1
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Tizabi D, Bachvaroff T, Hill RT. Complete genome sequence of Imperialibacter roseus strain P4 T. Microbiol Resour Announc 2024:e0098623. [PMID: 38780297 DOI: 10.1128/mra.00986-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Imperialibacter roseus strain P4T is a bacterial strain isolated from Permian groundwater. The complete genome of Imperialibacter roseus strain P4T was sequenced to reveal a single circular chromosome of 6,747,663 bp with a GC content of 46.5%.
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Affiliation(s)
- Daniela Tizabi
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Tsvetan Bachvaroff
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Russell T Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
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2
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Roch FF, Dzieciol M, Quijada NM, Alteio LV, Mester PJ, Selberherr E. Microbial community structure of plant-based meat alternatives. NPJ Sci Food 2024; 8:27. [PMID: 38740858 DOI: 10.1038/s41538-024-00269-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
A reduction in animal-based diets has driven market demand for alternative meat products, currently raising a new generation of plant-based meat alternatives (PBMAs). It remains unclear whether these substitutes are a short-lived trend or become established in the long term. Over the last few years, the trend of increasing sales and diversifying product range has continued, but publication activities in this field are currently limited mainly to market research and food technology topics. As their popularity increases, questions emerge about the safety and nutritional risks of these novel products. Even though all the examined products must be heated before consumption, consumers lack experience with this type of product and thus further research into product safety, is desirable. To consider these issues, we examined 32 PBMAs from Austrian supermarkets. Based on 16S rRNA gene amplicon sequencing, the majority of the products were dominated by lactic acid bacteria (either Leuconostoc or Latilactobacillus), and generally had low alpha diversity. Pseudomonadota (like Pseudomonas and Shewanella) dominated the other part of the products. In addition to LABs, a high diversity of different Bacillus, but also some Enterobacteriaceae and potentially pathogenic species were isolated with the culturing approach. We assume that especially the dominance of heterofermentative LABs has high relevance for the product stability and quality with the potential to increase shelf life of the products. The number of isolated Enterobacteriaceae and potential pathogens were low, but they still demonstrated that these products are suitable for their presence.
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Affiliation(s)
- Franz-Ferdinand Roch
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Monika Dzieciol
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Narciso M Quijada
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185, Villamayor (Salamanca), Spain
| | - Lauren V Alteio
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, 3430, Tulln, Austria
| | - Patrick-Julian Mester
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Evelyne Selberherr
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria.
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3
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Lamichhane J, Choi BI, Stegman N, Fontes Noronha M, Wolfe AJ. Macrolide Resistance in the Aerococcus urinae Complex: Implications for Integrative and Conjugative Elements. Antibiotics (Basel) 2024; 13:433. [PMID: 38786161 PMCID: PMC11117264 DOI: 10.3390/antibiotics13050433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The recognition of the Aerococcus urinae complex (AUC) as an emerging uropathogen has led to growing concerns due to a limited understanding of its disease spectrum and antibiotic resistance profiles. Here, we investigated the prevalence of macrolide resistance within urinary AUC isolates, shedding light on potential genetic mechanisms. Phenotypic testing revealed a high rate of macrolide resistance: 45%, among a total of 189 urinary AUC isolates. Genomic analysis identified integrative and conjugative elements (ICEs) as carriers of the macrolide resistance gene ermA, suggesting horizontal gene transfer as a mechanism of resistance. Furthermore, comparison with publicly available genomes of related pathogens revealed high ICE sequence homogeneity, highlighting the potential for cross-species dissemination of resistance determinants. Understanding mechanisms of resistance is crucial for developing effective surveillance strategies and improving antibiotic use. Furthermore, the findings underscore the importance of considering the broader ecological context of resistance dissemination, emphasizing the need for community-level surveillance to combat the spread of antibiotic resistance within the urinary microbiome.
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Affiliation(s)
- Jyoti Lamichhane
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA (M.F.N.)
| | - Brian I. Choi
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA (M.F.N.)
| | - Natalie Stegman
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA;
| | - Melline Fontes Noronha
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA (M.F.N.)
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA (M.F.N.)
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4
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Wennmann JT, Lim FS, Senger S, Gani M, Jehle JA, Keilwagen J. Haplotype determination of the Bombyx mori nucleopolyhedrovirus by Nanopore sequencing and linkage of single nucleotide variants. J Gen Virol 2024; 105. [PMID: 38767624 DOI: 10.1099/jgv.0.001983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
Naturally occurring isolates of baculoviruses, such as the Bombyx mori nucleopolyhedrovirus (BmNPV), usually consist of numerous genetically different haplotypes. Deciphering the different haplotypes of such isolates is hampered by the large size of the dsDNA genome, as well as the short read length of next generation sequencing (NGS) techniques that are widely applied for baculovirus isolate characterization. In this study, we addressed this challenge by combining the accuracy of NGS to determine single nucleotide variants (SNVs) as genetic markers with the long read length of Nanopore sequencing technique. This hybrid approach allowed the comprehensive analysis of genetically homogeneous and heterogeneous isolates of BmNPV. Specifically, this allowed the identification of two putative major haplotypes in the heterogeneous isolate BmNPV-Ja by SNV position linkage. SNV positions, which were determined based on NGS data, were linked by the long Nanopore reads in a Position Weight Matrix. Using a modified Expectation-Maximization algorithm, the Nanopore reads were assigned according to the occurrence of variable SNV positions by machine learning. The cohorts of reads were de novo assembled, which led to the identification of BmNPV haplotypes. The method demonstrated the strength of the combined approach of short- and long-read sequencing techniques to decipher the genetic diversity of baculovirus isolates.
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Affiliation(s)
- Jörg T Wennmann
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Fang-Shiang Lim
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Sergei Senger
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Mudasir Gani
- Division of Entomology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences & Technology, Kashmir 193 201, J&K, India
| | - Johannes A Jehle
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Jens Keilwagen
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Ernst-Baur-Str. 27, 06484 Quedlinburg, Germany
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Bouras G, Houtak G, Wick RR, Mallawaarachchi V, Roach MJ, Papudeshi B, Judd LM, Sheppard AE, Edwards RA, Vreugde S. Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies. Microb Genom 2024; 10. [PMID: 38717808 DOI: 10.1099/mgen.0.001244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024] Open
Abstract
Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- and long-reads) assembly approaches. Complete genomes allow a deeper understanding of bacterial evolution and genomic variation beyond single nucleotide variants. They are also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance genes. However, small plasmids are often missed or misassembled by long-read assembly algorithms. Here, we present Hybracter which allows for the fast, automatic and scalable recovery of near-perfect complete bacterial genomes using a long-read first assembly approach. Hybracter can be run either as a hybrid assembler or as a long-read only assembler. We compared Hybracter to existing automated hybrid and long-read only assembly tools using a diverse panel of samples of varying levels of long-read accuracy with manually curated ground truth reference genomes. We demonstrate that Hybracter as a hybrid assembler is more accurate and faster than the existing gold standard automated hybrid assembler Unicycler. We also show that Hybracter with long-reads only is the most accurate long-read only assembler and is comparable to hybrid methods in accurately recovering small plasmids.
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Affiliation(s)
- George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Ghais Houtak
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Ryan R Wick
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Michael J Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
- Adelaide Centre for Epigenetics and South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, Australia
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Lousie M Judd
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anna E Sheppard
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Robert A Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Sarah Vreugde
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
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6
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Choi BI, Fontes Noronha M, Kaindl J, Wolfe AJ. Complete genome sequences of Aerococcus loyolae ATCC TSD-300 T, Aerococcus mictus ATCC TSD-301 T, and Aerococcus tenax ATCC TSD-302 T. Microbiol Resour Announc 2024:e0015624. [PMID: 38651909 DOI: 10.1128/mra.00156-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
Previously identified under the single designation of Aerococcus urinae, three distinct taxonomic species have been distinguished as Aerococcus loyolae, Aerococcus mictus, and Aerococcus tenax. Here, we present the complete genome sequences of the type strains of these species assembled via a combination of short-read and long-read sequencing techniques.Registered at ClinicalTrials.gov (NCT01166438).
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Affiliation(s)
- Brian I Choi
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Melline Fontes Noronha
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Jacob Kaindl
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
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7
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Li H, Durbin R. Genome assembly in the telomere-to-telomere era. Nat Rev Genet 2024:10.1038/s41576-024-00718-w. [PMID: 38649458 DOI: 10.1038/s41576-024-00718-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 04/25/2024]
Abstract
Genome sequences largely determine the biology and encode the history of an organism, and de novo assembly - the process of reconstructing the genome sequence of an organism from sequencing reads - has been a central problem in bioinformatics for four decades. Until recently, genomes were typically assembled into fragments of a few megabases at best, but now technological advances in long-read sequencing enable the near-complete assembly of each chromosome - also known as telomere-to-telomere assembly - for many organisms. Here, we review recent progress on assembly algorithms and protocols, with a focus on how to derive near-telomere-to-telomere assemblies. We also discuss the additional developments that will be required to resolve remaining assembly gaps and to assemble non-diploid genomes.
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Affiliation(s)
- Heng Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Richard Durbin
- Department of Genetics, Cambridge University, Cambridge, UK.
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8
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Bouras G, Houtak G, Wick RR, Mallawaarachchi V, Roach MJ, Papudeshi B, Judd LM, Sheppard AE, Edwards RA, Vreugde S. Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.12.571215. [PMID: 38168369 PMCID: PMC10760025 DOI: 10.1101/2023.12.12.571215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- and long-reads) assembly approaches. Complete genomes allow a deeper understanding of bacterial evolution and genomic variation beyond single nucleotide variants (SNVs). They are also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance (AMR) genes. However, small plasmids are often missed or misassembled by long-read assembly algorithms. Here, we present Hybracter which allows for the fast, automatic, and scalable recovery of near-perfect complete bacterial genomes using a long-read first assembly approach. Hybracter can be run either as a hybrid assembler or as a long-read only assembler. We compared Hybracter to existing automated hybrid and long-read only assembly tools using a diverse panel of samples of varying levels of long-read accuracy with manually curated ground truth reference genomes. We demonstrate that Hybracter as a hybrid assembler is more accurate and faster than the existing gold standard automated hybrid assembler Unicycler. We also show that Hybracter with long-reads only is the most accurate long-read only assembler and is comparable to hybrid methods in accurately recovering small plasmids.
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Affiliation(s)
- George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, South Australia, Australia
| | - Ghais Houtak
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, South Australia, Australia
| | - Ryan R. Wick
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
- Adelaide Centre for Epigenetics and South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, Australia
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Lousie M. Judd
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anna E. Sheppard
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Sarah Vreugde
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, South Australia, Australia
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Yu W, Luo H, Yang J, Zhang S, Jiang H, Zhao X, Hui X, Sun D, Li L, Wei XQ, Lonardi S, Pan W. Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes. Genome Res 2024; 34:326-340. [PMID: 38428994 PMCID: PMC10984382 DOI: 10.1101/gr.278232.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/23/2024] [Indexed: 03/03/2024]
Abstract
Pacific Biosciences (PacBio) HiFi sequencing technology generates long reads (>10 kbp) with very high accuracy (<0.01% sequencing error). Although several de novo assembly tools are available for HiFi reads, there are no comprehensive studies on the evaluation of these assemblers. We evaluated the performance of 11 de novo HiFi assemblers on (1) real data for three eukaryotic genomes; (2) 34 synthetic data sets with different ploidy, sequencing coverage levels, heterozygosity rates, and sequencing error rates; (3) one real metagenomic data set; and (4) five synthetic metagenomic data sets with different composition abundance and heterozygosity rates. The 11 assemblers were evaluated using quality assessment tool (QUAST) and benchmarking universal single-copy ortholog (BUSCO). We also used several additional criteria, namely, completion rate, single-copy completion rate, duplicated completion rate, average proportion of largest category, average distance difference, quality value, run-time, and memory utilization. Results show that hifiasm and hifiasm-meta should be the first choice for assembling eukaryotic genomes and metagenomes with HiFi data. We performed a comprehensive benchmarking study of commonly used assemblers on complex eukaryotic genomes and metagenomes. Our study will help the research community to choose the most appropriate assembler for their data and identify possible improvements in assembly algorithms.
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Affiliation(s)
- Wenjuan Yu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Haohui Luo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jinbao Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shengchen Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Heling Jiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xianjia Zhao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Xingqi Hui
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Da Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Liang Li
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350002, China
| | - Xiu-Qing Wei
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350002, China;
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, California 92521, USA;
| | - Weihua Pan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China;
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10
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Wurzbacher CE, Haufschild T, Hammer J, van Teeseling MCF, Kallscheuer N, Jogler C. Planctoellipticum variicoloris gen. nov., sp. nov., a novel member of the family Planctomycetaceae isolated from wastewater of the aeration lagoon of a sugar processing plant in Northern Germany. Sci Rep 2024; 14:5741. [PMID: 38459238 PMCID: PMC10923784 DOI: 10.1038/s41598-024-56373-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/05/2024] [Indexed: 03/10/2024] Open
Abstract
In the present study, we characterise a strain isolated from the wastewater aeration lagoon of a sugar processing plant in Schleswig (Northern Germany) by Heinz Schlesner. As a pioneer in planctomycetal research, he isolated numerous strains belonging to the phylum Planctomycetota from aquatic habitats around the world. Phylogenetic analyses show that strain SH412T belongs to the family Planctomycetaceae and shares with 91.6% the highest 16S rRNA gene sequence similarity with Planctopirus limnophila DSM 3776T. Its genome has a length of 7.3 Mb and a G + C content of 63.6%. Optimal growth of strain SH412T occurs at pH 7.0-7.5 and 28 °C with its pigmentation depending on sunlight exposure. Strain SH412T reproduces by polar asymmetric division ("budding") and forms ovoid cells. The cell size determination was performed using a semi-automatic pipeline, which we first evaluated with the model species P. limnophila and then applied to strain SH412T. Furthermore, the data acquired during time-lapse analyses suggests a lifestyle switch from flagellated daughter cells to non-flagellated mother cells in the subsequent cycle. Based on our data, we suggest that strain SH412T represents a novel species within a novel genus, for which we propose the name Planctoellipticum variicoloris gen. nov., sp. nov., with strain SH412T (= CECT 30430T = STH00996T, the STH number refers to the Jena Microbial Resource Collection JMRC) as the type strain of the new species.
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Affiliation(s)
- Carmen E Wurzbacher
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Tom Haufschild
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Jonathan Hammer
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Muriel C F van Teeseling
- Junior Research Group "Prokaryotic Cell Biology", Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Nicolai Kallscheuer
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Christian Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
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11
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Guo S, Li Z, Li C, Liu Y, Liang X, Qin Y. Assembly and characterization of the complete mitochondrial genome of Ventilago leiocarpa. PLANT CELL REPORTS 2024; 43:77. [PMID: 38386216 DOI: 10.1007/s00299-023-03126-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/04/2023] [Indexed: 02/23/2024]
Abstract
KEY MESSAGE We reported the mitochondrial genome of Ventilago leiocarpa for the first time. Two and one sites lead to the generation of stop and stat codon through editing were verified. Ventilago leiocarpa, a member of the Rhamnaceae family, is frequently utilized in traditional medicine due to the medicinal properties of its roots. In this study, we successfully assembled the mitogenome of V. leiocarpa using both BGI short reads and Nanopore long reads. This mitogenome has a total length of 331,839 bp. The annotated results showed 36 unique protein-coding, 16 tRNA and 3 rRNA genes in this mitogenome. Furthermore, we confirmed the presence of a branched structure through the utilization of long reads mapping, PCR amplification, and Sanger sequencing. Specifically, the ctg1 can form a single circular molecule or combine with ctg4 to form a linear molecule. Likewise, ctg2 can form a single circular molecule or can be connected to ctg4 to form a linear molecule. Subsequently, through a comparative analysis of the mitogenome and cpgenome sequences, we identified ten mitochondrial plastid sequences (MTPTs), including two complete protein-coding genes and five complete tRNA genes. The existence of MTPTs was verified by long reads. Colinear analysis showed that the mitogenomes of Rosales were highly divergent in structure. Finally, we identified 545 RNA editing sites involving 36 protein-coding genes by Deepred-mt. To validate our findings, we conducted PCR amplification and Sanger sequencing, which confirmed the generation of stop codons in atp9-223 and rps10-391, as well as the generation of a start codon in nad4L-2. This project reported the complex structure and RNA editing event of the V. Leiocarpa mitogenome, which will provide valuable information for the study of mitochondrial gene expression.
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Affiliation(s)
- Song Guo
- College of Food and Biochemical Engineering, Guangxi Science and Technology Normal University, Guangxi Laibin, 546199, People's Republic of China
- Key Laboratory for Zhuang and Yao Pharmaceutical Quality Biology, Guangxi Science and Technology Normal University, Laibin, 546199, People's Republic of China
| | - Zeyang Li
- College of Food and Biochemical Engineering, Guangxi Science and Technology Normal University, Guangxi Laibin, 546199, People's Republic of China
- Key Laboratory for Zhuang and Yao Pharmaceutical Quality Biology, Guangxi Science and Technology Normal University, Laibin, 546199, People's Republic of China
| | - Chunlian Li
- College of Food and Biochemical Engineering, Guangxi Science and Technology Normal University, Guangxi Laibin, 546199, People's Republic of China
- Key Laboratory for Zhuang and Yao Pharmaceutical Quality Biology, Guangxi Science and Technology Normal University, Laibin, 546199, People's Republic of China
| | - Yu Liu
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530010, People's Republic of China
| | - Xianglan Liang
- College of Food and Biochemical Engineering, Guangxi Science and Technology Normal University, Guangxi Laibin, 546199, People's Republic of China
| | - Yiming Qin
- College of Food and Biochemical Engineering, Guangxi Science and Technology Normal University, Guangxi Laibin, 546199, People's Republic of China.
- Key Laboratory for Zhuang and Yao Pharmaceutical Quality Biology, Guangxi Science and Technology Normal University, Laibin, 546199, People's Republic of China.
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12
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Castillo M, Guevara G, Baldanta S, Rodríguez PS, Agudo L, Nogales J, Carrasco AD, Arribas-Aguilar F, Pérez-Pérez J, García JL, Galán B, Navarro Llorens JM. Characterization of Limnospira platensis PCC 9108 R-M and CRISPR-Cas systems. Microbiol Res 2024; 279:127572. [PMID: 38101163 DOI: 10.1016/j.micres.2023.127572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
The filamentous cyanobacterium Limnospira platensis, formerly known as Arthrospira platensis or spirulina, is one of the most commercially important species of microalgae. Due to its high nutritional value, pharmacological and industrial applications it is extensively cultivated on a large commercial scale. Despite its widespread use, its precise manipulation is still under development due to the lack of effective genetic protocols. Genetic transformation of Limnospira has been attempted but the methods reported have not been generally reproducible in other laboratories. Knowledge of the transformation defense mechanisms is essential for understanding its physiology and for broadening their applications. With the aim to understand more about the genetic defenses of L. platensis, in this work we have identified the restriction-modification and CRISPR-Cas systems and we have cloned and characterized thirteen methylases. In parallel, we have also characterized the methylome and orphan methyltransferases using genome-wide analysis of DNA methylation patterns and RNA-seq. The identification and characterization of these enzymes will be a valuable resource to know how this strain avoids being genetically manipulated and for further genomics studies.
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Affiliation(s)
- María Castillo
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Govinda Guevara
- Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain.
| | - Sara Baldanta
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain.
| | - Patricia Suárez Rodríguez
- Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain.
| | - Lucía Agudo
- Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain.
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain.
| | - Asunción Díaz Carrasco
- DNA Sequencing facility, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Fernando Arribas-Aguilar
- SECUGEN SL, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Julián Pérez-Pérez
- SECUGEN SL, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - José Luis García
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Beatriz Galán
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Juana María Navarro Llorens
- Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain.
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13
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Correa Pinto Junior D, Canal Delgado I, Yang H, Clemenceau A, Corvelo A, Narzisi G, Musunuri R, Meyer Berger J, Hendricks LE, Tokumura K, Luo N, Li H, Oury F, Ducy P, Yadav VK, Li X, Karsenty G. Osteocalcin of maternal and embryonic origins synergize to establish homeostasis in offspring. EMBO Rep 2024; 25:593-615. [PMID: 38228788 PMCID: PMC10897216 DOI: 10.1038/s44319-023-00031-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 01/18/2024] Open
Abstract
Many physiological osteocalcin-regulated functions are affected in adult offspring of mothers experiencing unhealthy pregnancy. Furthermore, osteocalcin signaling during gestation influences cognition and adrenal steroidogenesis in adult mice. Together these observations suggest that osteocalcin may broadly function during pregnancy to determine organismal homeostasis in adult mammals. To test this hypothesis, we analyzed in unchallenged wildtype and Osteocalcin-deficient, newborn and adult mice of various genotypes and origin maintained on different genetic backgrounds, the functions of osteocalcin in the pancreas, liver and testes and their molecular underpinnings. This analysis revealed that providing mothers are Osteocalcin-deficient, Osteocalcin haploinsufficiency in embryos hampers insulin secretion, liver gluconeogenesis, glucose homeostasis, testes steroidogenesis in adult offspring; inhibits cell proliferation in developing pancreatic islets and testes; and disrupts distinct programs of gene expression in these organs and in the brain. This study indicates that osteocalcin exerts dominant functions in most organs it influences. Furthermore, through their synergistic regulation of multiple physiological functions, osteocalcin of maternal and embryonic origins contributes to the establishment and maintenance of organismal homeostasis in newborn and adult offspring.
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Affiliation(s)
- Danilo Correa Pinto Junior
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Isabella Canal Delgado
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Haiyang Yang
- Guangdong Provincial Key Laboratory of Brain Connectome, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Alisson Clemenceau
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | | | | | | | - Julian Meyer Berger
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Lauren E Hendricks
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Kazuya Tokumura
- Department of Bioactive Molecules, Pharmacology, Gifu Pharmaceutical University, Gifu, Japan
| | - Na Luo
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Hongchao Li
- Guangdong Provincial Key Laboratory of Brain Connectome, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Franck Oury
- INSERM U1151, Institut Necker Enfants-Malades (INEM), Université Paris Descartes-Sorbonne, Paris Cité, Paris, France.
| | - Patricia Ducy
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
| | - Vijay K Yadav
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
| | - Xiang Li
- Guangdong Provincial Key Laboratory of Brain Connectome, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China.
| | - Gerard Karsenty
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
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14
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Delandre O, Lamer O, Loreau JM, Papa Mze N, Fonta I, Mosnier J, Gomez N, Javelle E, Pradines B. Long-Read Sequencing and De Novo Genome Assembly Pipeline of Two Plasmodium falciparum Clones ( Pf3D7, PfW2) Using Only the PromethION Sequencer from Oxford Nanopore Technologies without Whole-Genome Amplification. BIOLOGY 2024; 13:89. [PMID: 38392307 PMCID: PMC10886359 DOI: 10.3390/biology13020089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/24/2024]
Abstract
Antimalarial drug resistance has become a real public health problem despite WHO measures. New sequencing technologies make it possible to investigate genomic variations associated with resistant phenotypes at the genome-wide scale. Based on the use of hemisynthetic nanopores, the PromethION technology from Oxford Nanopore Technologies can produce long-read sequences, in contrast to previous short-read technologies used as the gold standard to sequence Plasmodium. Two clones of P. falciparum (Pf3D7 and PfW2) were sequenced in long-read using the PromethION sequencer from Oxford Nanopore Technologies without genomic amplification. This made it possible to create a processing analysis pipeline for human Plasmodium with ONT Fastq only. De novo assembly revealed N50 lengths of 18,488 kb and 17,502 kb for the Pf3D7 and PfW2, respectively. The genome size was estimated at 23,235,407 base pairs for the Pf3D7 clone and 21,712,038 base pairs for the PfW2 clone. The average genome coverage depth was estimated at 787X and 653X for the Pf3D7 and PfW2 clones, respectively. This study proposes an assembly processing pipeline for the human Plasmodium genome using software adapted to large ONT data and the high AT percentage of Plasmodium. This search provides all the parameters which were optimized for use with the software selected in the pipeline.
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Affiliation(s)
- Océane Delandre
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Ombeline Lamer
- Unité Bactériologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France
- Aix-Marseille Univ, INSERM, SSA, IRBA, MCT, 13005 Marseille, France
| | - Jean-Marie Loreau
- French Armed Forces Center for Epidemiology and Public Health (CESPA), 13014 Marseille, France
| | - Nasserdine Papa Mze
- Service de Biologie, Unité de Microbiologie, Hôpital Mignot, Centre Hospitalier de Versailles, 78150 Versailles, France
| | - Isabelle Fonta
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Joel Mosnier
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Nicolas Gomez
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Emilie Javelle
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Bruno Pradines
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
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15
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Eglit Y, Shiratori T, Jerlström-Hultqvist J, Williamson K, Roger AJ, Ishida KI, Simpson AGB. Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora. Curr Biol 2024; 34:451-459.e6. [PMID: 38262350 DOI: 10.1016/j.cub.2023.12.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 12/03/2023] [Accepted: 12/08/2023] [Indexed: 01/25/2024]
Abstract
"Kingdom-level" branches are being added to the tree of eukaryotes at a rate approaching one per year, with no signs of slowing down.1,2,3,4 Some are completely new discoveries, whereas others are morphologically unusual protists that were previously described but lacked molecular data. For example, Hemimastigophora are predatory protists with two rows of flagella that were known since the 19th century but proved to represent a new deep-branching eukaryote lineage when phylogenomic analyses were conducted.2Meteora sporadica5 is a protist with a unique morphology; cells glide over substrates along a long axis of anterior and posterior projections while a pair of lateral "arms" swing back and forth, a motility system without any obvious parallels. Originally, Meteora was described by light microscopy only, from a short-term enrichment of deep-sea sediment. A small subunit ribosomal RNA (SSU rRNA) sequence was reported recently, but the phylogenetic placement of Meteora remained unresolved.6 Here, we investigated two cultivated Meteora sporadica isolates in detail. Transmission electron microscopy showed that both the anterior-posterior projections and the arms are supported by microtubules originating from a cluster of subnuclear microtubule organizing centers (MTOCs). Neither have a flagellar axoneme-like structure. Sequencing the mitochondrial genome showed this to be among the most gene-rich known, outside jakobids. Remarkably, phylogenomic analyses of 254 nuclear protein-coding genes robustly support a close relationship with Hemimastigophora. Our study suggests that Meteora and Hemimastigophora together represent a morphologically diverse "supergroup" and thus are important for resolving the tree of eukaryote life and early eukaryote evolution.
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Affiliation(s)
- Yana Eglit
- Institute for Comparative Genomics, Department of Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Takashi Shiratori
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Jon Jerlström-Hultqvist
- Institute for Comparative Genomics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Kelsey Williamson
- Institute for Comparative Genomics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Andrew J Roger
- Institute for Comparative Genomics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Ken-Ichiro Ishida
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.
| | - Alastair G B Simpson
- Institute for Comparative Genomics, Department of Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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16
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Bello-López E, Escobedo-Muñoz AS, Hernández-Castro R, Cevallos MA. Genome sequence of an Acinetobacter pittii strain obtained from a red -lored parrot with pneumonia. Microbiol Resour Announc 2024; 13:e0103823. [PMID: 38112472 DOI: 10.1128/mra.01038-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023] Open
Abstract
Acinetobacter pittii 978-A_19 was obtained from a parrot with pneumonia. It is resistant to ampicillin, carbenicillin, cephalosporins, clindamycin, and trimethoprim + sulfamethoxazole. The genome encodes a new blaADC allele, a blaOXA-502 gene, possesses several virulence genes related to adherence and biofilm formation, and has types I, II, and IV secretion systems.
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Affiliation(s)
- E Bello-López
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México , Cuernavaca, Morelos, Mexico
| | - A S Escobedo-Muñoz
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México , Cuernavaca, Morelos, Mexico
| | - R Hernández-Castro
- Departmento de Ecología de Patógenos, Hospital General Dr. Manuel Gea González , Ciudad de México, Mexico
| | - M A Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México , Cuernavaca, Morelos, Mexico
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17
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Benoit G, Raguideau S, James R, Phillippy AM, Chikhi R, Quince C. High-quality metagenome assembly from long accurate reads with metaMDBG. Nat Biotechnol 2024:10.1038/s41587-023-01983-6. [PMID: 38168989 DOI: 10.1038/s41587-023-01983-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/08/2023] [Indexed: 01/05/2024]
Abstract
We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over sequences of minimizers to address variations in genome coverage depth and an abundance-based filtering strategy to simplify strain complexity. For complex communities, we obtained up to twice as many high-quality circularized prokaryotic metagenome-assembled genomes as existing methods and had better recovery of viruses and plasmids.
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Affiliation(s)
- Gaëtan Benoit
- Organisms and Ecosystems, Earlham Institute, Norwich, UK
| | | | - Robert James
- Gut Microbes and Health, Quadram Institute, Norwich, UK
| | - Adam M Phillippy
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA
| | - Rayan Chikhi
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Paris, France
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, UK.
- Gut Microbes and Health, Quadram Institute, Norwich, UK.
- School of Biological Sciences, University of East Anglia, Norwich, UK.
- Warwick Medical School, University of Warwick, Coventry, UK.
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18
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Corbera-Rubio F, Stouten GR, Bruins J, Dost SF, Merkel AY, Müller S, van Loosdrecht MCM, van Halem D, Laureni M. " Candidatus Siderophilus nitratireducens": a putative nap-dependent nitrate-reducing iron oxidizer within the new order Siderophiliales. ISME COMMUNICATIONS 2024; 4:ycae008. [PMID: 38577582 PMCID: PMC10993476 DOI: 10.1093/ismeco/ycae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 01/03/2024] [Accepted: 01/17/2024] [Indexed: 04/06/2024]
Abstract
Nitrate leaching from agricultural soils is increasingly found in groundwater, a primary source of drinking water worldwide. This nitrate influx can potentially stimulate the biological oxidation of iron in anoxic groundwater reservoirs. Nitrate-dependent iron-oxidizing (NDFO) bacteria have been extensively studied in laboratory settings, yet their ecophysiology in natural environments remains largely unknown. To this end, we established a pilot-scale filter on nitrate-rich groundwater to elucidate the structure and metabolism of nitrate-reducing iron-oxidizing microbiomes under oligotrophic conditions mimicking natural groundwaters. The enriched community stoichiometrically removed iron and nitrate consistently with the NDFO metabolism. Genome-resolved metagenomics revealed the underlying metabolic network between the dominant iron-dependent denitrifying autotrophs and the less abundant organoheterotrophs. The most abundant genome belonged to a new Candidate order, named Siderophiliales. This new species, "Candidatus Siderophilus nitratireducens," carries genes central genes to iron oxidation (cytochrome c cyc2), carbon fixation (rbc), and for the sole periplasmic nitrate reductase (nap). Using thermodynamics, we demonstrate that iron oxidation coupled to nap based dissimilatory reduction of nitrate to nitrite is energetically favorable under realistic Fe3+/Fe2+ and NO3-/NO2- concentration ratios. Ultimately, by bridging the gap between laboratory investigations and nitrate real-world conditions, this study provides insights into the intricate interplay between nitrate and iron in groundwater ecosystems, and expands our understanding of NDFOs taxonomic diversity and ecological role.
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Affiliation(s)
| | - Gerben R Stouten
- Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands
| | | | - Simon F Dost
- WMD Water Company Drenthe, Lauwers 3, 9405 BL Assen, the Netherlands
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia
| | - Simon Müller
- Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands
| | | | - Doris van Halem
- Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands
| | - Michele Laureni
- Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands
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19
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Kang X, Xu J, Luo X, Schönhuth A. Hybrid-hybrid correction of errors in long reads with HERO. Genome Biol 2023; 24:275. [PMID: 38041098 PMCID: PMC10690975 DOI: 10.1186/s13059-023-03112-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/16/2023] [Indexed: 12/03/2023] Open
Abstract
Although generally superior, hybrid approaches for correcting errors in third-generation sequencing (TGS) reads, using next-generation sequencing (NGS) reads, mistake haplotype-specific variants for errors in polyploid and mixed samples. We suggest HERO, as the first "hybrid-hybrid" approach, to make use of both de Bruijn graphs and overlap graphs for optimal catering to the particular strengths of NGS and TGS reads. Extensive benchmarking experiments demonstrate that HERO improves indel and mismatch error rates by on average 65% (27[Formula: see text]95%) and 20% (4[Formula: see text]61%). Using HERO prior to genome assembly significantly improves the assemblies in the majority of the relevant categories.
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Affiliation(s)
- Xiongbin Kang
- College of Biology, Hunan University, Changsha, China
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Jialu Xu
- College of Biology, Hunan University, Changsha, China
| | - Xiao Luo
- College of Biology, Hunan University, Changsha, China.
| | - Alexander Schönhuth
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany.
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20
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Strunov A, Kirchner S, Schindelar J, Kruckenhauser L, Haring E, Kapun M. Historic Museum Samples Provide Evidence for a Recent Replacement of Wolbachia Types in European Drosophila melanogaster. Mol Biol Evol 2023; 40:msad258. [PMID: 37995370 PMCID: PMC10701101 DOI: 10.1093/molbev/msad258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/23/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023] Open
Abstract
Wolbachia is one of the most common bacterial endosymbionts, which is frequently found in numerous arthropods and nematode taxa. Wolbachia infections can have a strong influence on the evolutionary dynamics of their hosts since these bacteria are reproductive manipulators that affect the fitness and life history of their host species for their own benefit. Host-symbiont interactions with Wolbachia are perhaps best studied in the model organism Drosophila melanogaster, which is naturally infected with at least 5 different variants among which wMel and wMelCS are the most frequent ones. Comparisons of infection types between natural flies and long-term lab stocks have previously indicated that wMelCS represents the ancestral type, which was only very recently replaced by the nowadays dominant wMel in most natural populations. In this study, we took advantage of recently sequenced museum specimens of D. melanogaster that have been collected 90 to 200 yr ago in Northern Europe to test this hypothesis. Our comparison to contemporary Wolbachia samples provides compelling support for the replacement hypothesis. Our analyses show that sequencing data from historic museum specimens and their bycatch are an emerging and unprecedented resource to address fundamental questions about evolutionary dynamics in host-symbiont interactions. However, we also identified contamination with DNA from crickets that resulted in co-contamination with cricket-specific Wolbachia in several samples. These results underpin the need for rigorous quality assessments of museomic data sets to account for contamination as a source of error that may strongly influence biological interpretations if it remains undetected.
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Affiliation(s)
- Anton Strunov
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Sandra Kirchner
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
| | - Julia Schindelar
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
| | - Luise Kruckenhauser
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
- Department for Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Elisabeth Haring
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
- Department for Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Martin Kapun
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
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21
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Lamas A, Garrido-Maestu A, Prieto A, Cepeda A, Franco CM. Whole genome sequencing in the palm of your hand: how to implement a MinION Galaxy-based workflow in a food safety laboratory for rapid Salmonella spp. serotyping, virulence, and antimicrobial resistance gene identification. Front Microbiol 2023; 14:1254692. [PMID: 38107857 PMCID: PMC10722185 DOI: 10.3389/fmicb.2023.1254692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/02/2023] [Indexed: 12/19/2023] Open
Abstract
Introduction Whole Genome Sequencing (WGS) implementation in food safety laboratories is a significant advancement in food pathogen control and outbreak tracking. However, the initial investment for acquiring next-generation sequencing platforms and the need for bioinformatic skills represented an obstacle for the widespread use of WGS. Long-reading technologies, such as the one developed by Oxford Nanopore Technologies, can be easily implemented with a minor initial investment and with simple protocols that can be performed with basic laboratory equipment. Methods Herein, we report a simple MinION Galaxy-based workflow with analysis parameters that allow its implementation in food safety laboratories with limited computer resources and without previous knowledge in bioinformatics for rapid Salmonella serotyping, virulence, and identification of antimicrobial resistance genes. For that purpose, the single use Flongle flow cells, along with the MinION Mk1B for WGS, and the community-driven web-based analysis platform Galaxy for bioinformatic analysis was used. Three strains belonging to three different serotypes, monophasic S. Typhimurium, S. Grancanaria, and S. Senftenberg, were sequenced. Results After 24 h of sequencing, enough coverage was achieved in order to perform de novo assembly in all three strains. After evaluating different tools, Flye de novo assemblies with medaka polishing were shown to be optimal for in silico Salmonella spp. serotyping with SISRT tool followed by antimicrobial and virulence gene identification with ABRicate. Discussion The implementation of the present workflow in food safety laboratories with limited computer resources allows a rapid characterization of Salmonella spp. isolates.
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Affiliation(s)
- Alexandre Lamas
- Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition and Bromatology, Veterinary School, Universidade da Santiago de Compostela, Lugo, Spain
| | - Alejandro Garrido-Maestu
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Alberto Prieto
- Department of Animal Pathology (INVESAGA Group), Faculty of Veterinary Sciences, Universidade de Santiago de Compostela, Lugo, Spain
| | - Alberto Cepeda
- Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition and Bromatology, Veterinary School, Universidade da Santiago de Compostela, Lugo, Spain
| | - Carlos Manuel Franco
- Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition and Bromatology, Veterinary School, Universidade da Santiago de Compostela, Lugo, Spain
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22
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Zorec TM, Alm E, Lind Karlberg M, Advani R, Hošnjak L, Poljak M. Comprehensive analysis of 66 complete molluscum contagiosum virus (MOCV) genomes: characterization and functional annotation of 47 novel complete MOCV genomes, including the first genome of MOCV genotype 3, and a proposal for harmonized MOCV genotyping indexing. mBio 2023; 14:e0222423. [PMID: 37947415 PMCID: PMC10746250 DOI: 10.1128/mbio.02224-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 10/05/2023] [Indexed: 11/12/2023] Open
Abstract
Four molluscum contagiosum virus (MOCV) genotypes (MOCV1-4) and four subtype variants (MOCV1p, MOCV1va, MOCV1vb, and MOCV1vc) were partially characterized using restriction enzyme profiling in the early 1980s/1990s. However, complete genome sequences of only MOCV1 and MOCV2 are available. The evolutionary pathways of MOCV genotypes and subtype variants with unavailable sequences remain unclear, and also whether all MOCV genotypes/subtype variants can be reliably detected and appropriately categorized using available PCR-based protocols. We de novo fully characterized and functionally annotated 47 complete MOCV genomes, including two putative non-MOCV1/2 isolates, expanding the number of fully characterized MOCV genomes to 66. To ascertain the placement of any putative novel MOCV sequence into the restriction profiling typing scheme, we developed an original framework for extracting complete MOCV genome sequence-based restriction profiles and matching them with reference restriction profiles. We confirmed that two putative non-MOCV1/2 isolates represent the first complete genomes of MOCV3. Comprehensive phylogenomic, recombination, and restriction enzyme recognition site analysis of all 66 currently available MOCV genomes showed that they can be agglomerated into six phylogenetic subgroups (PG1-6), corresponding to the subtype variants from the pioneering studies. PG5 was a novel subtype variant of MOCV2, but no PGs corresponded to the subtype variants MOCV1vb or MOCV4. We showed that the phylogenetic subgroups may have diverged from the prototype MOCV genotype lineages following large-scale recombination events and hinted at partial sequence content of MOCV4 and direction of recombinant transfer in the events that spawned PG5 and the yet undetected subtype variant MOCV1vb.IMPORTANCEFour molluscum contagiosum virus (MOCV) genotypes (MOCV1-4) and four subtype variants were partially characterized using restriction enzyme profiling in the 1980s/1990s, but complete genome sequences of only MOCV1 and MOCV2 are available. The evolutionary pathways whereby genotypes/subtype variants with unavailable sequences emerged and whether all MOCVs can be detected using current diagnostic approaches remain unclear. We fully characterized 47 novel complete MOCV genomes, including the first complete MOCV3 genome, expanding the number of fully characterized genomes to 66. For reliably classifying the novel non-MOCV1/2 genomes, we developed and validated a framework for matching sequence-derived restriction maps with those defining MOCV subtypes in pioneering studies. Six phylogenetic subgroups (PG1-6) were identified, PG5 representing a novel MOCV2 subtype. The phylogenetic subgroups diverged from the prototype lineages following large-scale recombination events and hinted at partial sequence content of MOCV4 and direction of recombinant transfer in the events spawning PG5 and yet undetected MOCV1vb variant.
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Affiliation(s)
- Tomaž Mark Zorec
- Laboratory for Molecular Microbiology and Slovenian HIV/AIDS Reference Center, Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Erik Alm
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | | | - Reza Advani
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Lea Hošnjak
- Laboratory for Molecular Microbiology and Slovenian HIV/AIDS Reference Center, Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Poljak
- Laboratory for Molecular Microbiology and Slovenian HIV/AIDS Reference Center, Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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23
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Singh A, Schnürer A, Dolfing J, Westerholm M. Syntrophic entanglements for propionate and acetate oxidation under thermophilic and high-ammonia conditions. THE ISME JOURNAL 2023; 17:1966-1978. [PMID: 37679429 PMCID: PMC10579422 DOI: 10.1038/s41396-023-01504-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023]
Abstract
Propionate is a key intermediate in anaerobic digestion processes and often accumulates in association with perturbations, such as elevated levels of ammonia. Under such conditions, syntrophic ammonia-tolerant microorganisms play a key role in propionate degradation. Despite their importance, little is known about these syntrophic microorganisms and their cross-species interactions. Here, we present metagenomes and metatranscriptomic data for novel thermophilic and ammonia-tolerant syntrophic bacteria and the partner methanogens enriched in propionate-fed reactors. A metagenome for a novel bacterium for which we propose the provisional name 'Candidatus Thermosyntrophopropionicum ammoniitolerans' was recovered, together with mapping of its highly expressed methylmalonyl-CoA pathway for syntrophic propionate degradation. Acetate was degraded by a novel thermophilic syntrophic acetate-oxidising candidate bacterium. Electron removal associated with syntrophic propionate and acetate oxidation was mediated by the hydrogen/formate-utilising methanogens Methanoculleus sp. and Methanothermobacter sp., with the latter observed to be critical for efficient propionate degradation. Similar dependence on Methanothermobacter was not seen for acetate degradation. Expression-based analyses indicated use of both H2 and formate for electron transfer, including cross-species reciprocation with sulphuric compounds and microbial nanotube-mediated interspecies interactions. Batch cultivation demonstrated degradation rates of up to 0.16 g propionate L-1 day-1 at hydrogen partial pressure 4-30 Pa and available energy was around -20 mol-1 propionate. These observations outline the multiple syntrophic interactions required for propionate oxidation and represent a first step in increasing knowledge of acid accumulation in high-ammonia biogas production systems.
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Affiliation(s)
- Abhijeet Singh
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Anna Schnürer
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Newcastle-upon-Tyne, NE18QH, UK
| | - Maria Westerholm
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden.
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24
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Felgate H, Sethi D, Faust K, Kiy C, Härtel C, Rupp J, Clifford R, Dean R, Tremlett C, Wain J, Langridge G, Clarke P, Page AJ, Webber MA. Characterisation of neonatal Staphylococcus capitis NRCS-A isolates compared with non NRCS-A Staphylococcus capitis from neonates and adults. Microb Genom 2023; 9:001106. [PMID: 37791541 PMCID: PMC10634448 DOI: 10.1099/mgen.0.001106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 09/04/2023] [Indexed: 10/05/2023] Open
Abstract
Staphylococcus capitis is a frequent cause of late-onset sepsis in neonates admitted to Neonatal Intensive Care Units (NICU). One clone of S. capitis, NRCS-A has been isolated from NICUs globally although the reasons for the global success of this clone are not well understood.We analysed a collection of S. capitis colonising babies admitted to two NICUs, one in the UK and one in Germany as well as corresponding pathological clinical isolates. Genome analysis identified a population structure of three groups; non-NRCS-A isolates, NRCS-A isolates, and a group of 'proto NRCS-A' - isolates closely related to NRCS-A but not associated with neonatal infection. All bloodstream isolates belonged to the NRCS-A group and were indistinguishable from strains carried on the skin or in the gut. NRCS-A isolates showed increased tolerance to chlorhexidine and antibiotics relative to the other S. capitis as well as enhanced ability to grow at higher pH values. Analysis of the pangenome of 138 isolates identified characteristic nsr and tarJ genes in both the NRCS-A and proto groups. A CRISPR-cas system was only seen in NRCS-A isolates which also showed enrichment of genes for metal acquisition and transport.We found evidence for transmission of S. capitis NRCS-A within NICU, with related isolates shared between babies and multiple acquisitions by some babies. Our data show NRCS-A strains commonly colonise uninfected babies in NICU representing a potential reservoir for potential infection. This work provides more evidence that adaptation to survive in the gut and on skin facilitates spread of NRCS-A, and that metal acquisition and tolerance may be important to the biology of NRCS-A. Understanding how NRCS-A survives in NICUs can help develop infection control procedures against this clone.
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Affiliation(s)
- Heather Felgate
- Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ, Norwich, UK
- Norwich Medical School, University of East Anglia (UEA), Norwich, UK
| | - Dheeraj Sethi
- Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ, Norwich, UK
- Norfolk and Norwich University Hospital (NNUH), NR4 7UY, Norwich, UK
| | - Kirsten Faust
- Department of Pediatrics, University of Lübeck, Lübeck, Germany
| | - Cemsid Kiy
- Department of Pediatrics, University of Lübeck, Lübeck, Germany
| | - Christoph Härtel
- Department of Pediatrics, University of Würzburg, Würzburg, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Rebecca Clifford
- Norwich Medical School, University of East Anglia (UEA), Norwich, UK
| | - Rachael Dean
- Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ, Norwich, UK
- Norfolk and Norwich University Hospital (NNUH), NR4 7UY, Norwich, UK
| | | | - John Wain
- Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ, Norwich, UK
- Norwich Medical School, University of East Anglia (UEA), Norwich, UK
| | - Gemma Langridge
- Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ, Norwich, UK
- Norwich Medical School, University of East Anglia (UEA), Norwich, UK
| | - Paul Clarke
- Norwich Medical School, University of East Anglia (UEA), Norwich, UK
- Norfolk and Norwich University Hospital (NNUH), NR4 7UY, Norwich, UK
| | - Andrew J. Page
- Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ, Norwich, UK
| | - Mark A. Webber
- Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ, Norwich, UK
- Norwich Medical School, University of East Anglia (UEA), Norwich, UK
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25
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Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Alvarez Jerez P, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P, Yang J, Rhie A, Scholz SW, Traynor BJ, Miga KH, Jain M, Timp W, Phillippy AM, Chaisson M, Sedlazeck FJ, Blauwendraat C, Paten B. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Nat Methods 2023; 20:1483-1492. [PMID: 37710018 DOI: 10.1038/s41592-023-01993-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 08/04/2023] [Indexed: 09/16/2023]
Abstract
Long-read sequencing technologies substantially overcome the limitations of short-reads but have not been considered as a feasible replacement for population-scale projects, being a combination of too expensive, not scalable enough or too error-prone. Here we develop an efficient and scalable wet lab and computational protocol, Napu, for Oxford Nanopore Technologies long-read sequencing that seeks to address those limitations. We applied our protocol to cell lines and brain tissue samples as part of a pilot project for the National Institutes of Health Center for Alzheimer's and Related Dementias. Using a single PromethION flow cell, we can detect single nucleotide polymorphisms with F1-score comparable to Illumina short-read sequencing. Small indel calling remains difficult within homopolymers and tandem repeats, but achieves good concordance to Illumina indel calls elsewhere. Further, we can discover structural variants with F1-score on par with state-of-the-art de novo assembly methods. Our protocol phases small and structural variants at megabase scales and produces highly accurate, haplotype-specific methylation calls.
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Affiliation(s)
- Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Kimberley J Billingsley
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
| | - Mira Mastoras
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | - Jean Monlong
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | - Mobin Asri
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Pilar Alvarez Jerez
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Ramita Dewan
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Xylena Reed
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Rylee M Genner
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kensuke Daida
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Sairam Behera
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Trevor Pesout
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Jeshuwin Prabakaran
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | | | - Jianzhi Yang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Bryan J Traynor
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Miten Jain
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
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26
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Wang L, Chen H, Liu W, Yang L, Xu Z, Chen D. Resistome and Genome Analysis of an Extensively Drug-Resistant Klebsiella michiganensis KMIB106: Characterization of a Novel KPC Plasmid pB106-1 and a Novel Cointegrate Plasmid pB106-IMP Harboring blaIMP-4 and blaSHV-12. Antibiotics (Basel) 2023; 12:1463. [PMID: 37760759 PMCID: PMC10525660 DOI: 10.3390/antibiotics12091463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Klebsiella michiganensis is a recently emerging human pathogen causing nosocomial infections. This study aimed to characterize the complete genome sequence of a clinical Klebsiella michiganensis strain KMIB106 which exhibited extensive drug-resistance. The whole genome of the strain was sequenced using PacBio RS III systems and Illumina Nextseq 500. Annotation, transposable elements and resistance gene identification were analyzed by RAST, prokka and Plasmid Finder, respectively. According to the results, KMIB106 was resistant to multiple antimicrobials, including carbapenems, but it remained susceptible to aztreonam. The genome of KMIB106 consisted of a single chromosome and three predicted plasmids. Importantly, a novel KPC plasmid pB106-1 was found to carry the array of resistance genes in a highly different order in its variable regions, including mphA, msrE, mphE, ARR-3, addA16, sul1, dfrA27, tetD and fosA3. Plasmid pB106-2 is a typical IncFII plasmid with no resistant gene. Plasmid pB106-IMP consists of the IncN and IncX3 backbones, and two resistance genes, blaIMP-4 and blaSHV-12, were identified. Our study for the first time reported an extensively drug-resistant Klebsiella michiganensis strain recovered from a child with a respiratory infection in Southern China, which carries three mega plasmids, with pB106-1 firstly identified to carry an array of resistance genes in a distinctive order, and pB106-IMP identified as a novel IncN-IncX3 cointegrate plasmid harboring two resistance genes blaIMP-4 and blaSHV-12.
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Affiliation(s)
- Linjing Wang
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Haijun Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Wanting Liu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Ling Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Zhenbo Xu
- School of Food Science and Engineering, Research Institute for Food Nutrition and Human Health, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou 510640, China
- Department of Laboratory Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515141, China
| | - Dingqiang Chen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
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27
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Alessiani A, La Bella G, Donatiello A, Occhiochiuso G, Faleo S, Didonna A, D’Attoli L, Selicato P, Pedarra C, La Salandra G, Mancini ME, Di Taranto P, Goffredo E. Occurrence of a New Variant of Salmonella Infantis Lacking Somatic Antigen. Microorganisms 2023; 11:2274. [PMID: 37764118 PMCID: PMC10538023 DOI: 10.3390/microorganisms11092274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Salmonella Infantis is one of the most frequent serovars reported in broilers and is also regularly identified in human salmonellosis cases, representing a relevant public health problem. In the laboratories of the Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata (IZSPB), six Salmonella Infantis strains with antigenic formula -:r:1,5 have been isolated from the litter and carcass of broilers between 2018 and 2022. The strains were investigated to evaluate their phenotype, antibiotic resistance and genomic profiles. Genomic analysis confirmed that the isolates belonged to the Infantis serotype and to the sequence type ST32. Moreover, all strains showed a multidrug-resistant (MDR) profile and were characterised by the presence of the IncFIB plasmid incompatibility group. Three strains had the blaCTX-M-1 gene, and one of them carried IncX1. The presence of this new variant of S. Infantis is particularly relevant because it could expand the landscape of the S. Infantis population. The absence of the somatic antigen could pose a problem in both isolation and serotyping and a consequent public health concern due to the spread of Salmonella infection.
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Affiliation(s)
- Alessandra Alessiani
- Istituto Zooprofilattico Sperimentare della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Via Campo Boario 1, 64100 Teramo, Italy
| | - Gianfranco La Bella
- Istituto Zooprofilattico Sperimentare della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Adelia Donatiello
- Istituto Zooprofilattico Sperimentare della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Gilda Occhiochiuso
- Istituto Zooprofilattico Sperimentare della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Simona Faleo
- Istituto Zooprofilattico Sperimentare della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Antonella Didonna
- Istituto Zooprofilattico Sperimentare della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Luigi D’Attoli
- Istituto Zooprofilattico Sperimentare della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Patrizia Selicato
- Istituto Zooprofilattico Sperimentare della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Carmine Pedarra
- Istituto Zooprofilattico Sperimentare della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Giovanna La Salandra
- Istituto Zooprofilattico Sperimentare della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Maria Emanuela Mancini
- Istituto Zooprofilattico Sperimentare della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Pietro Di Taranto
- Istituto Zooprofilattico Sperimentare della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Elisa Goffredo
- Istituto Zooprofilattico Sperimentare della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
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28
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Chen JC, Patel K, Smith PA, Vidyaprakash E, Snyder C, Tagg KA, Webb HE, Schroeder MN, Katz LS, Rowe LA, Howard D, Griswold T, Lindsey RL, Carleton HA. Reoccurring Escherichia coli O157:H7 Strain Linked to Leafy Greens-Associated Outbreaks, 2016-2019. Emerg Infect Dis 2023; 29:1895-1899. [PMID: 37610207 PMCID: PMC10461648 DOI: 10.3201/eid2909.230069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023] Open
Abstract
Genomic characterization of an Escherichia coli O157:H7 strain linked to leafy greens-associated outbreaks dates its emergence to late 2015. One clade has notable accessory genomic content and a previously described mutation putatively associated with increased arsenic tolerance. This strain is a reoccurring, emerging, or persistent strain causing illness over an extended period.
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Affiliation(s)
| | | | - Peyton A. Smith
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Eshaw Vidyaprakash
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Caroline Snyder
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Kaitlin A. Tagg
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Hattie E. Webb
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Morgan N. Schroeder
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Lee S. Katz
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | | | - Dakota Howard
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Taylor Griswold
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Rebecca L. Lindsey
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
| | - Heather A. Carleton
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.C. Chen, K. Patel, P.A. Smith, E. Vidyaprakash, C. Snyder, K.A. Tagg, H.E. Webb, M.N. Schroeder, L.S. Katz, L.A. Rowe, D. Howard, T. Griswold, R.L. Lindsey, H.A. Carleton)
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA (K. Patel, C. Snyder)
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Awate S, Mubarka S, Huber RG. Whole Genomic Characterization of Streptococcus iniae Isolates from Barramundi ( Lates calcarifer) and Preliminary Evidence of Cross-Protective Immunization. Vaccines (Basel) 2023; 11:1443. [PMID: 37766120 PMCID: PMC10537698 DOI: 10.3390/vaccines11091443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/20/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Lates calcarifer, also known as Barramundi or Asian seabass, is a highly productive and fast-growing species that is well suited to large-scale aquaculture due to its attractive harvestable yields (premium fish). This fish has been envisioned as having the potential to be the "Salmon of Tropics". Cultivating Lates calcarifer in aquaculture poses challenges, as the dense populations that make such aquaculture commercially viable facilitate the rapid spread of infectious diseases, which in turn significantly impact yield. Hence, the immunization of juveniles is necessary, and the development of new immunization agents enhances the efficiency of aquaculture and improves food security. In our study, we characterize seven novel strains of the bacterial pathogen Streptococcus iniae that were collected from commercial fish farms in Singapore and Australia. We find that the capsular operon in our strains is highly conserved and identify a number of major surface antigens previously described in Streptococcus. A genome analysis indicates that the present strains are closely related but form distinct strains within the S. iniae species. We then proceed to demonstrate that inoculation with the inactivated strain P3SAB cross-protects Lates calcarifer against S. iniae infections in vivo from a variety of strains found in both Singapore and Australia.
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Affiliation(s)
- Sunita Awate
- UVAXX Pte Ltd., 203 Henderson Industrial Road, #12-01, Singapore 159546, Singapore;
| | - Salma Mubarka
- UVAXX Pte Ltd., 203 Henderson Industrial Road, #12-01, Singapore 159546, Singapore;
| | - Roland G. Huber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix #07-01, 30 Biopolis Street, Singapore 138671, Singapore
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Minio A, Figueroa-Balderas R, Cohen SP, Ali SS, Carriel D, Britto D, Stack C, Baruah IK, Marelli JP, Cantu D, Bailey BA. Clonal reproduction of Moniliophthora roreri and the emergence of unique lineages with distinct genomes during range expansion. G3 (BETHESDA, MD.) 2023; 13:jkad125. [PMID: 37337677 PMCID: PMC10468315 DOI: 10.1093/g3journal/jkad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 04/27/2023] [Accepted: 05/30/2023] [Indexed: 06/21/2023]
Abstract
The basidiomycete Moniliophthora roreri causes frosty pod rot of cacao (Theobroma cacao) in the western hemisphere. Moniliophthora roreri is considered asexual and haploid throughout its hemibiotrophic life cycle. To understand the processes driving genome modification, using long-read sequencing technology, we sequenced and assembled 5 high-quality M. roreri genomes out of a collection of 99 isolates collected throughout the pathogen's range. We obtained chromosome-scale assemblies composed of 11 scaffolds. We used short-read technology to sequence the genomes of 22 similarly chosen isolates. Alignments among the 5 reference assemblies revealed inversions, translocations, and duplications between and within scaffolds. Isolates at the front of the pathogens' expanding range tend to share lineage-specific structural variants, as confirmed by short-read sequencing. We identified, for the first time, 3 new mating type A locus alleles (5 in total) and 1 new potential mating type B locus allele (3 in total). Currently, only 2 mating type combinations, A1B1 and A2B2, are known to exist outside of Colombia. A systematic survey of the M. roreri transcriptome across 2 isolates identified an expanded candidate effector pool and provided evidence that effector candidate genes unique to the Moniliophthoras are preferentially expressed during the biotrophic phase of disease. Notably, M. roreri isolates in Costa Rica carry a chromosome segment duplication that has doubled the associated gene complement and includes secreted proteins and candidate effectors. Clonal reproduction of the haploid M. roreri genome has allowed lineages with unique genome structures and compositions to dominate as it expands its range, displaying a significant founder effect.
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Affiliation(s)
- Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis 95616, CA, USA
- Genome Center, University of California Davis, 95616 Davis, CA, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis 95616, CA, USA
| | - Stephen P Cohen
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville 20705, MD, USA
| | - Shahin S Ali
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville 20705, MD, USA
| | - Denny Carriel
- Mars La Chola (MLCH), Mars Inc., Guayaquil 090103, Ecuador
| | - Dahyana Britto
- Mars Center for Cocoa Science, Mars Inc., Fazenda Almirante, Caixa Postal 55, Itajuípe, BA, CEP 45630-000, Brazil
| | - Conrad Stack
- Mars Digital Technologies, Mars Inc., Chicago 60642, IL, USA
| | - Indrani K Baruah
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville 20705, MD, USA
| | | | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis 95616, CA, USA
| | - Bryan A Bailey
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville 20705, MD, USA
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31
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Yap ZL, Motnenko A, Cardona S. Complete Genome Sequence of Burkholderia vietnamiensis LMG16232. Microbiol Resour Announc 2023; 12:e0032823. [PMID: 37395660 PMCID: PMC10443308 DOI: 10.1128/mra.00328-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/09/2023] [Indexed: 07/04/2023] Open
Abstract
We report here the complete annotated closed genome sequence of Burkholderia vietnamiensis LMG16232. There were three contigs, with a combined size of 6,739,172 bp and a GC content of 67%.
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Affiliation(s)
- Zhong Ling Yap
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Anna Motnenko
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Silvia Cardona
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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32
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Pinto DC, Delgado IC, Yang H, Clemenceau A, Corvelo A, Narzisi G, Musunuri R, Berger JM, Hendricks LE, Tokumura K, Luo N, Li H, Oury F, Ducy P, Yadav VK, Li X, Karsenty G. Osteocalcin of maternal and embryonic origins synergize to establish homeostasis in offspring. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.552969. [PMID: 37645714 PMCID: PMC10462025 DOI: 10.1101/2023.08.11.552969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Many physiological functions regulated by osteocalcin are affected in adult offspring of mothers experiencing an unhealthy pregnancy. Furthermore, osteocalcin signaling during gestation influences cognition and adrenal steroidogenesis in adult mice. Together these observations suggest that osteocalcin functions during pregnancy may be a broader determinant of organismal homeostasis in adult mammals than previously thought. To test this hypothesis, we analyzed in unchallenged wildtype and Osteocalcin -deficient, newborn, and adult mice of various genotypes and origin, and that were maintained on different genetic backgrounds, the functions of osteocalcin in the pancreas, liver and testes and their molecular underpinnings. This analysis revealed that providing mothers are themselves Osteocalcin -deficient, Osteocalcin haploinsufficiency in embryos hampers insulin secretion, liver gluconeogenesis, glucose homeostasis, testes steroidogenesis in adult offspring; inhibits cell proliferation in developing pancreatic islets and testes; and disrupts distinct programs of gene expression in these organs and in the brain. This study indicates that through their synergistic regulation of multiple physiological functions, osteocalcin ofmaternal and embryonic origins contributes to the establishment and maintenance of organismal homeostasis in newborn and adult offspring.
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Elek CKA, Brown TL, Le Viet T, Evans R, Baker DJ, Telatin A, Tiwari SK, Al-Khanaq H, Thilliez G, Kingsley RA, Hall LJ, Webber MA, Adriaenssens EM. A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses. Microb Genom 2023; 9:mgen001065. [PMID: 37463032 PMCID: PMC10438801 DOI: 10.1099/mgen.0.001065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/17/2023] [Indexed: 07/21/2023] Open
Abstract
Bacteriophages (phages) within the genus Przondovirus are T7-like podoviruses belonging to the subfamily Studiervirinae, within the family Autographiviridae, and have a highly conserved genome organisation. The genomes of these phages range from 37 to 42 kb in size, encode 50-60 genes and are characterised by the presence of direct terminal repeats (DTRs) flanking the linear chromosome. These DTRs are often deleted during short-read-only and hybrid assemblies. Moreover, long-read-only assemblies are often littered with sequencing and/or assembly errors and require additional curation. Here, we present the isolation and characterisation of ten novel przondoviruses targeting Klebsiella spp. We describe HYPPA, a HYbrid and Poly-polish Phage Assembly workflow, which utilises long-read assemblies in combination with short-read sequencing to resolve phage DTRs and correcting errors, negating the need for laborious primer walking and Sanger sequencing validation. Our assembly workflow utilised Oxford Nanopore Technologies for long-read sequencing for its accessibility, making it the more relevant long-read sequencing technology at this time, and Illumina DNA Prep for short-read sequencing, representing the most commonly used technologies globally. Our data demonstrate the importance of careful curation of phage assemblies before publication, and prior to using them for comparative genomics.
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Affiliation(s)
- Claire K. A. Elek
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
| | - Teagan L. Brown
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Thanh Le Viet
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Rhiannon Evans
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - David J. Baker
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Andrea Telatin
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Sumeet K. Tiwari
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Haider Al-Khanaq
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Gaëtan Thilliez
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
| | - Robert A. Kingsley
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
| | - Lindsay J. Hall
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
- Chair of Intestinal Microbiome, ZIEL—Institute for Food and Health, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mark A. Webber
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
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Li X, Shi Q, Chen K, Shao M. Seeding with minimized subsequence. Bioinformatics 2023; 39:i232-i241. [PMID: 37387132 DOI: 10.1093/bioinformatics/btad218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION Modern methods for computation-intensive tasks in sequence analysis (e.g. read mapping, sequence alignment, genome assembly, etc.) often first transform each sequence into a list of short, regular-length seeds so that compact data structures and efficient algorithms can be employed to handle the ever-growing large-scale data. Seeding methods using kmers (substrings of length k) have gained tremendous success in processing sequencing data with low mutation/error rates. However, they are much less effective for sequencing data with high error rates as kmers cannot tolerate errors. RESULTS We propose SubseqHash, a strategy that uses subsequences, rather than substrings, as seeds. Formally, SubseqHash maps a string of length n to its smallest subsequence of length k, k < n, according to a given order overall length-k strings. Finding the smallest subsequence of a string by enumeration is impractical as the number of subsequences grows exponentially. To overcome this barrier, we propose a novel algorithmic framework that consists of a specifically designed order (termed ABC order) and an algorithm that computes the minimized subsequence under an ABC order in polynomial time. We first show that the ABC order exhibits the desired property and the probability of hash collision using the ABC order is close to the Jaccard index. We then show that SubseqHash overwhelmingly outperforms the substring-based seeding methods in producing high-quality seed-matches for three critical applications: read mapping, sequence alignment, and overlap detection. SubseqHash presents a major algorithmic breakthrough for tackling the high error rates and we expect it to be widely adapted for long-reads analysis. AVAILABILITY AND IMPLEMENTATION SubseqHash is freely available at https://github.com/Shao-Group/subseqhash.
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Affiliation(s)
- Xiang Li
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Qian Shi
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ke Chen
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Mingfu Shao
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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35
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Gach J, Grzelczyk J, Strzała T, Boratyński F, Olejniczak T. Microbial Metabolites of 3- n-butylphthalide as Monoamine Oxidase A Inhibitors. Int J Mol Sci 2023; 24:10605. [PMID: 37445788 DOI: 10.3390/ijms241310605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Novel compounds with antidepressant activity via monoamine oxidase inhibition are being sought. Among these, derivatives of 3-n-butylphthalide, a neuroprotective lactone from Apiaceae plants, may be prominent candidates. This study aimed to obtain the oxidation products of 3-n-butylphthalide and screen them regarding their activity against the monoamine oxidase A (MAO-A) isoform. Such activity of these compounds has not been previously tested. To obtain the metabolites, we used fungi as biocatalysts because of their high oxidative capacity. Overall, 37 strains were used, among which Penicillium and Botrytis spp. were the most efficient, leading to the obtaining of three main products: 3-n-butyl-10-hydroxyphthalide, 3-n-butylphthalide-11-oic acid, and 3-n-butyl-11-hydroxyphthalide, with a total yield of 0.38-0.82 g per g of the substrate, depending on the biocatalyst used. The precursor-3-n-butylphthalide and abovementioned metabolites inhibited the MAO-A enzyme; the most active was the carboxylic acid derivative of the lactone with inhibitory constant (Ki) < 0.001 µmol/L. The in silico prediction of the drug-likeness of the metabolites matches the assumptions of Lipinski, Ghose, Veber, Egan, and Muegge. All the compounds are within the optimal range for the lipophilicity value, which is connected to adequate permeability and solubility.
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Affiliation(s)
- Joanna Gach
- Department of Food Chemistry and Biocatalysis, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland
| | - Joanna Grzelczyk
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, 90-924 Łódź, Poland
| | - Tomasz Strzała
- Department of Genetics, Wrocław University of Environmental and Life Sciences, Kożuchowska 7, 51-631 Wrocław, Poland
| | - Filip Boratyński
- Department of Food Chemistry and Biocatalysis, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland
| | - Teresa Olejniczak
- Department of Food Chemistry and Biocatalysis, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland
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36
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Catto MA, Labadie PE, Jacobson AL, Kennedy GG, Srinivasan R, Hunt BG. Pest status, molecular evolution, and epigenetic factors derived from the genome assembly of Frankliniella fusca, a thysanopteran phytovirus vector. BMC Genomics 2023; 24:343. [PMID: 37344773 DOI: 10.1186/s12864-023-09375-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 05/13/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND The tobacco thrips (Frankliniella fusca Hinds; family Thripidae; order Thysanoptera) is an important pest that can transmit viruses such as the tomato spotted wilt orthotospovirus to numerous economically important agricultural row crops and vegetables. The structural and functional genomics within the order Thysanoptera has only begun to be explored. Within the > 7000 known thysanopteran species, the melon thrips (Thrips palmi Karny) and the western flower thrips (Frankliniella occidentalis Pergrande) are the only two thysanopteran species with assembled genomes. RESULTS A genome of F. fusca was assembled by long-read sequencing of DNA from an inbred line. The final assembly size was 370 Mb with a single copy ortholog completeness of ~ 99% with respect to Insecta. The annotated genome of F. fusca was compared with the genome of its congener, F. occidentalis. Results revealed many instances of lineage-specific differences in gene content. Analyses of sequence divergence between the two Frankliniella species' genomes revealed substitution patterns consistent with positive selection in ~ 5% of the protein-coding genes with 1:1 orthologs. Further, gene content related to its pest status, such as xenobiotic detoxification and response to an ambisense-tripartite RNA virus (orthotospovirus) infection was compared with F. occidentalis. Several F. fusca genes related to virus infection possessed signatures of positive selection. Estimation of CpG depletion, a mutational consequence of DNA methylation, revealed that F. fusca genes that were downregulated and alternatively spliced in response to virus infection were preferentially targeted by DNA methylation. As in many other insects, DNA methylation was enriched in exons in Frankliniella, but gene copies with homology to DNA methyltransferase 3 were numerous and fragmented. This phenomenon seems to be relatively unique to thrips among other insect groups. CONCLUSIONS The F. fusca genome assembly provides an important resource for comparative genomic analyses of thysanopterans. This genomic foundation allows for insights into molecular evolution, gene regulation, and loci important to agricultural pest status.
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Affiliation(s)
- Michael A Catto
- Department of Entomology, University of Georgia, Athens, GA, 30602, USA
| | - Paul E Labadie
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Alana L Jacobson
- Department of Entomology and Plant Pathology, Auburn University College of Agriculture, Auburn, AL, 36849, USA
| | - George G Kennedy
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | | | - Brendan G Hunt
- Department of Entomology, University of Georgia, Griffin, GA, 30223, USA.
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Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Jerez PA, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P, Yang J, Rhie A, Scholz SW, Traynor BJ, Miga KH, Jain M, Timp W, Phillippy AM, Chaisson M, Sedlazeck FJ, Blauwendraat C, Paten B. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523790. [PMID: 36711673 PMCID: PMC9882142 DOI: 10.1101/2023.01.12.523790] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Long-read sequencing technologies substantially overcome the limitations of short-reads but to date have not been considered as feasible replacement at scale due to a combination of being too expensive, not scalable enough, or too error-prone. Here, we develop an efficient and scalable wet lab and computational protocol for Oxford Nanopore Technologies (ONT) long-read sequencing that seeks to provide a genuine alternative to short-reads for large-scale genomics projects. We applied our protocol to cell lines and brain tissue samples as part of a pilot project for the NIH Center for Alzheimer's and Related Dementias (CARD). Using a single PromethION flow cell, we can detect SNPs with F1-score better than Illumina short-read sequencing. Small indel calling remains to be difficult inside homopolymers and tandem repeats, but is comparable to Illumina calls elsewhere. Further, we can discover structural variants with F1-score comparable to state-of the-art methods involving Pacific Biosciences HiFi sequencing and trio information (but at a lower cost and greater throughput). Using ONT based phasing, we can then combine and phase small and structural variants at megabase scales. Our protocol also produces highly accurate, haplotype-specific methylation calls. Overall, this makes large-scale long-read sequencing projects feasible; the protocol is currently being used to sequence thousands of brain-based genomes as a part of the NIH CARD initiative. We provide the protocol and software as open-source integrated pipelines for generating phased variant calls and assemblies.
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Affiliation(s)
- Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, USA
| | - Kimberley J. Billingsley
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Mira Mastoras
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | - Jean Monlong
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | - Mobin Asri
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Pilar Alvarez Jerez
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Ramita Dewan
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Xylena Reed
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Rylee M. Genner
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kensuke Daida
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Sairam Behera
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Kishwar Shafin
- Google LLC, 1600 Amphitheatre Pkwy, Mountain View, CA, USA
| | - Trevor Pesout
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Jeshuwin Prabakaran
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, USA
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | | | | | - Jianzhi Yang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sonja W. Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Bryan J. Traynor
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Miten Jain
- Department of Bioengineering, Department of Physics, Northeastern University, Boston, MA, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, Texas, USA
| | - Cornelis Blauwendraat
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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Rohlfing K, Yue L, Franke S, Zeng C, Podsiadlowski L, Dobler S. When does the female bias arise? Insights from the sex determination cascade of a flea beetle with a strongly skewed sex ratio. Funct Integr Genomics 2023; 23:112. [PMID: 37000335 PMCID: PMC10066108 DOI: 10.1007/s10142-023-01023-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 04/01/2023]
Abstract
Reproduction-manipulating bacteria like Wolbachia can shift sex ratios in insects towards females, but skewed sex ratios may also arise from genetic conflicts. The flea beetle Altica lythri harbors three main mtDNA strains that are coupled to three different Wolbachia infections. Depending on the mtDNA types, the females produce either offspring with a balanced sex ratio or exclusively daughters. To obtain markers that can monitor when sex bias arises in the beetle's ontogeny, we elucidated the sex determination cascade of A. lythri. We established a RT-PCR method based on length variants of dsx (doublesex) transcripts to determine the sex of morphologically indistinguishable eggs and larvae. In females of one mtDNA type (HT1/HT1*) known to produce only daughters, male offspring were already missing at the egg stage while for females of another type (HT2), the dsx splice variants revealed a balanced sex ratio among eggs and larvae. Our data suggest that the sex determination cascade in A. lythri is initiated by maternally transmitted female-specific tra (transformer) mRNA as primary signal. This tra mRNA seems to be involved in a positive feedback loop that maintains the production of the female splice variant, as known for female offspring in Tribolium castaneum. The translation of the maternally transmitted female tra mRNA must be inhibited in male offspring, but the underlying primary genetic signal remains to be identified. We discuss which differences between the mtDNA types can influence sex determination and lead to the skewed sex ratio of HT1.
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Affiliation(s)
- Kim Rohlfing
- Institute of Animal Cell and Systems Biology, Universität Hamburg, Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany.
| | - Lennart Yue
- Institute of Animal Cell and Systems Biology, Universität Hamburg, Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany
| | - Sebastian Franke
- Institute of Animal Cell and Systems Biology, Universität Hamburg, Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany
| | - Cen Zeng
- Institute of Animal Cell and Systems Biology, Universität Hamburg, Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany
| | - Lars Podsiadlowski
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Susanne Dobler
- Institute of Animal Cell and Systems Biology, Universität Hamburg, Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany.
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Sarton-Lohéac G, Nunes da Silva CG, Mazel F, Baud G, de Bakker V, Das S, El Chazli Y, Ellegaard K, Garcia-Garcera M, Glover N, Liberti J, Nacif Marçal L, Prasad A, Somerville V, Bonilla-Rosso G, Engel P. Deep Divergence and Genomic Diversification of Gut Symbionts of Neotropical Stingless Bees. mBio 2023; 14:e0353822. [PMID: 36939321 PMCID: PMC10128065 DOI: 10.1128/mbio.03538-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
Social bees harbor conserved gut microbiotas that may have been acquired in a common ancestor of social bees and subsequently codiversified with their hosts. However, most of this knowledge is based on studies on the gut microbiotas of honey bees and bumblebees. Much less is known about the gut microbiotas of the third and most diverse group of social bees, the stingless bees. Specifically, the absence of genomic data from their microbiotas presents an important knowledge gap in understanding the evolution and functional diversity of the social bee microbiota. Here, we combined community profiling with culturing and genome sequencing of gut bacteria from six neotropical stingless bee species from Brazil. Phylogenomic analyses show that most stingless bee gut isolates form deep-branching sister clades of core members of the honey bee and bumblebee gut microbiota with conserved functional capabilities, confirming the common ancestry and ecology of their microbiota. However, our bacterial phylogenies were not congruent with those of the host, indicating that the evolution of the social bee gut microbiota was not driven by strict codiversification but included host switches and independent symbiont gain and losses. Finally, as reported for the honey bee and bumblebee microbiotas, we found substantial genomic divergence among strains of stingless bee gut bacteria, suggesting adaptation to different host species and glycan niches. Our study offers first insights into the genomic diversity of the stingless bee microbiota and highlights the need for broader samplings to understand the evolution of the social bee gut microbiota. IMPORTANCE Stingless bees are the most diverse group of the corbiculate bees and represent important pollinator species throughout the tropics and subtropics. They harbor specialized microbial communities in their gut that are related to those found in honey bees and bumblebees and that are likely important for bee health. Few bacteria have been cultured from the gut of stingless bees, which has prevented characterization of their genomic diversity and functional potential. Here, we established cultures of major members of the gut microbiotas of six stingless bee species and sequenced their genomes. We found that most stingless bee isolates belong to novel bacterial species distantly related to those found in honey bees and bumblebees and encoding similar functional capabilities. Our study offers a new perspective on the evolution of the social bee gut microbiota and presents a basis for characterizing the symbiotic relationships between gut bacteria and stingless bees.
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Affiliation(s)
- Garance Sarton-Lohéac
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Gilles Baud
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Vincent de Bakker
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sudip Das
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Yassine El Chazli
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Kirsten Ellegaard
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Natasha Glover
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joanito Liberti
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Lorena Nacif Marçal
- Department of Morphology, Instituto de Ciências Biológicas, Federal University of Amazonas, Manaus, Brazil
| | - Aiswarya Prasad
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Germán Bonilla-Rosso
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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Characterization of Escherichia coli and Other Enterobacterales Resistant to Extended-Spectrum Cephalosporins Isolated from Dairy Manure in Ontario, Canada. Appl Environ Microbiol 2023; 89:e0186922. [PMID: 36695602 PMCID: PMC9972979 DOI: 10.1128/aem.01869-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Extended-spectrum cephalosporins (ESCs) resistance genes, such as blaCTX-M, blaCMY, and blaSHV, have been found regularly in bacteria from livestock. However, information on their distribution in dairy cattle in Canada and on the associated genome sequences of ESC-resistant Enterobacterales is sparse. In this study, the diversity and distribution of ESC-resistant Escherichia coli throughout manure treatments in six farms in Southern Ontario were assessed over a one-year period, and their ESC-resistance plasmids were characterized. The manure samples were enriched using selective media. The resulting isolates were screened via polymerase chain reaction for blaCTX-M, blaCMY, and blaSHV. No E. coli carrying blaSHV were detected. Escherichia coli (n = 248) carrying blaCTX-M or blaCMY underwent whole-genome sequencing using an Illumina MiSeq/NextSeq. These isolates were typed using multilocus sequence typing (MLST) and their resistance gene profiles. A subset of E. coli (n = 28) were sequenced using Oxford Nanopore Technologies. Plasmids were assembled using Unicycler and characterized via the resistance genes pattern, replicon type, plasmid MLST, phylogenetic analysis, and Mauve alignments. The recovery of ESC-resistant Enterobacterales (18 species, 8 genera) was drastically reduced in manure outputs. However, multiple treatment stages were needed to attain a significant reduction. 62 sequence types were identified, with ST10, ST46, ST58, ST155, ST190, ST398, ST685, and ST8761 being detected throughout the treatment pipeline. These STs overlapped with those found on multiple farms. The ESC-resistance determinants included CTX-M-1, -14, -15, -17, -24, -32, -55, and CMY-2. The plasmids carrying blaCTX-M were more diverse than were the plasmids carrying blaCMY. Known "epidemic plasmids" were detected for both blaCTX-M and blaCMY. IMPORTANCE The increase in antimicrobial resistance is of concern for human and animal health, especially when resistance is conferred to extended-spectrum cephalosporins, which are used to treat serious infections in both human and veterinary medicine. Bacteria carrying extended-spectrum cephalosporin resistance genes, including blaCTX-M and blaCMY, are frequently found in dairy manure. Manure treatment influences the loads and diversity of bacteria, including those carrying antimicrobial resistance genes, such as Enterobacterales and Escherichia coli. Any bacteria that survive the treatment process are subsequently applied to the environment. Enterobacterales carrying blaCTX-M or blaCMY can contaminate soil and crops consumed by humans and animals, thereby increasing the potential for antimicrobial resistance genes to integrate into the human gut microflora through horizontal gene transfer. This furthers the dissemination of resistance. Therefore, it is imperative to understand the effects manure treatments have on ESC-resistance in environmentally applied manure.
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Zhang F, Chen F, Schwarzacher T, Heslop-Harrison JS, Teng N. The nature and genomic landscape of repetitive DNA classes in Chrysanthemum nankingense shows recent genomic changes. ANNALS OF BOTANY 2023; 131:215-228. [PMID: 35639931 PMCID: PMC9904347 DOI: 10.1093/aob/mcac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Tandemly repeated DNA and transposable elements represent most of the DNA in higher plant genomes. High-throughput sequencing allows a survey of the DNA in a genome, but whole-genome assembly can miss a substantial fraction of highly repeated sequence motifs. Chrysanthemum nankingense (2n = 2x = 18; genome size = 3.07 Gb; Asteraceae), a diploid reference for the many auto- and allopolyploids in the genus, was considered as an ancestral species and serves as an ornamental plant and high-value food. We aimed to characterize the major repetitive DNA motifs, understand their structure and identify key features that are shaped by genome and sequence evolution. METHODS Graph-based clustering with RepeatExplorer was used to identify and classify repetitive motifs in 2.14 millions of 250-bp paired-end Illumina reads from total genomic DNA of C. nankingense. Independently, the frequency of all canonical motifs k-bases long was counted in the raw read data and abundant k-mers (16, 21, 32, 64 and 128) were extracted and assembled to generate longer contigs for repetitive motif identification. For comparison, long terminal repeat retrotransposons were checked in the published C. nankingense reference genome. Fluorescent in situ hybridization was performed to show the chromosomal distribution of the main types of repetitive motifs. KEY RESULTS Apart from rDNA (0.86 % of the total genome), a few microsatellites (0.16 %), and telomeric sequences, no highly abundant tandem repeats were identified. There were many transposable elements: 40 % of the genome had sequences with recognizable domains related to transposable elements. Long terminal repeat retrotransposons showed widespread distribution over chromosomes, although different sequence families had characteristic features such as abundance at or exclusion from centromeric or subtelomeric regions. Another group of very abundant repetitive motifs, including those most identified as low-complexity sequences (9.07 %) in the genome, showed no similarity to known sequence motifs or tandemly repeated elements. CONCLUSIONS The Chrysanthemum genome has an unusual structure with a very low proportion of tandemly repeated sequences (~1.02 %) in the genome, and a high proportion of low-complexity sequences, most likely degenerated remains of transposable elements. Identifying the presence, nature and genomic organization of major genome fractions enables inference of the evolutionary history of sequences, including degeneration and loss, critical to understanding biodiversity and diversification processes in the genomes of diploid and polyploid Chrysanthemum, Asteraceae and plants more widely.
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Affiliation(s)
- Fengjiao Zhang
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Fadi Chen
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
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Valenti I, Saracchi M, Degradi L, Kunova A, Cortesi P, Pasquali M. A Genome Resource for Ciborinia camelliae, the Causal Agent of Camellia Flower Blight. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:131-133. [PMID: 36513026 DOI: 10.1094/mpmi-09-22-0175-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Ciborinia camelliae Kohn is a camellia pathogen belonging to family Sclerotiniaceae, infecting only flowers of camellias. To better understand the virulence mechanism in this species, the draft genome sequence of the Italian strain of C. camelliae was obtained with a hybrid approach, combining Illumina HiSeq paired reads and MinIon Nanopore long-read sequencing. This combination improved significantly the existing National Center for Biotechnology Information reference genome. The assembly contiguity was implemented decreasing the contig number from 2,604 to 49. The N50 contig size increased from 31,803 to 2,726,972 bp and the completeness of assembly increased from 94.5 to 97.3% according to BUSCO analysis. This work is foundational to allow functional analysis of the infection process in this scarcely known floral pathogen. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Irene Valenti
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Marco Saracchi
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Luca Degradi
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Andrea Kunova
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Paolo Cortesi
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
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Zelendova M, Papagiannitsis CC, Sismova P, Medvecky M, Pomorska K, Palkovicova J, Nesporova K, Jakubu V, Jamborova I, Zemlickova H, Dolejska M. Plasmid-mediated colistin resistance among human clinical Enterobacterales isolates: national surveillance in the Czech Republic. Front Microbiol 2023; 14:1147846. [PMID: 37180238 PMCID: PMC10174314 DOI: 10.3389/fmicb.2023.1147846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/05/2023] [Indexed: 05/16/2023] Open
Abstract
The occurrence of colistin resistance has increased rapidly among Enterobacterales around the world. We performed a national survey of plasmid-mediated colistin resistance in human clinical isolates through a retrospective analysis of samples from 2009 to 2017 and a prospective sampling in 2018-2020. The aim of this study was to identify and characterize isolates with mcr genes from various regions of the Czech Republic using whole genome sequencing (WGS). Of all 1932 colistin-resistant isolates analyzed, 73 (3.8%) were positive for mcr genes. Most isolates carried mcr-1 (48/73) and were identified as Escherichia coli (n = 44) and Klebsiella pneumoniae (n = 4) of various sequence types (ST). Twenty-five isolates, including Enterobacter spp. (n = 24) and Citrobacter freundii (n = 1) carrying the mcr-9 gene were detected; three of them (Enterobacter kobei ST54) co-harbored the mcr-4 and mcr-9 genes. Multi-drug resistance phenotype was a common feature of mcr isolates and 14% (10/73) isolates also co-harbored clinically important beta-lactamases, including two isolates with carbapenemases KPC-2 and OXA-48. Phylogenetic analysis of E. coli ST744, the dominant genotype in this study, with the global collection showed Czech isolates belonged to two major clades, one containing isolates from Europe, while the second composed of isolates from diverse geographical areas. The mcr-1 gene was carried by IncX4 (34/73, 47%), IncHI2/ST4 (6/73, 8%) and IncI2 (8/73, 11%) plasmid groups. Small plasmids belonging to the ColE10 group were associated with mcr-4 in three isolates, while mcr-9 was carried by IncHI2/ST1 plasmids (4/73, 5%) or the chromosome (18/73, 25%). We showed an overall low level of occurrence of mcr genes in colistin-resistant bacteria from human clinical samples in the Czech Republic.
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Affiliation(s)
- Marketa Zelendova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | | | - Petra Sismova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Matej Medvecky
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, Czechia
| | - Katarina Pomorska
- NRL for ATB, The National Institute of Public Health, Centre for Epidemiology and Microbiology, Prague, Czechia
| | - Jana Palkovicova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | | | - Vladislav Jakubu
- NRL for ATB, The National Institute of Public Health, Centre for Epidemiology and Microbiology, Prague, Czechia
- Department of Microbiology, 3rd Faculty of Medicine, Kralovske Vinohrady University Hospital and National Institute of Public Health, Charles University, Prague, Czechia
| | - Ivana Jamborova
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Helena Zemlickova
- NRL for ATB, The National Institute of Public Health, Centre for Epidemiology and Microbiology, Prague, Czechia
- Department of Microbiology, 3rd Faculty of Medicine, Kralovske Vinohrady University Hospital and National Institute of Public Health, Charles University, Prague, Czechia
| | - Monika Dolejska
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
- Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Brno, Czechia
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Pilsen, Czechia
- *Correspondence: Monika Dolejska,
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Campolo A, Pifer R, Walters R, Thomas M, Miller E, Harris V, King J, Rice CA, Shannon P, Patterson B, Crary M. Acanthamoeba spp. aggregate and encyst on contact lens material increasing resistance to disinfection. Front Microbiol 2022; 13:1089092. [PMID: 36601401 PMCID: PMC9806144 DOI: 10.3389/fmicb.2022.1089092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction Acanthamoeba keratitis is often caused when Acanthamoeba contaminate contact lenses and infect the cornea. Acanthamoeba is pervasive in the environment as a motile, foraging trophozoite or biocide-resistant and persistent cyst. As contact lens contamination is a potential first step in infection, we studied Acanthamoeba's behavior and interactions on different contact lens materials. We hypothesized that contact lenses may induce aggregation, which is a precursor to encystment, and that aggregated encystment would be more difficult to disinfect than motile trophozoites. Methods Six clinically and/or scientifically relevant strains of Acanthamoeba (ATCC 30010, ATCC 30461, ATCC 50370, ATCC 50702, ATCC 50703, and ATCC PRA-115) were investigated on seven different common silicone hydrogel contact lenses, and a no-lens control, for aggregation and encystment for 72 h. Cell count and size were used to determine aggregation, and fluorescent staining was used to understand encystment. RNA seq was performed to describe the genome of Acanthamoeba which was individually motile or aggregated on different lens materials. Disinfection efficacy using three common multi-purpose solutions was calculated to describe the potential disinfection resistance of trophozoites, individual cysts, or spheroids. Results Acanthamoeba trophozoites of all strains examined demonstrated significantly more aggregation on specific contact lens materials than others, or the no-lens control. Fluorescent staining demonstrated encystment in as little as 4 hours on contact lens materials, which is substantially faster than previously reported in natural or laboratory settings. Gene expression profiles corroborated encystment, with significantly differentially expressed pathways involving actin arrangement and membrane complexes. High disinfection resistance of cysts and spheroids with multi-purpose solutions was observed. Discussion Aggregation/encystment is a protective mechanism which may enable Acanthamoeba to be more disinfection resistant than individual trophozoites. This study demonstrates that some contact lens materials promote Acanthamoeba aggregation and encystment, and Acanthamoeba spheroids obstruct multi-purpose solutions from disinfecting Acanthamoeba.
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Affiliation(s)
| | - Reed Pifer
- Alcon Research, LLC, Fort Worth, TX, United States
| | | | - Megan Thomas
- Alcon Research, LLC, Fort Worth, TX, United States
| | - Elise Miller
- Alcon Research, LLC, Fort Worth, TX, United States
| | | | - Jamie King
- Alcon Research, LLC, Fort Worth, TX, United States
| | - Christopher A. Rice
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States,Purdue Institute for Drug Discovery (PIDD), Purdue University, West Lafayette, IN, United States,Purdue Institute of Inflammation, Immunology and Infectious Disease (PI4D), Purdue University, West Lafayette, IN, United States
| | - Paul Shannon
- Alcon Research, LLC, Fort Worth, TX, United States
| | | | - Monica Crary
- Alcon Research, LLC, Fort Worth, TX, United States,*Correspondence: Monica Crary,
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Armstrong EE, Campana MG, Solari KA, Morgan SR, Ryder OA, Naude VN, Samelius G, Sharma K, Hadly EA, Petrov DA. Genome report: chromosome-level draft assemblies of the snow leopard, African leopard, and tiger (Panthera uncia, Panthera pardus pardus, and Panthera tigris). G3 (BETHESDA, MD.) 2022; 12:jkac277. [PMID: 36250809 PMCID: PMC9713438 DOI: 10.1093/g3journal/jkac277] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/14/2022] [Indexed: 04/07/2024]
Abstract
The big cats (genus Panthera) represent some of the most popular and charismatic species on the planet. Although some reference genomes are available for this clade, few are at the chromosome level, inhibiting high-resolution genomic studies. We assembled genomes from 3 members of the genus, the tiger (Panthera tigris), the snow leopard (Panthera uncia), and the African leopard (Panthera pardus pardus), at chromosome or near-chromosome level. We used a combination of short- and long-read technologies, as well as proximity ligation data from Hi-C technology, to achieve high continuity and contiguity for each individual. We hope that these genomes will aid in further evolutionary and conservation research of this iconic group of mammals.
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Affiliation(s)
- Ellie E Armstrong
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Washington State University, Pullman, WA 99164, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC 20008, USA
| | | | - Simon R Morgan
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Wildlife ACT Fund Trust, Cape Town 8001, South Africa
| | - Oliver A Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA
| | - Vincent N Naude
- Department of Conservation Ecology and Entomology, University of Stellenbosch, Stellenbosch, 7602, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | | | - Koustubh Sharma
- Snow Leopard Trust, Seattle, WA 98103, USA
- Nature Conservation Foundation, Mysore 570 017, India
| | | | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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Freire B, Ladra S, Parama JR. Memory-Efficient Assembly Using Flye. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3564-3577. [PMID: 34469305 DOI: 10.1109/tcbb.2021.3108843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In the past decade, next-generation sequencing (NGS) enabled the generation of genomic data in a cost-effective, high-throughput manner. The most recent third-generation sequencing technologies produce longer reads; however, their error rates are much higher, which complicates the assembly process. This generates time- and space- demanding long-read assemblers. Moreover, the advances in these technologies have allowed portable and real-time DNA sequencing, enabling in-field analysis. In these scenarios, it becomes crucial to have more efficient solutions that can be executed in computers or mobile devices with minimum hardware requirements. We re-implemented an existing assembler devoted for long reads, more concretely Flye, using compressed data structures. We then compare our version with the original software using real datasets, and evaluate their performance in terms of memory requirements, execution speed, and energy consumption. The assembly results are not affected, as the core of the algorithm is maintained, but the usage of advanced compact data structures leads to improvements in memory consumption that range from 22% to 47% less space, and in the processing time, which range from being on a par up to decreases of 25%. These improvements also cause reductions in energy consumption of around 3-8%, with some datasets obtaining decreases up to 26%.
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Gao M, Feng C, Ji Y, Shi Y, Shi W, Zhang L, Liu S, Li A, Zhang X, Li Q, Lu J, Bao Q, Zhang H. AadA36, a novel chromosomal aminoglycoside nucleotidyltransferase from a clinical isolate of Providencia stuartii. Front Microbiol 2022; 13:1035651. [PMID: 36386671 PMCID: PMC9663854 DOI: 10.3389/fmicb.2022.1035651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/06/2022] [Indexed: 01/25/2023] Open
Abstract
In this study, we characterized a novel chromosome-encoded aminoglycoside nucleotidyltransferase (ANT), AadA36, from the Providencia stuartii strain P14 isolated from the sputum specimen of a burn patient at a hospital in Wenzhou, China. Among the functionally characterized ANTs, AadA36 shared the highest amino acid sequence identity of 51.91% with AadA14. The whole genome of P. stuartii P14 consisted of one chromosome and two plasmids (designated pP14-166 and pP14-114). A total of 19 genes with ≥80% similarity with functionally characterized antimicrobial resistance genes (ARGs) were identified in the whole genome, including aminoglycosides [aac(2')-Ia, aph(6)-Id, aph(3″)-Ib, aac(6')-Ib, ant(3″)-IIa, aph(3')-Ia], β-lactams (bla CMY-2 and bla OXA-10) and so on. Antimicrobial susceptibility testing showed that the aadA36 gene conferred specific resistance to spectinomycin and streptomycin, and the minimum inhibitory concentration (MIC) of these antimicrobials increased 128- and 64-fold compared with the control strain. The kinetic parameters of AadA36 were consistent with the MIC data of spectinomycin and streptomycin, with kcat /Km ratios of (1.07 ± 2.23) × 104 M-1 s-1 and (8.96 ± 1.01) × 103 M-1 s-1, respectively. The identification of a novel aminoglycoside resistance gene will help us further understand the complexity of the resistance mechanisms and provide deep insights into the dissemination of resistance genes in the microbial population.
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Affiliation(s)
- Mengdi Gao
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Chunlin Feng
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yongan Ji
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yaokai Shi
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Weina Shi
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lei Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shuang Liu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Anqi Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xueya Zhang
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiaoling Li
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Qiyu Bao
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China,Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China,*Correspondence: Qiyu Bao,
| | - Hailin Zhang
- Department of Children’s Respiration Disease, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China,Hailin Zhang,
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Matson MEH, Liang Q, Lonardi S, Judelson HS. Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the plant pathogen Phytophthora infestans revealed using its first chromosome-scale assembly. PLoS Pathog 2022; 18:e1010869. [PMID: 36215336 PMCID: PMC9584435 DOI: 10.1371/journal.ppat.1010869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/20/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022] Open
Abstract
Natural isolates of the potato and tomato pathogen Phytophthora infestans exhibit substantial variation in virulence, chemical sensitivity, ploidy, and other traits. A chromosome-scale assembly was developed to expand genomic resources for this oomyceteous microbe, and used to explore the basis of variation. Using PacBio and Illumina data, a long-range linking library, and an optical map, an assembly was created and coalesced into 15 pseudochromosomes spanning 219 Mb using SNP-based genetic linkage data. De novo gene prediction combined with transcript evidence identified 19,981 protein-coding genes, plus about eight thousand tRNA genes. The chromosomes were comprised of a mosaic of gene-rich and gene-sparse regions plus very long centromeres. Genes exhibited a biased distribution across chromosomes, especially members of families encoding RXLR and CRN effectors which clustered on certain chromosomes. Strikingly, half of F1 progeny of diploid parents were polyploid or aneuploid. Substantial expression level polymorphisms between strains were identified, much of which could be attributed to differences in chromosome dosage, transposable element insertions, and adjacency to repetitive DNA. QTL analysis identified a locus on the right arm of chromosome 3 governing sensitivity to the crop protection chemical metalaxyl. Strains heterozygous for resistance often experienced megabase-sized deletions of that part of the chromosome when cultured on metalaxyl, increasing resistance due to loss of the sensitive allele. This study sheds light on diverse phenomena affecting variation in P. infestans and relatives, helps explain the prevalence of polyploidy in natural populations, and provides a new foundation for biologic and genetic investigations.
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Affiliation(s)
- Michael E. H. Matson
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Qihua Liang
- Department of Computer Science and Engineering, University of California, Riverside, California, United States of America
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, California, United States of America
| | - Howard S. Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
- * E-mail:
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Triponney P, Bour M, Beyrouthy R, Bonnet R, Plésiat P, Jeannot K. Role of megaplasmids and chromosomal integration in acquisition of CTX-M-encoding genes by Pseudomonas aeruginosa. J Antimicrob Chemother 2022; 77:3194-3198. [PMID: 36177785 DOI: 10.1093/jac/dkac302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Pauline Triponney
- Centre National de Référence de la résistance aux antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | - Maxime Bour
- Centre National de Référence de la résistance aux antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | - Racha Beyrouthy
- Clermont Université, Université d'Auvergne, Inserm U1071, INRA USC2018, Clermont-Ferrand, France.,CHU Clermont-Ferrand, Laboratoire de Bactériologie Clinique, Clermont-Ferrand, France.,Centre National de Référence de la Résistance aux Antibiotiques, laboratoire associé, Clermont-Ferrand, France
| | - Richard Bonnet
- Clermont Université, Université d'Auvergne, Inserm U1071, INRA USC2018, Clermont-Ferrand, France.,CHU Clermont-Ferrand, Laboratoire de Bactériologie Clinique, Clermont-Ferrand, France.,Centre National de Référence de la Résistance aux Antibiotiques, laboratoire associé, Clermont-Ferrand, France
| | - Patrick Plésiat
- Centre National de Référence de la résistance aux antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France.,UMR6249 CNRS Chrono-Environnement, Université de Franche-Comté, Besançon, France
| | - Katy Jeannot
- Centre National de Référence de la résistance aux antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France.,UMR6249 CNRS Chrono-Environnement, Université de Franche-Comté, Besançon, France.,CHU Jean Minjoz, Laboratoire de Bactériologie, Besançon, France
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Khan J, Kokot M, Deorowicz S, Patro R. Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2. Genome Biol 2022; 23:190. [PMID: 36076275 PMCID: PMC9454175 DOI: 10.1186/s13059-022-02743-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
The de Bruijn graph is a key data structure in modern computational genomics, and construction of its compacted variant resides upstream of many genomic analyses. As the quantity of genomic data grows rapidly, this often forms a computational bottleneck. We present Cuttlefish 2, significantly advancing the state-of-the-art for this problem. On a commodity server, it reduces the graph construction time for 661K bacterial genomes, of size 2.58Tbp, from 4.5 days to 17-23 h; and it constructs the graph for 1.52Tbp white spruce reads in approximately 10 h, while the closest competitor requires 54-58 h, using considerably more memory.
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Affiliation(s)
- Jamshed Khan
- Department of Computer Science, University of Maryland, College Park, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA
| | - Marek Kokot
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland
| | - Sebastian Deorowicz
- Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland
| | - Rob Patro
- Department of Computer Science, University of Maryland, College Park, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA
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