sequence divergence are host adaptability mechanisms for Magnaporthe species, and this coevolution processes is greatly driven by directional selection from host plants.
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Affiliation(s)
- Zhenhui Zhong
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Justice Norvienyeku
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meilian Chen
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiandong Bao
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianyu Lin
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liqiong Chen
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yahong Lin
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoxian Wu
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zena Cai
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qi Zhang
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoye Lin
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yonghe Hong
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jun Huang
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Linghong Xu
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Honghong Zhang
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Long Chen
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Tang
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huakun Zheng
- Haixia Institute of Science and Technology (HIST), Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaofeng Chen
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanli Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Bi Lian
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liangsheng Zhang
- Haixia Institute of Science and Technology (HIST), Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Haibao Tang
- Haixia Institute of Science and Technology (HIST), Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guodong Lu
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Daniel J. Ebbole
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Baohua Wang
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zonghua Wang
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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423
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Complete Genome Sequences of Seven Helicoverpa armigera SNPV-AC53-Derived Strains. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00260-16. [PMID: 27151787 PMCID: PMC4859169 DOI: 10.1128/genomea.00260-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Wild-type baculovirus isolates typically consist of multiple strains. We report the full genome sequences of seven alphabaculovirus strains derived by passage through tissue culture from Helicoverpa armigera SNPV-AC53 (KJ909666).
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424
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Lopes MR, Morais CG, Kominek J, Cadete RM, Soares MA, Uetanabaro APT, Fonseca C, Lachance MA, Hittinger CT, Rosa CA. Genomic analysis and D-xylose fermentation of three novel Spathaspora species: Spathaspora girioi sp. nov., Spathaspora hagerdaliae f. a., sp. nov. and Spathaspora gorwiae f. a., sp. nov. FEMS Yeast Res 2016; 16:fow044. [PMID: 27188884 DOI: 10.1093/femsyr/fow044] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2016] [Indexed: 02/03/2023] Open
Abstract
Three novel D-xylose-fermenting yeast species of Spathaspora clade were recovered from rotting wood in regions of the Atlantic Rainforest ecosystem in Brazil. Differentiation of new species was based on analyses of the gene encoding the D1/D2 sequences of large subunit of rRNA and on 642 conserved, single-copy, orthologous genes from genome sequence assemblies from the newly described species and 15 closely-related Debaryomycetaceae/Metschnikowiaceae species. Spathaspora girioi sp. nov. produced unconjugated asci with a single elongated ascospore with curved ends; ascospore formation was not observed for the other two species. The three novel species ferment D-xylose with different efficiencies. Spathaspora hagerdaliae sp. nov. and Sp. girioi sp. nov. showed xylose reductase (XR) activity strictly dependent on NADPH, whereas Sp. gorwiae sp. nov. had XR activity that used both NADH and NADPH as co-factors. The genes that encode enzymes involved in D-xylose metabolism (XR, xylitol dehydrogenase and xylulokinase) were also identified for these novel species. The type strains are Sp. girioi sp. nov. UFMG-CM-Y302(T) (=CBS 13476), Sp. hagerdaliae f.a., sp. nov. UFMG-CM-Y303(T) (=CBS 13475) and Sp. gorwiae f.a., sp. nov. UFMG-CM-Y312(T) (=CBS 13472).
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Affiliation(s)
- Mariana R Lopes
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Camila G Morais
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil Laboratório Nacional de Energia e Geologia, I.P., Unidade de Bioenergia, Estrada do Paço do Lumiar 22, 1649-038 Lisboa, Portugal
| | - Jacek Kominek
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Raquel M Cadete
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Marco A Soares
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Ana Paula T Uetanabaro
- Departamento de Ciências Biológicas e Agroindústria, Universidade Estadual Santa Cruz, Ilhéus, BA 45662-900, Brazil
| | - César Fonseca
- Laboratório Nacional de Energia e Geologia, I.P., Unidade de Bioenergia, Estrada do Paço do Lumiar 22, 1649-038 Lisboa, Portugal Section for Sustainable Biotechnology, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450 Copenhagen SV, Denmark
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, 1151 Richmond St. N., N6A 5B7, London, Ontario, Canada
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
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425
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Durai DA, Schulz MH. Informed kmer selection for de novo transcriptome assembly. Bioinformatics 2016; 32:1670-7. [PMID: 27153653 PMCID: PMC4892416 DOI: 10.1093/bioinformatics/btw217] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 04/17/2016] [Indexed: 11/23/2022] Open
Abstract
Motivation:De novo transcriptome assembly is an integral part for many RNA-seq workflows. Common applications include sequencing of non-model organisms, cancer or meta transcriptomes. Most de novo transcriptome assemblers use the de Bruijn graph (DBG) as the underlying data structure. The quality of the assemblies produced by such assemblers is highly influenced by the exact word length k. As such no single kmer value leads to optimal results. Instead, DBGs over different kmer values are built and the assemblies are merged to improve sensitivity. However, no studies have investigated thoroughly the problem of automatically learning at which kmer value to stop the assembly. Instead a suboptimal selection of kmer values is often used in practice. Results: Here we investigate the contribution of a single kmer value in a multi-kmer based assembly approach. We find that a comparative clustering of related assemblies can be used to estimate the importance of an additional kmer assembly. Using a model fit based algorithm we predict the kmer value at which no further assemblies are necessary. Our approach is tested with different de novo assemblers for datasets with different coverage values and read lengths. Further, we suggest a simple post processing step that significantly improves the quality of multi-kmer assemblies. Conclusion: We provide an automatic method for limiting the number of kmer values without a significant loss in assembly quality but with savings in assembly time. This is a step forward to making multi-kmer methods more reliable and easier to use. Availability and Implementation:A general implementation of our approach can be found under: https://github.com/SchulzLab/KREATION. Supplementary information:Supplementary data are available at Bioinformatics online. Contact:mschulz@mmci.uni-saarland.de
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Affiliation(s)
- Dilip A Durai
- Cluster of Excellence on Multimodal Computing and Interaction, Saarland University, Saarbrücken, 66123, Germany Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, 66123, Germany
| | - Marcel H Schulz
- Cluster of Excellence on Multimodal Computing and Interaction, Saarland University, Saarbrücken, 66123, Germany Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, 66123, Germany
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426
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Draft Genome Sequence of Biocontrol Agent Pythium oligandrum Strain Po37, an Oomycota. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00215-16. [PMID: 27081125 PMCID: PMC4832153 DOI: 10.1128/genomea.00215-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The oomycotaPythium oligandrumPo37 is used as a biocontrol agent of plant diseases. Here, we present the first draft of theP. oligandrumPo37 genome sequence, which comprises 725 scaffolds with a total length of 35.9 Mb and 11,695 predicted protein-coding genes.
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427
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Holley G, Wittler R, Stoye J. Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage. Algorithms Mol Biol 2016; 11:3. [PMID: 27087830 PMCID: PMC4832552 DOI: 10.1186/s13015-016-0066-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/31/2016] [Indexed: 12/21/2022] Open
Abstract
Background High throughput sequencing technologies have become fast and cheap in the past years. As a result, large-scale projects started to sequence tens to several thousands of genomes per species, producing a high number of sequences sampled from each genome. Such a highly redundant collection of very similar sequences is called a pan-genome. It can be transformed into a set of sequences “colored” by the genomes to which they belong. A colored de Bruijn graph (C-DBG) extracts from the sequences all colored k-mers, strings of length k, and stores them in vertices. Results In this paper, we present an alignment-free, reference-free and incremental data structure for storing a pan-genome as a C-DBG: the bloom filter trie (BFT). The data structure allows to store and compress a set of colored k-mers, and also to efficiently traverse the graph. Bloom filter trie was used to index and query different pangenome datasets. Compared to another state-of-the-art data structure, BFT was up to two times faster to build while using about the same amount of main memory. For querying k-mers, BFT was about 52–66 times faster while using about 5.5–14.3 times less memory. Conclusion We present a novel succinct data structure called the Bloom Filter Trie for indexing a pan-genome as a colored de Bruijn graph. The trie stores k-mers and their colors based on a new representation of vertices that compress and index shared substrings. Vertices use basic data structures for lightweight substrings storage as well as Bloom filters for efficient trie and graph traversals. Experimental results prove better performance compared to another state-of-the-art data structure. Availability https://www.github.com/GuillaumeHolley/BloomFilterTrie.
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428
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Nguyen HDT, McMullin DR, Ponomareva E, Riley R, Pomraning KR, Baker SE, Seifert KA. Ochratoxin A production by Penicillium thymicola. Fungal Biol 2016; 120:1041-1049. [PMID: 27521635 DOI: 10.1016/j.funbio.2016.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 04/04/2016] [Accepted: 04/04/2016] [Indexed: 10/21/2022]
Abstract
Ochratoxin A (OTA) is a mycotoxin produced by some Aspergillus and Penicillium species that grow on economically important agricultural crops and food products. OTA is classified as Group 2B carcinogen and is potently nephrotoxic, which is the basis for its regulation in some jurisdictions. Using high resolution mass spectroscopy, OTA and ochratoxin B (OTB) were detected in liquid culture extracts of Penicillium thymicola DAOMC 180753 isolated from Canadian cheddar cheese. The genome of this strain was sequenced, assembled and annotated to probe for putative genes involved in OTA biosynthesis. Known OTA biosynthetic genes from Penicillium verrucosum or Penicillium nordicum, two related Penicillium species that produce OTA, were not found in P. thymicola. However, a gene cluster containing a polyketide synthase (PKS) and PKS-nonribosomal peptide synthase (NRPS) hybrid encoding genes were located in the P. thymicola genome that showed a high degree of similarity to OTA biosynthetic enzymes of Aspergillus carbonarius and Aspergillus ochraceus. This is the first report of ochratoxin from P. thymicola and a new record of the species in Canada.
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Affiliation(s)
- Hai D T Nguyen
- University of Ottawa, Department of Biology, 30 Marie-Curie Private, Ottawa, ON, K1N 6N5, Canada; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada.
| | - David R McMullin
- Carleton University, Department of Chemistry, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Ekaterina Ponomareva
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Robert Riley
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, 3335 Innovation Boulevard, Richland, WA, 99354, USA
| | - Scott E Baker
- Pacific Northwest National Laboratory, Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, 3335 Innovation Boulevard, Richland, WA, 99354, USA
| | - Keith A Seifert
- University of Ottawa, Department of Biology, 30 Marie-Curie Private, Ottawa, ON, K1N 6N5, Canada; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
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429
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Cha S, Bird DM. Optimizing k-mer size using a variant grid search to enhance de novo genome assembly. Bioinformation 2016; 12:36-40. [PMID: 28104957 PMCID: PMC5237644 DOI: 10.6026/97320630012036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/06/2016] [Accepted: 04/06/2016] [Indexed: 11/23/2022] Open
Abstract
Largely driven by huge reductions in per-base costs, sequencing nucleic acids has become a near-ubiquitous technique in laboratories performing biological and biomedical research. Most of the effort goes to re-sequencing, but assembly of de novogenerated, raw sequence reads into contigs that span as much of the genome as possible is central to many projects. Although truly complete coverage is not realistically attainable, maximizing the amount of sequence that can be correctly assembled into contigs contributes to coverage. Here we compare three commonly used assembly algorithms (ABySS, Velvet and SOAPdenovo2), and show that empirical optimization of k-mer values has a disproportionate influence on de novo assembly of a eukaryotic genome, the nematode parasite Meloidogynechitwoodi. Each assembler was challenged with about 40 million Iluumina II paired-end reads, and assemblies performed under a range of k-mer sizes. In each instance, the optimal k-mer was 127, although based on N50 values,ABySS was more efficient than the others. That the assembly was not spurious was established using the "Core Eukaryotic Gene Mapping Approach", which indicated that 98.79% of the M. chitwoodi genome was accounted for by the assembly. Subsequent gene finding and annotation are consistent with this and suggest that k-mer optimization contributes to the robustness of assembly.
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Affiliation(s)
- Soyeon Cha
- Bioinformatics Research Center and Department of Plant Pathology, NC State University, Raleigh, NC, USA
| | - David McK Bird
- Bioinformatics Research Center and Department of Plant Pathology, NC State University, Raleigh, NC, USA
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430
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Ropars J, Toro KS, Noel J, Pelin A, Charron P, Farinelli L, Marton T, Krüger M, Fuchs J, Brachmann A, Corradi N. Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi. Nat Microbiol 2016; 1:16033. [PMID: 27572831 DOI: 10.1038/nmicrobiol.2016.33] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/23/2016] [Indexed: 12/30/2022]
Abstract
Sexual reproduction is ubiquitous among eukaryotes, and fully asexual lineages are extremely rare. Prominent among ancient asexual lineages are the arbuscular mycorrhizal fungi (AMF), a group of plant symbionts with a multinucleate cytoplasm. Genomic divergence among co-existing nuclei was proposed to drive the evolutionary success of AMF in the absence of sex(1), but this hypothesis has been contradicted by recent genome analyses that failed to find significant genetic diversity within an AMF isolate(2,3). Here, we set out to resolve issues surrounding the genome organization and sexual potential of AMF by exploring the genomes of five isolates of Rhizophagus irregularis, a model AMF. We find that genetic diversity in this species varies among isolates and is structured in a homo-dikaryon-like manner usually linked with the existence of a sexual life cycle. We also identify a putative AMF mating-type locus, containing two genes with structural and evolutionary similarities with the mating-type locus of some Dikarya. Our analyses suggest that this locus may be multi-allelic and that AMF could be heterothallic and bipolar. These findings reconcile opposing views on the genome organization of these ubiquitous plant symbionts and open avenues for strain improvement and environmental application of these organisms.
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Affiliation(s)
- Jeanne Ropars
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Jessica Noel
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Adrian Pelin
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Philippe Charron
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Laurent Farinelli
- FASTERIS S.A., Ch. du Pont-du-Centenaire 109, PO Box 28, CH-1228 Plan-les-Ouates, Switzerland
| | - Timea Marton
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Manuela Krüger
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.,Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, Průhonice, CZ-25243, Czech Republic
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Andreas Brachmann
- LMU Munich, Faculty of Biology, Genetics, D-82152 Planegg-Martinsried, Germany
| | - Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
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431
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Abu Bakar S, Sampathrajan S, Loke KK, Goh HH, Mohd Noor N. DNA-seq analysis of Garcinia mangostana. GENOMICS DATA 2016; 7:62-3. [PMID: 26981362 PMCID: PMC4778587 DOI: 10.1016/j.gdata.2015.11.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 11/22/2015] [Indexed: 11/05/2022]
Abstract
Mangosteen (Garcinia mangostana Linn.) is a tropical tree mainly found in South East Asia and considered as “the queen of fruits”. The asexually produced fruit is dark purple or reddish in color, with white flesh which is slightly acidic with sweet flavor and a pleasant aroma. The purple pericarp tissue is rich in xanthones which are useful for medical purposes. We performed the first genome sequencing of this commercially important fruit tree to study its genome composition and attempted draft genome assembly. Raw reads of the DNA sequencing project have been deposited to SRA database with the accession number SRX1426419.
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Affiliation(s)
- Syuhaidah Abu Bakar
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Sureshkumar Sampathrajan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Kok-Keong Loke
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Normah Mohd Noor
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
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432
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Vincent AT, Derome N, Boyle B, Culley AI, Charette SJ. Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money. J Microbiol Methods 2016; 138:60-71. [PMID: 26995332 DOI: 10.1016/j.mimet.2016.02.016] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/26/2016] [Accepted: 02/24/2016] [Indexed: 12/16/2022]
Abstract
The Sanger sequencing method produces relatively long DNA sequences of unmatched quality and has been considered for long time as the gold standard for sequencing DNA. Many improvements of the Sanger method that culminated with fluorescent dyes coupled with automated capillary electrophoresis enabled the sequencing of the first genomes. Nevertheless, using this technology to sequence whole genomes was costly, laborious and time consuming even for genomes that are relatively small in size. A major technological advance was the introduction of next-generation sequencing (NGS) pioneered by 454 Life Sciences in the early part of the 21th century. NGS allowed scientists to sequence thousands to millions of DNA molecules in a single machine run. Since then, new NGS technologies have emerged and existing NGS platforms have been improved, enabling the production of genome sequences at an unprecedented rate as well as broadening the spectrum of NGS applications. The current affordability of generating genomic information, especially with microbial samples, has resulted in a false sense of simplicity that belies the fact that many researchers still consider these technologies a black box. In this review, our objective is to identify and discuss four steps that we consider crucial to the success of any NGS-related project. These steps are: (1) the definition of the research objectives beyond sequencing and appropriate experimental planning, (2) library preparation, (3) sequencing and (4) data analysis. The goal of this review is to give an overview of the process, from sample to analysis, and discuss how to optimize your resources to achieve the most from your NGS-based research. Regardless of the evolution and improvement of the sequencing technologies, these four steps will remain relevant.
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Affiliation(s)
- Antony T Vincent
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC G1V 0A6, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC G1V 4G5, Canada
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; Département de biologie, Faculté des sciences et de génie, Université Laval, Quebec City G1V 0A6, Canada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Alexander I Culley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC G1V 0A6, Canada; Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC G1V 0A6, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, QC G1V 4G5, Canada.
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433
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Bonizzoni P, Vedova GD, Pirola Y, Previtali M, Rizzi R. LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly. J Comput Biol 2016; 23:137-49. [PMID: 26953874 DOI: 10.1089/cmb.2015.0172] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The large amount of short read data that has to be assembled in future applications, such as in metagenomics or cancer genomics, strongly motivates the investigation of disk-based approaches to index next-generation sequencing (NGS) data. Positive results in this direction stimulate the investigation of efficient external memory algorithms for de novo assembly from NGS data. Our article is also motivated by the open problem of designing a space-efficient algorithm to compute a string graph using an indexing procedure based on the Burrows-Wheeler transform (BWT). We have developed a disk-based algorithm for computing string graphs in external memory: the light string graph (LSG). LSG relies on a new representation of the FM-index that is exploited to use an amount of main memory requirement that is independent from the size of the data set. Moreover, we have developed a pipeline for genome assembly from NGS data that integrates LSG with the assembly step of SGA (Simpson and Durbin, 2012 ), a state-of-the-art string graph-based assembler, and uses BEETL for indexing the input data. LSG is open source software and is available online. We have analyzed our implementation on a 875-million read whole-genome dataset, on which LSG has built the string graph using only 1GB of main memory (reducing the memory occupation by a factor of 50 with respect to SGA), while requiring slightly more than twice the time than SGA. The analysis of the entire pipeline shows an important decrease in memory usage, while managing to have only a moderate increase in the running time.
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Affiliation(s)
- Paola Bonizzoni
- Dipartimento di Informatica Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca , Milan, Italy
| | - Gianluca Della Vedova
- Dipartimento di Informatica Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca , Milan, Italy
| | - Yuri Pirola
- Dipartimento di Informatica Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca , Milan, Italy
| | - Marco Previtali
- Dipartimento di Informatica Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca , Milan, Italy
| | - Raffaella Rizzi
- Dipartimento di Informatica Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca , Milan, Italy
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434
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Fagerlund A, Langsrud S, Schirmer BCT, Møretrø T, Heir E. Genome Analysis of Listeria monocytogenes Sequence Type 8 Strains Persisting in Salmon and Poultry Processing Environments and Comparison with Related Strains. PLoS One 2016; 11:e0151117. [PMID: 26953695 PMCID: PMC4783014 DOI: 10.1371/journal.pone.0151117] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/22/2016] [Indexed: 12/19/2022] Open
Abstract
Listeria monocytogenes is an important foodborne pathogen responsible for the disease listeriosis, and can be found throughout the environment, in many foods and in food processing facilities. The main cause of listeriosis is consumption of food contaminated from sources in food processing environments. Persistence in food processing facilities has previously been shown for the L. monocytogenes sequence type (ST) 8 subtype. In the current study, five ST8 strains were subjected to whole-genome sequencing and compared with five additionally available ST8 genomes, allowing comparison of strains from salmon, poultry and cheese industry, in addition to a human clinical isolate. Genome-wide analysis of single-nucleotide polymorphisms (SNPs) confirmed that almost identical strains were detected in a Danish salmon processing plant in 1996 and in a Norwegian salmon processing plant in 2001 and 2011. Furthermore, we show that L. monocytogenes ST8 was likely to have been transferred between two poultry processing plants as a result of relocation of processing equipment. The SNP data were used to infer the phylogeny of the ST8 strains, separating them into two main genetic groups. Within each group, the plasmid and prophage content was almost entirely conserved, but between groups, these sequences showed strong divergence. The accessory genome of the ST8 strains harbored genetic elements which could be involved in rendering the ST8 strains resilient to incoming mobile genetic elements. These included two restriction-modification loci, one of which was predicted to show phase variable recognition sequence specificity through site-specific domain shuffling. Analysis indicated that the ST8 strains harbor all important known L. monocytogenes virulence factors, and ST8 strains are commonly identified as the causative agents of invasive listeriosis. Therefore, the persistence of this L. monocytogenes subtype in food processing facilities poses a significant concern for food safety.
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Affiliation(s)
- Annette Fagerlund
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
- * E-mail:
| | - Solveig Langsrud
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Bjørn C. T. Schirmer
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Trond Møretrø
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Even Heir
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
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435
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Al-Okaily AA. HGA: de novo genome assembly method for bacterial genomes using high coverage short sequencing reads. BMC Genomics 2016; 17:193. [PMID: 26945881 PMCID: PMC4779561 DOI: 10.1186/s12864-016-2515-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 02/23/2016] [Indexed: 11/15/2022] Open
Abstract
Background Current high-throughput sequencing technologies generate large numbers of relatively short and error-prone reads, making the de novo assembly problem challenging. Although high quality assemblies can be obtained by assembling multiple paired-end libraries with both short and long insert sizes, the latter are costly to generate. Recently, GAGE-B study showed that a remarkably good assembly quality can be obtained for bacterial genomes by state-of-the-art assemblers run on a single short-insert library with very high coverage. Results In this paper, we introduce a novel hierarchical genome assembly (HGA) methodology that takes further advantage of such very high coverage by independently assembling disjoint subsets of reads, combining assemblies of the subsets, and finally re-assembling the combined contigs along with the original reads. Conclusions We empirically evaluated this methodology for 8 leading assemblers using 7 GAGE-B bacterial datasets consisting of 100 bp Illumina HiSeq and 250 bp Illumina MiSeq reads, with coverage ranging from 100x– ∼200x. The results show that for all evaluated datasets and using most evaluated assemblers (that were used to assemble the disjoint subsets), HGA leads to a significant improvement in the quality of the assembly based on N50 and corrected N50 metrics. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2515-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anas A Al-Okaily
- Computer Science & Engineering Department, University of Connecticut, Storrs, 06269, CT, USA.
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436
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Madoui MA, Dossat C, d'Agata L, van Oeveren J, van der Vossen E, Aury JM. MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data. BMC Bioinformatics 2016; 17:115. [PMID: 26936254 PMCID: PMC4776351 DOI: 10.1186/s12859-016-0969-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/23/2016] [Indexed: 12/20/2022] Open
Abstract
Background Scaffolding is an essential step in the genome assembly process. Current methods based on large fragment paired-end reads or long reads allow an increase in contiguity but often lack consistency in repetitive regions, resulting in fragmented assemblies. Here, we describe a novel tool to link assemblies to a genome map to aid complex genome reconstruction by detecting assembly errors and allowing scaffold ordering and anchoring. Results We present MaGuS (map-guided scaffolding), a modular tool that uses a draft genome assembly, a Whole Genome Profiling™ (WGP) map, and high-throughput paired-end sequencing data to estimate the quality and to enhance the contiguity of an assembly. We generated several assemblies of the Arabidopsis genome using different scaffolding programs and applied MaGuS to select the best assembly using quality metrics. Then, we used MaGuS to perform map-guided scaffolding to increase contiguity by creating new scaffold links in low-covered and highly repetitive regions where other commonly used scaffolding methods lack consistency. Conclusions MaGuS is a powerful reference-free evaluator of assembly quality and a WGP map-guided scaffolder that is freely available at https://github.com/institut-de-genomique/MaGuS. Its use can be extended to other high-throughput sequencing data (e.g., long-read data) and also to other map data (e.g., genetic maps) to improve the quality and the contiguity of large and complex genome assemblies. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0969-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mohammed-Amin Madoui
- CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057, Evry, France.
| | - Carole Dossat
- CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057, Evry, France.
| | - Léo d'Agata
- CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057, Evry, France.
| | - Jan van Oeveren
- Keygene NV, Agro Business Park 90, 6708 PW, Wageningen, The Netherlands.
| | | | - Jean-Marc Aury
- CEA, DSV, Institut de Génomique, Genoscope, 2 rue Gaston Crémieux, CP5706, 91057, Evry, France.
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437
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Draft Genome Sequence of a Salmonella enterica subsp. enterica Serovar Gallinarum bv. Gallinarum Isolate Associated with Fowl Typhoid Outbreaks in Brazil. GENOME ANNOUNCEMENTS 2016; 4:4/1/e00019-16. [PMID: 26950322 PMCID: PMC4767912 DOI: 10.1128/genomea.00019-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Salmonella enterica subsp. enterica serovar Gallinarum bv. Gallinarum strains are bird pathogens causing fowl typhoid (FT). Isolate BR_RS12 was obtained from a poultry flock with FT in 2014. The sequencing of this genome will enable to track the origin of the recent outbreaks in Brazil.
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438
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Liu MS, Kuo TCY, Ko CY, Wu DC, Li KY, Lin WJ, Lin CP, Wang YW, Schafleitner R, Lo HF, Chen CY, Chen LFO. Genomic and transcriptomic comparison of nucleotide variations for insights into bruchid resistance of mungbean (Vigna radiata [L.] R. Wilczek). BMC PLANT BIOLOGY 2016; 16:46. [PMID: 26887961 PMCID: PMC4756517 DOI: 10.1186/s12870-016-0736-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 02/09/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Mungbean (Vigna radiata [L.] R. Wilczek) is an important legume crop with high nutritional value in South and Southeast Asia. The crop plant is susceptible to a storage pest caused by bruchids (Callosobruchus spp.). Some wild and cultivated mungbean accessions show resistance to bruchids. Genomic and transcriptomic comparison of bruchid-resistant and -susceptible mungbean could reveal bruchid-resistant genes (Br) for this pest and give insights into the bruchid resistance of mungbean. RESULTS Flow cytometry showed that the genome size varied by 61 Mb (mega base pairs) among the tested mungbean accessions. Next generation sequencing followed by de novo assembly of the genome of the bruchid-resistant recombinant inbred line 59 (RIL59) revealed more than 42,000 genes. Transcriptomic comparison of bruchid-resistant and -susceptible parental lines and their offspring identified 91 differentially expressed genes (DEGs) classified into 17 major and 74 minor bruchid-resistance-associated genes. We found 408 nucleotide variations (NVs) between bruchid-resistant and -susceptible lines in regions spanning 2 kb (kilo base pairs) of the promoters of 68 DEGs. Furthermore, 282 NVs were identified on exons of 148 sequence-changed-protein genes (SCPs). DEGs and SCPs comprised genes involved in resistant-related, transposable elements (TEs) and conserved metabolic pathways. A large number of these genes were mapped to a region on chromosome 5. Molecular markers designed for variants of putative bruchid-resistance-associated genes were highly diagnostic for the bruchid-resistant genotype. CONCLUSIONS In addition to identifying bruchid-resistance-associated genes, we found that conserved metabolism and TEs may be modifier factors for bruchid resistance of mungbean. The genome sequence of a bruchid-resistant inbred line, candidate genes and sequence variations in promoter regions and exons putatively conditioning resistance as well as markers detecting these variants could be used for development of bruchid-resistant mungbean varieties.
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Affiliation(s)
- Mao-Sen Liu
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.
| | - Tony Chien-Yen Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, 106, Taiwan.
| | - Chia-Yun Ko
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.
| | - Dung-Chi Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, 106, Taiwan.
| | - Kuan-Yi Li
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, 106, Taiwan.
| | - Wu-Jui Lin
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 106, Taiwan.
| | - Ching-Ping Lin
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.
| | - Yen-Wei Wang
- AVRDC-the World Vegetable Center, 60 Yi-min Liao, Shanhua, Tainan, 74151, Taiwan.
| | - Roland Schafleitner
- AVRDC-the World Vegetable Center, 60 Yi-min Liao, Shanhua, Tainan, 74151, Taiwan.
| | - Hsiao-Feng Lo
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, 106, Taiwan.
| | - Chien-Yu Chen
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, 106, Taiwan.
| | - Long-Fang O Chen
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.
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439
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Aluome C, Aubert G, Alves Carvalho S, Le Paslier MC, Burstin J, Brunel D. De novo construction of a "Gene-space" for diploid plant genome rich in repetitive sequences by an iterative Process of Extraction and Assembly of NGS reads (iPEA protocol) with limited computing resources. BMC Res Notes 2016; 9:81. [PMID: 26864345 PMCID: PMC4750290 DOI: 10.1186/s13104-016-1903-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/02/2016] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The continuing increase in size and quality of the "short reads" raw data is a significant help for the quality of the assembly obtained through various bioinformatics tools. However, building a reference genome sequence for most plant species remains a significant challenge due to the large number of repeated sequences which are problematic for a whole-genome quality de novo assembly. Furthermore, for most SNP identification approaches in plant genetics and breeding, only the "Gene-space" regions including the promoter, exon and intron sequences are considered. RESULTS We developed the iPea protocol to produce a de novo Gene-space assembly by reconstructing, in an iterative way, the non-coding sequence flanking the Unigene cDNA sequence through addition of next-generation DNA-seq data. The approach was elaborated with the large diploid genome of pea (Pisum sativum L.), rich in repetitive sequences. The final Gene-space assembly included 35,400 contigs (97 Mb), covering 88 % of the 40,227 contigs (53.1 Mb) of the PsCam_low-copy Unigen set. Its accuracy was validated by the results of the built GenoPea 13.2 K SNP Array. CONCLUSION The iPEA protocol allows the reconstruction of a Gene-space based from RNA-Seq and DNA-seq data with limited computing resources.
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Affiliation(s)
- Christelle Aluome
- INRA Institut National de la Recherche Agronomique, US1279 Etude du Polymorphisme des génomes Végétaux, CEA-IG/CNG Centre National de Génotypage, 2 rue Gaston Crémieux, 91057, Evry, France.
| | - Grégoire Aubert
- INRA Institut National de la Recherche Agronomique, UMR1347 Agroécologie, 17 rue Sully, 21065, Dijon Cedex, France.
| | - Susete Alves Carvalho
- INRA Institut National de la Recherche Agronomique, UMR1347 Agroécologie, 17 rue Sully, 21065, Dijon Cedex, France.
| | - Marie-Christine Le Paslier
- INRA Institut National de la Recherche Agronomique, US1279 Etude du Polymorphisme des génomes Végétaux, CEA-IG/CNG Centre National de Génotypage, 2 rue Gaston Crémieux, 91057, Evry, France.
| | - Judith Burstin
- INRA Institut National de la Recherche Agronomique, UMR1347 Agroécologie, 17 rue Sully, 21065, Dijon Cedex, France.
| | - Dominique Brunel
- INRA Institut National de la Recherche Agronomique, US1279 Etude du Polymorphisme des génomes Végétaux, CEA-IG/CNG Centre National de Génotypage, 2 rue Gaston Crémieux, 91057, Evry, France.
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440
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Tian RM, Sun J, Cai L, Zhang WP, Zhou GW, Qiu JW, Qian PY. The deep-sea glass sponge Lophophysema eversa harbours potential symbionts responsible for the nutrient conversions of carbon, nitrogen and sulfur. Environ Microbiol 2016; 18:2481-94. [PMID: 26637128 DOI: 10.1111/1462-2920.13161] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/27/2015] [Indexed: 11/30/2022]
Abstract
Glass sponge (Hexactinellida, Porifera) is a special lineage because of its unique tissue organization and skeleton material. Structure and physiology of glass sponge have been extensively studied. However, our knowledge of the glass sponge-associated microbial community and of the interaction with the host is rather limited. Here, we performed genomic studies on the microbial community in the glass sponge Lophophysema eversa in seamount. The microbial community was dominated by an ammonia-oxidizing archaeum (AOA), a nitrite-oxidizing bacterium (NOB) and a sulfur-oxidizing bacterium (SOB), all of which were autotrophs. Genomic analysis on the AOA, NOB and SOB in the sponge revealed specific functional features of sponge-associated microorganisms in comparison with the closely related free-living relatives, including chemotaxis, phage defence, vitamin biosynthesis and nutrient uptake among others, which are related to ecological functions. The three autotrophs play essential roles in the cycles of carbon, nitrogen and sulfur in the microenvironment inside the sponge body, and they are considered to play symbiotic roles in the host as scavengers of toxic ammonia, nitrite and sulfide. Our study extends knowledge regarding the metabolism and the evolution of chemolithotrophs inside the invertebrate body.
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Affiliation(s)
- Ren-Mao Tian
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Jin Sun
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Lin Cai
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Wei-Peng Zhang
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Guo-Wei Zhou
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong
| | - Pei-Yuan Qian
- Divison of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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441
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Laehnemann D, Borkhardt A, McHardy AC. Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction. Brief Bioinform 2016; 17:154-79. [PMID: 26026159 PMCID: PMC4719071 DOI: 10.1093/bib/bbv029] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/09/2015] [Indexed: 12/23/2022] Open
Abstract
Characterizing the errors generated by common high-throughput sequencing platforms and telling true genetic variation from technical artefacts are two interdependent steps, essential to many analyses such as single nucleotide variant calling, haplotype inference, sequence assembly and evolutionary studies. Both random and systematic errors can show a specific occurrence profile for each of the six prominent sequencing platforms surveyed here: 454 pyrosequencing, Complete Genomics DNA nanoball sequencing, Illumina sequencing by synthesis, Ion Torrent semiconductor sequencing, Pacific Biosciences single-molecule real-time sequencing and Oxford Nanopore sequencing. There is a large variety of programs available for error removal in sequencing read data, which differ in the error models and statistical techniques they use, the features of the data they analyse, the parameters they determine from them and the data structures and algorithms they use. We highlight the assumptions they make and for which data types these hold, providing guidance which tools to consider for benchmarking with regard to the data properties. While no benchmarking results are included here, such specific benchmarks would greatly inform tool choices and future software development. The development of stand-alone error correctors, as well as single nucleotide variant and haplotype callers, could also benefit from using more of the knowledge about error profiles and from (re)combining ideas from the existing approaches presented here.
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442
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Schill KM, Wang Y, Butler RR, Pombert JF, Reddy NR, Skinner GE, Larkin JW. Genetic Diversity of Clostridium sporogenes PA 3679 Isolates Obtained from Different Sources as Resolved by Pulsed-Field Gel Electrophoresis and High-Throughput Sequencing. Appl Environ Microbiol 2016; 82:384-93. [PMID: 26519392 PMCID: PMC4702626 DOI: 10.1128/aem.02616-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/21/2015] [Indexed: 12/27/2022] Open
Abstract
Clostridium sporogenes PA 3679 is a nonpathogenic, nontoxic model organism for proteolytic Clostridium botulinum used in the validation of conventional thermal food processes due to its ability to produce highly heat-resistant endospores. Because of its public safety importance, the uncertain taxonomic classification and genetic diversity of PA 3679 are concerns. Therefore, isolates of C. sporogenes PA 3679 were obtained from various sources and characterized using pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. The phylogenetic relatedness and genetic variability were assessed based on 16S rRNA gene sequencing and whole-genome single nucleotide polymorphism (SNP) analysis. All C. sporogenes PA 3679 isolates were categorized into two clades (clade I containing ATCC 7955 NCA3679 isolates 1961-2, 1990, and 2007 and clade II containing PA 3679 isolates NFL, UW, FDA, and Campbell and ATCC 7955 NCA3679 isolate 1961-4). The 16S maximum likelihood (ML) tree clustered both clades within proteolytic C. botulinum strains, with clade I forming a distinct cluster with other C. sporogenes non-PA 3679 strains. SNP analysis revealed that clade I isolates were more similar to the genomic reference PA 3679 (NCTC8594) genome (GenBank accession number AGAH00000000.1) than clade II isolates were. The genomic reference C. sporogenes PA 3679 (NCTC8594) genome and clade I C. sporogenes isolates were genetically distinct from those obtained from other sources (University of Wisconsin, National Food Laboratory, U.S. Food and Drug Administration, and Campbell's Soup Company). Thermal destruction studies revealed that clade I isolates were more sensitive to high temperature than clade II isolates were. Considering the widespread use of C. sporogenes PA 3679 and its genetic information in numerous studies, the accurate identification and genetic characterization of C. sporogenes PA 3679 are of critical importance.
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Affiliation(s)
- Kristin M Schill
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Bedford Park, Illinois, USA
| | - Yun Wang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Bedford Park, Illinois, USA
| | - Robert R Butler
- Illinois Institute of Technology, Department of Biology, Chicago, Illinois, USA
| | | | - N Rukma Reddy
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Bedford Park, Illinois, USA
| | - Guy E Skinner
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Bedford Park, Illinois, USA
| | - John W Larkin
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Bedford Park, Illinois, USA
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443
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Dos Santos RAC, Berretta AA, Barud HDS, Ribeiro SJL, González-García LN, Zucchi TD, Goldman GH, Riaño-Pachón DM. Draft Genome Sequence of Komagataeibacter intermedius Strain AF2, a Producer of Cellulose, Isolated from Kombucha Tea. GENOME ANNOUNCEMENTS 2015; 3:e01404-15. [PMID: 26634755 PMCID: PMC4669396 DOI: 10.1128/genomea.01404-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 10/16/2015] [Indexed: 11/20/2022]
Abstract
Here, we present the draft genome sequence of Komagataeibacter intermedius strain AF2, which was isolated from Kombucha tea and is capable of producing cellulose, although at lower levels compared to another bacterium from the same environment, K. rhaeticus strain AF1.
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Affiliation(s)
- Renato Augusto Corrêa Dos Santos
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - Andresa Aparecida Berretta
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil Laboratório de Pesquisa, Desenvolvimento e Inovação, Apis Flora Industrial e Comercial Ltda., Ribeirão Preto, São Paulo, Brazil
| | | | | | | | | | - Gustavo H Goldman
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Diego M Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
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Wingfield BD, Barnes I, Wilhelm de Beer Z, De Vos L, Duong TA, Kanzi AM, Naidoo K, Nguyen HD, Santana QC, Sayari M, Seifert KA, Steenkamp ET, Trollip C, van der Merwe NA, van der Nest MA, Markus Wilken P, Wingfield MJ. IMA Genome-F 5: Draft genome sequences of Ceratocystis eucalypticola, Chrysoporthe cubensis, C. deuterocubensis, Davidsoniella virescens, Fusarium temperatum,Graphilbum fragrans, Penicillium nordicum, and Thielaviopsis musarum. IMA Fungus 2015; 6:493-506. [PMID: 26734552 PMCID: PMC4681265 DOI: 10.5598/imafungus.2015.06.02.13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/23/2015] [Indexed: 12/05/2022] Open
Abstract
The genomes of Ceratocystis eucalypticola, Chrysoporthe cubensis, Chrysoporthe deuterocubensis, Davidsoniella virescens, Fusarium temperatum, Graphilbum fragrans, Penicillium nordicum and Thielaviopsis musarum are presented in this genome announcement. These seven genomes are from plant pathogens and otherwise economically important fungal species. The genome sizes range from 28 Mb in the case of T. musarum to 45 Mb for Fusarium temperatum. These genomes include the first reports of genomes for the genera Davidsoniella, Graphilbum and Thielaviopsis. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these pathogens cause disease.
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Affiliation(s)
- Brenda D. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Irene Barnes
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Z. Wilhelm de Beer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Lieschen De Vos
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Tuan A. Duong
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Aquillah M. Kanzi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Kershney Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Hai D.T. Nguyen
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Quentin C. Santana
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Mohammad Sayari
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Keith A. Seifert
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Emma T. Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Conrad Trollip
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Nicolaas A. van der Merwe
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Magriet A. van der Nest
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - P. Markus Wilken
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
| | - Michael J. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028 South Africa
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Van Hoeck A, Horemans N, Monsieurs P, Cao HX, Vandenhove H, Blust R. The first draft genome of the aquatic model plant Lemna minor opens the route for future stress physiology research and biotechnological applications. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:188. [PMID: 26609323 PMCID: PMC4659200 DOI: 10.1186/s13068-015-0381-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/10/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Freshwater duckweed, comprising the smallest, fastest growing and simplest macrophytes has various applications in agriculture, phytoremediation and energy production. Lemna minor, the so-called common duckweed, is a model system of these aquatic plants for ecotoxicological bioassays, genetic transformation tools and industrial applications. Given the ecotoxic relevance and high potential for biomass production, whole-genome information of this cosmopolitan duckweed is needed. RESULTS The 472 Mbp assembly of the L. minor genome (2n = 40; estimated 481 Mbp; 98.1 %) contains 22,382 protein-coding genes and 61.5 % repetitive sequences. The repeat content explains 94.5 % of the genome size difference in comparison with the greater duckweed, Spirodela polyrhiza (2n = 40; 158 Mbp; 19,623 protein-coding genes; and 15.79 % repetitive sequences). Comparison of proteins from other monocot plants, protein ortholog identification, OrthoMCL, suggests 1356 duckweed-specific groups (3367 proteins, 15.0 % total L. minor proteins) and 795 Lemna-specific groups (2897 proteins, 12.9 % total L. minor proteins). Interestingly, proteins involved in biosynthetic processes in response to various stimuli and hydrolase activities are enriched in the Lemna proteome in comparison with the Spirodela proteome. CONCLUSIONS The genome sequence and annotation of L. minor protein-coding genes provide new insights in biological understanding and biomass production applications of Lemna species.
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Affiliation(s)
- Arne Van Hoeck
- />Biosphere Impact Studies, SCK•CEN, Boeretang 200, 2400 Mol, Belgium
- />Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Nele Horemans
- />Biosphere Impact Studies, SCK•CEN, Boeretang 200, 2400 Mol, Belgium
- />Centre for Environmental Research, University of Hasselt, Universiteitslaan 1, 3590 Diepenbeek, Belgium
| | | | - Hieu Xuan Cao
- />Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466 Stadt Seeland, Germany
| | | | - Ronny Blust
- />Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
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446
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Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes. J Clin Microbiol 2015; 54:333-42. [PMID: 26607978 PMCID: PMC4733179 DOI: 10.1128/jcm.02344-15] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/10/2015] [Indexed: 12/31/2022] Open
Abstract
Whole-genome sequencing (WGS) has emerged as a powerful tool for comparing bacterial isolates in outbreak detection and investigation. Here we demonstrate that WGS performed prospectively for national epidemiologic surveillance of Listeria monocytogenes has the capacity to be superior to our current approaches using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), multilocus variable-number tandem-repeat analysis (MLVA), binary typing, and serotyping. Initially 423 L. monocytogenes isolates underwent WGS, and comparisons uncovered a diverse genetic population structure derived from three distinct lineages. MLST, binary typing, and serotyping results inferred in silico from the WGS data were highly concordant (>99%) with laboratory typing performed in parallel. However, WGS was able to identify distinct nested clusters within groups of isolates that were otherwise indistinguishable using our current typing methods. Routine WGS was then used for prospective epidemiologic surveillance on a further 97 L. monocytogenes isolates over a 12-month period, which provided a greater level of discrimination than that of conventional typing for inferring linkage to point source outbreaks. A risk-based alert system based on WGS similarity was used to inform epidemiologists required to act on the data. Our experience shows that WGS can be adopted for prospective L. monocytogenes surveillance and investigated for other pathogens relevant to public health.
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447
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Prasad P, Varshney D, Adholeya A. Whole genome annotation and comparative genomic analyses of bio-control fungus Purpureocillium lilacinum. BMC Genomics 2015; 16:1004. [PMID: 26607873 PMCID: PMC4658809 DOI: 10.1186/s12864-015-2229-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/18/2015] [Indexed: 01/11/2023] Open
Abstract
Background The fungus Purpureocillium lilacinum is widely known as a biological control agent against plant parasitic nematodes. This research article consists of genomic annotation of the first draft of whole genome sequence of P. lilacinum. The study aims to decipher the putative genetic components of the fungus involved in nematode pathogenesis by performing comparative genomic analysis with nine closely related fungal species in Hypocreales. Results de novo genomic assembly was done and a total of 301 scaffolds were constructed for P. lilacinum genomic DNA. By employing structural genome prediction models, 13, 266 genes coding for proteins were predicted in the genome. Approximately 73 % of the predicted genes were functionally annotated using Blastp, InterProScan and Gene Ontology. A 14.7 % fraction of the predicted genes shared significant homology with genes in the Pathogen Host Interactions (PHI) database. The phylogenomic analysis carried out using maximum likelihood RAxML algorithm provided insight into the evolutionary relationship of P. lilacinum. In congruence with other closely related species in the Hypocreales namely, Metarhizium spp., Pochonia chlamydosporia, Cordyceps militaris, Trichoderma reesei and Fusarium spp., P. lilacinum has large gene sets coding for G-protein coupled receptors (GPCRs), proteases, glycoside hydrolases and carbohydrate esterases that are required for degradation of nematode-egg shell components. Screening of the genome by Antibiotics & Secondary Metabolite Analysis Shell (AntiSMASH) pipeline indicated that the genome potentially codes for a variety of secondary metabolites, possibly required for adaptation to heterogeneous lifestyles reported for P. lilacinum. Significant up-regulation of subtilisin-like serine protease genes in presence of nematode eggs in quantitative real-time analyses suggested potential role of serine proteases in nematode pathogenesis. Conclusions The data offer a better understanding of Purpureocillium lilacinum genome and will enhance our understanding on the molecular mechanism involved in nematophagy. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2229-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pushplata Prasad
- TERI Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gual Pahari,Faridabad Road, Gurgaon, Haryana, 122 001, India.
| | - Deepti Varshney
- TERI Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gual Pahari,Faridabad Road, Gurgaon, Haryana, 122 001, India.
| | - Alok Adholeya
- TERI Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gual Pahari,Faridabad Road, Gurgaon, Haryana, 122 001, India.
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448
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Nishimura O, Hosoda K, Kawaguchi E, Yazawa S, Hayashi T, Inoue T, Umesono Y, Agata K. Unusually Large Number of Mutations in Asexually Reproducing Clonal Planarian Dugesia japonica. PLoS One 2015; 10:e0143525. [PMID: 26588467 PMCID: PMC4654569 DOI: 10.1371/journal.pone.0143525] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/05/2015] [Indexed: 11/21/2022] Open
Abstract
We established a laboratory clonal strain of freshwater planarian (Dugesia japonica) that was derived from a single individual and that continued to undergo autotomous asexual reproduction for more than 20 years, and we performed large-scale genome sequencing and transcriptome analysis on it. Despite the fact that a completely clonal strain of the planarian was used, an unusually large number of mutations were detected. To enable quantitative genetic analysis of such a unique organism, we developed a new model called the Reference Gene Model, and used it to conduct large-scale transcriptome analysis. The results revealed large numbers of mutations not only outside but also inside gene-coding regions. Non-synonymous SNPs were detected in 74% of the genes for which valid ORFs were predicted. Interestingly, the high-mutation genes, such as metabolism- and defense-related genes, were correlated with genes that were previously identified as diverse genes among different planarian species. Although a large number of amino acid substitutions were apparently accumulated during asexual reproduction over this long period of time, the planarian maintained normal body-shape, behaviors, and physiological functions. The results of the present study reveal a unique aspect of asexual reproduction.
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Affiliation(s)
- Osamu Nishimura
- Global COE Program: Evolution and Biodiversity, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Kazutaka Hosoda
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Eri Kawaguchi
- Global COE Program: Evolution and Biodiversity, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Shigenobu Yazawa
- Global COE Program: Evolution and Biodiversity, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
- Cellular and Structural Physiology Institute, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Tetsutaro Hayashi
- Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-Nakamachi, Chuo-ku, Kobe, Hyogo, Japan
- Advanced Center for Computing and Communication, RIKEN, 2–1 Hirosawa, Wako, Saitama, Japan
| | - Takeshi Inoue
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Yoshihiko Umesono
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo, Japan
| | - Kiyokazu Agata
- Global COE Program: Evolution and Biodiversity, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
- * E-mail:
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449
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A supergene determines highly divergent male reproductive morphs in the ruff. Nat Genet 2015; 48:79-83. [PMID: 26569125 PMCID: PMC5218575 DOI: 10.1038/ng.3443] [Citation(s) in RCA: 324] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/16/2015] [Indexed: 12/13/2022]
Abstract
Three strikingly different alternative male mating morphs (aggressive “Independents”, semi-cooperative “Satellites” and female mimic “Faeders”) coexist as a balanced polymorphism in the ruff, Philomachus pugnax, a lek-breeding wading bird1,2,3. Major differences in body size, ornamentation, and aggressive and mating behaviour are inherited as an autosomal polymorphism4,5. We show that development into Satellites and Faeders is determined by a supergene6,7,8 consisting of divergent alternative, dominant, non-recombining haplotypes of an inversion on chromosome 11, which contains 125 predicted genes. Independents are homozygous for the ancestral sequence. One breakpoint of the inversion disrupts the essential Centromere protein N (CENP-N) gene, and pedigree analysis confirms lethality of inversion homozygotes. We describe novel behavioural, testes size, and steroid metabolic differences among morphs, and identify polymorphic genes within the inversion that are likely to contribute to the differences among morphs in reproductive traits.
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450
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Massive horizontal gene transfer, strictly vertical inheritance and ancient duplications differentially shape the evolution of Bacillus cereus enterotoxin operons hbl, cytK and nhe. BMC Evol Biol 2015; 15:246. [PMID: 26555390 PMCID: PMC4641410 DOI: 10.1186/s12862-015-0529-4] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/30/2015] [Indexed: 11/10/2022] Open
Abstract
Background Bacillus cereus sensu lato comprises eight closely related species including the human pathogens Bacillus anthracis and Bacillus cereus. Within B. cereus sensu lato, chromosomally and plasmid-encoded toxins exist. While plasmid-mediated horizontal gene transfer of the emetic toxin, anthrax and insecticidal toxins is known, evolution of enterotoxin genes within the group has not been studied. Results We report draft genome assemblies of 25 strains, a phylogenetic network of 142 strains based on ANI derived from genome sequences and a phylogeny based on whole-genome SNP analysis. The data clearly support subdivision of B. cereus sensu lato into seven phylogenetic groups. While group I, V and VII represent B. pseudomycoides, B. toyonensis and B. cytotoxicus, which are distinguishable at species level (ANI border ≥ 96 %), strains ascribed to the other five species do not match phylogenic groups. The chromosomal enterotoxin operons nheABC and hblCDAB are abundant within B. cereus both isolated from infections and from the environment. While the duplicated hbl variant hbla is present in 22 % of all strains investigated, duplication of nheABC is extremely rare (0.02 %) and appears to be phylogenetically unstable. Distribution of toxin genes was matched to a master tree based on seven concatenated housekeeping genes, which depicts species relationships in B. cereus sensu lato as accurately as whole-genome comparisons. Comparison to the phylogeny of enterotoxin genes uncovered ample evidence for horizontal transfer of hbl, cytK and plcR, as well as frequent deletion of both toxins and duplication of hbl. No evidence for nhe deletion was found and stable horizontal transfer of nhe is rare. Therefore, evolution of B. cereus enterotoxin operons is shaped unexpectedly different for yet unknown reasons. Conclusions Frequent exchange of the pathogenicity factors hbl, cytK and plcR in B. cereus sensu lato appears to be an important mechanism of B. cereus virulence evolution, including so-called probiotic or non-pathogenic species, which might have consequences for risk assessment procedures. In contrast, exclusively vertical inheritance of nhe was observed, and since nhe-negative strains appear to be extremely rare, we suggest that fitness loss may be associated with deletion or horizontal transfer of the nhe operon. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0529-4) contains supplementary material, which is available to authorized users.
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