1
|
Dobner J, Nguyen T, Pavez-Giani MG, Cyganek L, Distelmaier F, Krutmann J, Prigione A, Rossi A. mtDNA analysis using Mitopore. Mol Ther Methods Clin Dev 2024; 32:101231. [PMID: 38572068 PMCID: PMC10988129 DOI: 10.1016/j.omtm.2024.101231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/08/2024] [Indexed: 04/05/2024]
Abstract
Mitochondrial DNA (mtDNA) analysis is crucial for the diagnosis of mitochondrial disorders, forensic investigations, and basic research. Existing pipelines are complex, expensive, and require specialized personnel. In many cases, including the diagnosis of detrimental single nucleotide variants (SNVs), mtDNA analysis is still carried out using Sanger sequencing. Here, we developed a simple workflow and a publicly available webserver named Mitopore that allows the detection of mtDNA SNVs, indels, and haplogroups. To simplify mtDNA analysis, we tailored our workflow to process noisy long-read sequencing data for mtDNA analysis, focusing on sequence alignment and parameter optimization. We implemented Mitopore with eliBQ (eliminate bad quality reads), an innovative quality enhancement that permits the increase of per-base quality of over 20% for low-quality data. The whole Mitopore workflow and webserver were validated using patient-derived and induced pluripotent stem cells harboring mtDNA mutations. Mitopore streamlines mtDNA analysis as an easy-to-use fast, reliable, and cost-effective analysis method for both long- and short-read sequencing data. This significantly enhances the accessibility of mtDNA analysis and reduces the cost per sample, contributing to the progress of mtDNA-related research and diagnosis.
Collapse
Affiliation(s)
- Jochen Dobner
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Thach Nguyen
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Mario Gustavo Pavez-Giani
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Lukas Cyganek
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jean Krutmann
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
- Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Alessandro Prigione
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Andrea Rossi
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| |
Collapse
|
2
|
Tahsin A, Hasan M, Rahman S, Jubair M, Afrad MH, Khan MH, Alam MS, Begum MN, Karim MY, Mukta SA, Habib MT, Alam AN, Chowdhury EK, Rahman MR, Ryan ET, Shirin T, Rahman M, Qadri F. Coding-complete genomes of 18 SARS-CoV-2 Omicron JN.1, JN.1.4, and JN.1.11 sub-lineages in Bangladesh. Microbiol Resour Announc 2024:e0013524. [PMID: 38656213 DOI: 10.1128/mra.00135-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 03/22/2024] [Indexed: 04/26/2024] Open
Abstract
We report 18 coding-complete genome sequences of emerging SARS-CoV-2 Omicron sub-lineages JN.1, JN.1.4, and JN.1.11 from Bangladesh. Nasopharyngeal swab samples were obtained from individuals with COVID-19 symptoms between December 2023 and January 2024. Whole genome sequencing was performed following the ARTIC Network-based protocol using Oxford Nanopore Technology.
Collapse
Affiliation(s)
- Anika Tahsin
- Institute for Developing Science and Health initiatives, Dhaka, Bangladesh
| | - Mahin Hasan
- Institute for Developing Science and Health initiatives, Dhaka, Bangladesh
| | - Saikt Rahman
- Institute for Developing Science and Health initiatives, Dhaka, Bangladesh
| | - Mohammad Jubair
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | | | - Md Shaheen Alam
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | - Md Yeasir Karim
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | | | - Ahmed Nawsher Alam
- Institute of Epidemiology, Disease Control, and Research, Dhaka, Bangladesh
| | - Emran Kabir Chowdhury
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Md Rofiqur Rahman
- Institute for Developing Science and Health initiatives, Dhaka, Bangladesh
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control, and Research, Dhaka, Bangladesh
| | - Mustafizur Rahman
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Firdausi Qadri
- Institute for Developing Science and Health initiatives, Dhaka, Bangladesh
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| |
Collapse
|
3
|
Gand M, Navickaite I, Bartsch LJ, Grützke J, Overballe-Petersen S, Rasmussen A, Otani S, Michelacci V, Matamoros BR, González-Zorn B, Brouwer MSM, Di Marcantonio L, Bloemen B, Vanneste K, Roosens NHCJ, AbuOun M, De Keersmaecker SCJ. Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes. Front Microbiol 2024; 15:1336532. [PMID: 38659981 PMCID: PMC11042533 DOI: 10.3389/fmicb.2024.1336532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/29/2024] [Indexed: 04/26/2024] Open
Abstract
Metagenomic sequencing is a promising method that has the potential to revolutionize the world of pathogen detection and antimicrobial resistance (AMR) surveillance in food-producing environments. However, the analysis of the huge amount of data obtained requires performant bioinformatics tools and databases, with intuitive and straightforward interpretation. In this study, based on long-read metagenomics data of chicken fecal samples with a spike-in mock community, we proposed confidence levels for taxonomic identification and AMR gene detection, with interpretation guidelines, to help with the analysis of the output data generated by KMA, a popular k-mer read alignment tool. Additionally, we demonstrated that the completeness and diversity of the genomes present in the reference databases are key parameters for accurate and easy interpretation of the sequencing data. Finally, we explored whether KMA, in a two-step procedure, can be used to link the detected AMR genes to their bacterial host chromosome, both detected within the same long-reads. The confidence levels were successfully tested on 28 metagenomics datasets which were obtained with sequencing of real and spiked samples from fecal (chicken, pig, and buffalo) or food (minced beef and food enzyme products) origin. The methodology proposed in this study will facilitate the analysis of metagenomics sequencing datasets for KMA users. Ultimately, this will contribute to improvements in the rapid diagnosis and surveillance of pathogens and AMR genes in food-producing environments, as prioritized by the EU.
Collapse
Affiliation(s)
- Mathieu Gand
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Indre Navickaite
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Lee-Julia Bartsch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Josephine Grützke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Astrid Rasmussen
- Bacterial Reference Center, Statens Serum Institute, Copenhagen, Denmark
| | - Saria Otani
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Valeria Michelacci
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - Bruno González-Zorn
- Department of Animal Health, Complutense University of Madrid, Madrid, Spain
| | - Michael S. M. Brouwer
- Wageningen Bioveterinary Research Part of Wageningen University and Research, Lelystad, Netherlands
| | - Lisa Di Marcantonio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Bram Bloemen
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | | |
Collapse
|
4
|
Poliakov E, Kaplun L, Rogozin IB. Editorial: Novel applications of ONT technologies in genomics and transcriptomics. Front Genet 2024; 15:1384584. [PMID: 38572417 PMCID: PMC10987952 DOI: 10.3389/fgene.2024.1384584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/08/2024] [Indexed: 04/05/2024] Open
Affiliation(s)
- Eugenia Poliakov
- Laboratory of Retinal Cell and Molecular Biology, National Eye Institute (NEI), National Institutes of Health, Bethesda, MD, United States
| | | | - Igor B. Rogozin
- Life Science Research Center, Faculty of Science, University of Ostrava, Ostrava, Czechia
| |
Collapse
|
5
|
Kim C, Pongpanich M, Porntaveetus T. Unraveling metagenomics through long-read sequencing: a comprehensive review. J Transl Med 2024; 22:111. [PMID: 38282030 PMCID: PMC10823668 DOI: 10.1186/s12967-024-04917-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 01/21/2024] [Indexed: 01/30/2024] Open
Abstract
The study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of shotgun metagenomics. However, a new era has emerged with the advent of long-read sequencing (LRS), which offers substantial improvements over its predecessor, short-read sequencing (SRS). LRS produces reads that are several kilobases long, enabling researchers to obtain more complete and contiguous genomic information, characterize structural variations, and study epigenetic modifications. The current leaders in LRS technologies are Pacific Biotechnologies (PacBio) and Oxford Nanopore Technologies (ONT), each offering a distinct set of advantages. This review covers the workflow of long-read metagenomics sequencing, including sample preparation (sample collection, sample extraction, and library preparation), sequencing, processing (quality control, assembly, and binning), and analysis (taxonomic annotation and functional annotation). Each section provides a concise outline of the key concept of the methodology, presenting the original concept as well as how it is challenged or modified in the context of LRS. Additionally, the section introduces a range of tools that are compatible with LRS and can be utilized to execute the LRS process. This review aims to present the workflow of metagenomics, highlight the transformative impact of LRS, and provide researchers with a selection of tools suitable for this task.
Collapse
Affiliation(s)
- Chankyung Kim
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
- Graduate Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence for Cancer and Inflammation, Chulalongkorn University, Bangkok, Thailand
| | - Thantrira Porntaveetus
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
- Graduate Program in Geriatric and Special Patients Care, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
| |
Collapse
|
6
|
Tshiabuila D, Choga W, James SE, Maponga T, Preiser W, van Zyl G, Moir M, van Wyk S, Giandhari J, Pillay S, Anyaneji UJ, Lessells RJ, Naidoo Y, Sanko TJ, Wilkinson E, Tegally H, Baxter C, Martin DP, de Oliveira T. An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable For Genomic Surveillance Within Clinical Diagnostic Settings. medRxiv 2024:2024.01.19.24301519. [PMID: 38293032 PMCID: PMC10827254 DOI: 10.1101/2024.01.19.24301519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Chronic hepatitis B virus (HBV) infection remains a significant public health concern, particularly in Africa, where there is a substantial burden. HBV is an enveloped virus, with isolates being classified into ten phylogenetically distinct genotypes (A - J) determined based on full-genome sequence data or reverse hybridization-based diagnostic tests. In practice, limitations are noted in that diagnostic sequencing, generally using Sanger sequencing, tends to focus only on the S-gene, yielding little or no information on intra-patient HBV genetic diversity with very low-frequency variants and reverse hybridization detects only known genotype-specific mutations. To resolve these limitations, we developed an Oxford Nanopore Technology (ONT)-based HBV genotyping protocol suitable for clinical virology, yielding complete HBV genome sequences and extensive data on intra-patient HBV diversity. Specifically, the protocol involves tiling-based PCR amplification of HBV sequences, library preparation using the ONT Rapid Barcoding Kit, ONT GridION sequencing, genotyping using Genome Detective software, recombination analysis using jpHMM and RDP5 software, and drug resistance profiling using Geno2pheno software. We prove the utility of our protocol by efficiently generating and characterizing high-quality near full-length HBV genomes from 148 left-over diagnostic Hepatitis B patient samples obtained in the Western Cape province of South Africa, providing valuable insights into the genetic diversity and epidemiology of HBV in this region of the world.
Collapse
Affiliation(s)
- Derek Tshiabuila
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Wonderful Choga
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - San E. James
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa & National Health Laboratory Service
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa & National Health Laboratory Service
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa & National Health Laboratory Service
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Stephanie van Wyk
- Collaborating Centre for Optimizing Antimalarial Therapy (CCOAT), Mitigating Antimalarial Resistance Consortium in South East Africa (MARC SEA), Department of Medicine, Division of Clinical Pharmacology, University of Cape Town, South Africa
| | - Jennifer Giandhari
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Ugochukwu J. Anyaneji
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Richard J. Lessells
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Yeshnee Naidoo
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Tomasz Janusz Sanko
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Darren P. Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| |
Collapse
|
7
|
Safar HA, Alatar F, Mustafa AS. Three Rounds of Read Correction Significantly Improve Eukaryotic Protein Detection in ONT Reads. Microorganisms 2024; 12:247. [PMID: 38399651 PMCID: PMC10893331 DOI: 10.3390/microorganisms12020247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Eukaryotes' whole-genome sequencing is crucial for species identification, gene detection, and protein annotation. Oxford Nanopore Technology (ONT) is an affordable and rapid platform for sequencing eukaryotes; however, the relatively higher error rates require computational and bioinformatic efforts to produce more accurate genome assemblies. Here, we evaluated the effect of read correction tools on eukaryote genome completeness, gene detection and protein annotation. METHODS Reads generated by ONT of four eukaryotes, C. albicans, C. gattii, S. cerevisiae, and P. falciparum, were assembled using minimap2 and underwent three rounds of read correction using flye, medaka and racon. The generates consensus FASTA files were compared for total length (bp), genome completeness, gene detection, and protein-annotation by QUAST, BUSCO, BRAKER1 and InterProScan, respectively. RESULTS Genome completeness was dependent on the assembly method rather than on the read correction tool; however, medaka performed better than flye and racon. Racon significantly performed better than flye and medaka in gene detection, while both racon and medaka significantly performed better than flye in protein-annotation. CONCLUSION We show that three rounds of read correction significantly affect gene detection and protein annotation, which are dependent on assembly quality in preference to assembly completeness.
Collapse
Affiliation(s)
- Hussain A. Safar
- OMICS Research Unit, Health Science Centre, Kuwait University, Kuwait City 13110, Kuwait;
| | - Fatemah Alatar
- Serology and Molecular Microbiology Reference Laboratory, Mubarak Al-Kabeer Hospital, Ministry of Health, Kuwait City 13110, Kuwait;
| | - Abu Salim Mustafa
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City 13110, Kuwait
| |
Collapse
|
8
|
Henares D, Lo SW, Perez-Argüello A, Redin A, Ciruela P, Garcia-Garcia JJ, Brotons P, Yuste J, Sá-Leão R, Muñoz-Almagro C. Comparison of next generation technologies and bioinformatics pipelines for capsular typing of Streptococcus pneumoniae. J Clin Microbiol 2023; 61:e0074123. [PMID: 38092657 PMCID: PMC10729682 DOI: 10.1128/jcm.00741-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/01/2023] [Indexed: 12/20/2023] Open
Abstract
Whole genome sequencing (WGS)-based approaches for pneumococcal capsular typing have become an alternative to serological methods. In silico serotyping from WGS has not yet been applied to long-read sequences produced by third-generation technologies. The objective of the study was to determine the capsular types of pneumococci causing invasive disease in Catalonia (Spain) using serological typing and WGS and to compare the performance of different bioinformatics pipelines using short- and long-read data from WGS. All invasive pneumococcal pediatric isolates collected in Hospital Sant Joan de Déu (Barcelona) from 2013 to 2019 were included. Isolates were assigned a capsular type by serological testing based on anticapsular antisera and by different WGS-based pipelines: Illumina sequencing followed by serotyping with PneumoCaT, SeroBA, and Pathogenwatch vs MinION-ONT sequencing coupled with serotyping by Pathogenwatch from pneumococcal assembled genomes. A total of 119 out of 121 pneumococcal isolates were available for sequencing. Twenty-nine different serotypes were identified by serological typing, with 24F (n = 17; 14.3%), 14 (n = 10; 8.4%), and 15B/C (n = 8; 6.7%) being the most common serotypes. WGS-based pipelines showed initial concordance with serological typing (>91% of accuracy). The main discrepant results were found at the serotype level within a serogroup: 6A/B, 6C/D, 9A/V, 11A/D, and 18B/C. Only one discrepancy at the serogroup level was observed: serotype 29 by serological testing and serotype 35B/D by all WGS-based pipelines. Thus, bioinformatics WGS-based pipelines, including those using third-generation sequencing, are useful for pneumococcal capsular assignment. Possible discrepancies between serological typing and WGS-based approaches should be considered in pneumococcal capsular-type surveillance studies.
Collapse
Affiliation(s)
- Desiree Henares
- Department of RDI Microbiology, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Stephanie W. Lo
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Milner Center for Evolution, Life Sciences Department, University of Bath, Bath, United Kingdom
| | - Amaresh Perez-Argüello
- Department of RDI Microbiology, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Alba Redin
- Department of RDI Microbiology, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Pilar Ciruela
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Surveillance and Public Health Emergency Response, Public Health Agency of Catalonia (ASPCAT), Barcelona, Spain
| | - Juan Jose Garcia-Garcia
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Pediatrics Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Department of Surgery and Medical-Surgical Specialties, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Pedro Brotons
- Department of RDI Microbiology, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Jose Yuste
- Spanish Pneumococcal Reference Laboratory, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- CIBER of Respiratory Diseases (CIBERES), Instituto de salud Carlos III, Madrid, Spain
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Carmen Muñoz-Almagro
- Department of RDI Microbiology, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| |
Collapse
|
9
|
Mollova D, Gozmanova M, Apostolova E, Yahubyan G, Iliev I, Baev V. Illuminating the Genomic Landscape of Lactiplantibacillus plantarum PU3-A Novel Probiotic Strain Isolated from Human Breast Milk, Explored through Nanopore Sequencing. Microorganisms 2023; 11:2440. [PMID: 37894099 PMCID: PMC10609609 DOI: 10.3390/microorganisms11102440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/11/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Lactiplantibacillus plantarum stands out as a remarkably diverse species of lactic acid bacteria, occupying a myriad of ecological niches. Particularly noteworthy is its presence in human breast milk, which can serve as a reservoir of probiotic bacteria, contributing significantly to the establishment and constitution of infant gut microbiota. In light of this, our study attempted to conduct an initial investigation encompassing both genomic and phenotypic aspects of the L. plantarum PU3 strain, that holds potential as a probiotic agent. By employing the cutting-edge third-generation Nanopore sequencing technology, L. plantarum PU3 revealed a circular chromosome of 3,180,940 bp and nine plasmids of various lengths. The L. plantarum PU3 genome has a total of 2962 protein-coding and non-coding genes. Our in-depth investigations revealed more than 150 probiotic gene markers that unfold the genetic determinants for acid tolerance, bile resistance, adhesion, and oxidative and osmotic stress. The in vivo analysis showed the strain's proficiency in utilizing various carbohydrates as growth substrates, complementing the in silico analysis of the genes involved in metabolic pathways. Notably, the strain demonstrated a pronounced affinity for D-sorbitol, D-mannitol, and D-Gluconic acid, among other carbohydrate sources. The in vitro experimental verification of acid, osmotic and bile tolerance validated the robustness of the strain in challenging environments. Encouragingly, no virulence factors were detected in the genome of PU3, suggesting its safety profile. In search of beneficial properties, we found potential bacteriocin biosynthesis clusters, suggesting its capability for antimicrobial activity. The characteristics exhibited by L. plantarum PU3 pave the way for promising strain potential, warranting further investigations to unlock its full capacity and contributions to probiotic and therapeutic avenues.
Collapse
Affiliation(s)
- Daniela Mollova
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (D.M.); (I.I.)
| | - Mariyana Gozmanova
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
| | - Elena Apostolova
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
| | - Galina Yahubyan
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
| | - Ilia Iliev
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (D.M.); (I.I.)
| | - Vesselin Baev
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (M.G.); (E.A.); (G.Y.)
| |
Collapse
|
10
|
Espinosa E, Bautista R, Fernandez I, Larrosa R, Zapata EL, Plata O. Comparing assembly strategies for third-generation sequencing technologies across different genomes. Genomics 2023; 115:110700. [PMID: 37598732 DOI: 10.1016/j.ygeno.2023.110700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 08/22/2023]
Abstract
The recent advent of long-read sequencing technologies, such as Pacific Biosciences (PacBio) and Oxford Nanopore technology (ONT), has led to substantial accuracy and computational cost improvements. However, de novo whole-genome assembly still presents significant challenges related to the computational cost and the quality of the results. Accordingly, sequencing accuracy and throughput continue to improve, and many tools are constantly emerging. Therefore, selecting the correct sequencing platform, the proper sequencing depth and the assembly tools are necessary to perform high-quality assembly. This paper evaluates the primary assembly reconstruction from recent hybrid and non-hybrid pipelines on different genomes. We find that using PacBio high-fidelity long-read (HiFi) plays an essential role in haplotype construction with respect to ONT reads. However, we observe a substantial improvement in the correctness of the assembly from high-fidelity ONT datasets and combining it with HiFi or short-reads.
Collapse
Affiliation(s)
- Elena Espinosa
- Department of Computer Architecture, University of Malaga, Louis Pasteur, 35, Campus de Teatinos, Malaga 29071, Spain.
| | - Rocio Bautista
- Supercomputing and Bioinnovation Center, University of Malaga, C. Severo Ochoa, 34, Malaga 29590, Spain.
| | - Ivan Fernandez
- Department of Computer Architecture, University of Malaga, Louis Pasteur, 35, Campus de Teatinos, Malaga 29071, Spain; Departament d'Arquitectura de Computadors, Universitat Politècnica de Catalunya, C. Jordi Girona, 1-3, Barcelona 08034, Spain.
| | - Rafael Larrosa
- Department of Computer Architecture, University of Malaga, Louis Pasteur, 35, Campus de Teatinos, Malaga 29071, Spain; Supercomputing and Bioinnovation Center, University of Malaga, C. Severo Ochoa, 34, Malaga 29590, Spain.
| | - Emilio L Zapata
- Department of Computer Architecture, University of Malaga, Louis Pasteur, 35, Campus de Teatinos, Malaga 29071, Spain; Supercomputing and Bioinnovation Center, University of Malaga, C. Severo Ochoa, 34, Malaga 29590, Spain.
| | - Oscar Plata
- Department of Computer Architecture, University of Malaga, Louis Pasteur, 35, Campus de Teatinos, Malaga 29071, Spain.
| |
Collapse
|
11
|
Meckoni SN, Nass B, Pucker B. Phylogenetic placement of Ceratophyllum submersum based on a complete plastome sequence derived from nanopore long read sequencing data. BMC Res Notes 2023; 16:187. [PMID: 37626355 PMCID: PMC10464454 DOI: 10.1186/s13104-023-06459-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
OBJECTIVE Eutrophication poses a mounting concern in today's world. Ceratophyllum submersum L. is one of many plants capable of living in eutrophic conditions, therefore it could play a critical role in addressing the problem of eutrophication. This study aimed to take a first genomic look at C. submersum. RESULTS Sequencing of gDNA from C. submersum yielded enough reads to assemble a plastome. Subsequent annotation and phylogenetic analysis validated existing information regarding angiosperm relationships and the positioning of Ceratophylalles in a wider phylogenetic context.
Collapse
Affiliation(s)
- Samuel Nestor Meckoni
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology, TU Braunschweig, 38106, Braunschweig, Germany
| | - Benneth Nass
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology, TU Braunschweig, 38106, Braunschweig, Germany
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6 - Suchdol, CZ-165 21, Prague, Czech Republic
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology, TU Braunschweig, 38106, Braunschweig, Germany.
- Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, 38106, Braunschweig, Germany.
| |
Collapse
|
12
|
Safar HA, Alatar F, Nasser K, Al-Ajmi R, Alfouzan W, Mustafa AS. The impact of applying various de novo assembly and correction tools on the identification of genome characterization, drug resistance, and virulence factors of clinical isolates using ONT sequencing. BMC Biotechnol 2023; 23:26. [PMID: 37525145 PMCID: PMC10391896 DOI: 10.1186/s12896-023-00797-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/21/2023] [Indexed: 08/02/2023] Open
Abstract
Oxford Nanopore sequencing technology (ONT) is currently widely used due to its affordability, simplicity, and reliability. Despite the advantage ONT has over next-generation sequencing in detecting resistance genes in mobile genetic elements, its relatively high error rate (10-15%) is still a deterrent. Several bioinformatic tools are freely available for raw data processing and obtaining complete and more accurate genome assemblies. In this study, we evaluated the impact of using mix-and-matched read assembly (Flye, Canu, Wtdbg2, and NECAT) and read correction (Medaka, NextPolish, and Racon) tools in generating complete and accurate genome assemblies, and downstream genomic analysis of nine clinical Escherichia coli isolates. Flye and Canu assemblers were the most robust in genome assembly, and Medaka and Racon correction tools significantly improved assembly parameters. Flye functioned well in pan-genome analysis, while Medaka increased the number of core genes detected. Flye, Canu, and NECAT assembler functioned well in detecting antimicrobial resistance genes (AMR), while Wtdbg2 required correction tools for better detection. Flye was the best assembler for detecting and locating both virulence and AMR genes (i.e., chromosomal vs. plasmid). This study provides insight into the performance of several read assembly and read correction tools for analyzing ONT sequencing reads for clinical isolates.
Collapse
Affiliation(s)
- Hussain A Safar
- OMICS Research Unit, Health Science Centre, Kuwait University, Hawalli Governorate, Kuwait
| | - Fatemah Alatar
- Serology and Molecular Microbiology Reference Laboratory, Mubarak Al-Kabeer Hospital, Ministry of Health, Hawalli Governorate, Kuwait
| | - Kother Nasser
- Serology and Molecular Microbiology Reference Laboratory, Mubarak Al-Kabeer Hospital, Ministry of Health, Hawalli Governorate, Kuwait
| | - Rehab Al-Ajmi
- Department of Microbiology, Faculty of Medicine, Kuwait University, Hawalli Governorate, Kuwait
| | - Wadha Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Hawalli Governorate, Kuwait
- Microbiology Unit, Farwaniya Hospital, Ministry of Health, Al Farwaniyah Governorate, Kuwait
| | - Abu Salim Mustafa
- Department of Microbiology, Faculty of Medicine, Kuwait University, Hawalli Governorate, Kuwait.
| |
Collapse
|
13
|
Krøvel AV, Hetland MAK, Bernhoff E, Bjørheim AS, Soma MA, Löhr IH. Long-read sequencing for reliably calling the mompS allele in Legionella pneumophila sequence-based typing. Front Cell Infect Microbiol 2023; 13:1176182. [PMID: 37256104 PMCID: PMC10226664 DOI: 10.3389/fcimb.2023.1176182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/21/2023] [Indexed: 06/01/2023] Open
Abstract
Sequence-based typing (SBT) of Legionella pneumophila is a valuable tool in epidemiological studies and outbreak investigations of Legionnaires' disease. In the L. pneumophila SBT scheme, mompS2 is one of seven genes that determine the sequence type (ST). The Legionella genome typically contains two copies of mompS (mompS1 and mompS2). When they are non-identical it can be challenging to determine the mompS2 allele, and subsequently the ST, from Illumina short-reads. In our collection of 233 L. pneumophila genomes, there were 62 STs, 18 of which carried non-identical mompS copies. Using short-reads, the mompS2 allele was misassembled or untypeable in several STs. Genomes belonging to ST154 and ST574, which carried mompS1 allele 7 and mompS2 allele 15, were assigned an incorrect mompS2 allele and/or mompS gene copy number when short-read assembled. For other isolates, mainly those carrying non-identical mompS copies, short-read assemblers occasionally failed to resolve the structure of the mompS-region, also resulting in untypeability from the short-read data. In this study, we wanted to understand the challenges we observed with calling the mompS2 allele from short-reads, assess if other short-read methods were able to resolve the mompS-region, and investigate the possibility of using long-reads to obtain the mompS alleles, and thereby perform L. pneumophila SBT from long-reads only. We found that the choice of short-read assembler had a major impact on resolving the mompS-region and thus SBT from short-reads, but no method consistently solved the mompS2 allele. By using Oxford Nanopore Technology (ONT) sequencing together with Trycycler and Medaka for long-read assembly and polishing we were able to resolve the mompS copies and correctly identify the mompS2 allele, in accordance with Sanger sequencing/EQA results for all tested isolates (n=35). The remaining six genes of the SBT profile could also be determined from the ONT-only reads. The STs called from ONT-only assemblies were also consistent with hybrid-assemblies of Illumina and ONT reads. We therefore propose ONT sequencing as an alternative method to perform L. pneumophila SBT to overcome the mompS challenge observed with short-reads. To facilitate this, we have developed ONTmompS (https://github.com/marithetland/ONTmompS), an in silico approach to determine L. pneumophila ST from long-read or hybrid assemblies.
Collapse
Affiliation(s)
- Anne Vatland Krøvel
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- National Reference Laboratory for Legionella, Stavanger University Hospital, Stavanger, Norway
| | - Marit A. K. Hetland
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- Department of Biological Sciences, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway
| | - Eva Bernhoff
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- National Reference Laboratory for Legionella, Stavanger University Hospital, Stavanger, Norway
| | - Anna Steensen Bjørheim
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- National Reference Laboratory for Legionella, Stavanger University Hospital, Stavanger, Norway
| | - Markus André Soma
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Iren H. Löhr
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- National Reference Laboratory for Legionella, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| |
Collapse
|
14
|
Roberts MB, Schultz DT, Gatins R, Escalona M, Bernardi G. Chromosome-level genome of the three-spot damselfish, Dascyllus trimaculatus. G3 (Bethesda) 2023; 13:jkac339. [PMID: 36905099 PMCID: PMC10085752 DOI: 10.1093/g3journal/jkac339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/14/2022] [Indexed: 04/12/2023]
Abstract
Damselfishes (Family: Pomacentridae) are a group of ecologically important, primarily coral reef fishes that include over 400 species. Damselfishes have been used as model organisms to study recruitment (anemonefishes), the effects of ocean acidification (spiny damselfish), population structure, and speciation (Dascyllus). The genus Dascyllus includes a group of small-bodied species, and a complex of relatively larger bodied species, the Dascyllus trimaculatus species complex that is comprised of several species including D. trimaculatus itself. The three-spot damselfish, D. trimaculatus, is a widespread and common coral reef fish species found across the tropical Indo-Pacific. Here, we present the first-genome assembly of this species. This assembly contains 910 Mb, 90% of the bases are in 24 chromosome-scale scaffolds, and the Benchmarking Universal Single-Copy Orthologs score of the assembly is 97.9%. Our findings confirm previous reports of a karyotype of 2n = 47 in D. trimaculatus in which one parent contributes 24 chromosomes and the other 23. We find evidence that this karyotype is the result of a heterozygous Robertsonian fusion. We also find that the D. trimaculatus chromosomes are each homologous with single chromosomes of the closely related clownfish species, Amphiprion percula. This assembly will be a valuable resource in the population genomics and conservation of Damselfishes, and continued studies of the karyotypic diversity in this clade.
Collapse
Affiliation(s)
- May B Roberts
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Darrin T Schultz
- Department of Molecular Evolution and Development, University of Vienna, Vienna 1010, Austria
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
- Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Remy Gatins
- Department of Marine Sciences, Northeastern University, Boston, MA 02115, USA
| | - Merly Escalona
- Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| |
Collapse
|
15
|
Ikemoto K, Fujimoto H, Fujimoto A. Localized assembly for long reads enables genome-wide analysis of repetitive regions at single-base resolution in human genomes. Hum Genomics 2023; 17:21. [PMID: 36895025 PMCID: PMC9996862 DOI: 10.1186/s40246-023-00467-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/01/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Long-read sequencing technologies have the potential to overcome the limitations of short reads and provide a comprehensive picture of the human genome. However, the characterization of repetitive sequences by reconstructing genomic structures at high resolution solely from long reads remains difficult. Here, we developed a localized assembly method (LoMA) that constructs highly accurate consensus sequences (CSs) from long reads. METHODS We developed LoMA by combining minimap2, MAFFT, and our algorithm, which classifies diploid haplotypes based on structural variants and CSs. Using this tool, we analyzed two human samples (NA18943 and NA19240) sequenced with the Oxford Nanopore sequencer. We defined target regions in each genome based on mapping patterns and then constructed a high-quality catalog of the human insertion solely from the long-read data. RESULTS The assessment of LoMA showed a high accuracy of CSs (error rate < 0.3%) compared with raw data (error rate > 8%) and superiority to a previous study. The genome-wide analysis of NA18943 and NA19240 identified 5516 and 6542 insertions (≥ 100 bp), respectively. Most insertions (~ 80%) were derived from tandem repeats and transposable elements. We also detected processed pseudogenes, insertions in transposable elements, and long insertions (> 10 kbp). Finally, our analysis suggested that short tandem duplications are associated with gene expression and transposons. CONCLUSIONS Our analysis showed that LoMA constructs high-quality sequences from long reads with substantial errors. This study revealed the true structures of the insertions with high accuracy and inferred the mechanisms for the insertions, thus contributing to future human genome studies. LoMA is available at our GitHub page: https://github.com/kolikem/loma .
Collapse
Affiliation(s)
- Ko Ikemoto
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo, Japan
| | - Hinano Fujimoto
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo, Japan
| | - Akihiro Fujimoto
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo, Japan.
| |
Collapse
|
16
|
Tsuiko O, El Ayeb Y, Jatsenko T, Allemeersch J, Melotte C, Ding J, Debrock S, Peeraer K, Vanhie A, De Leener A, Pirard C, Kluyskens C, Denayer E, Legius E, Vermeesch JR, Brems H, Dimitriadou E. Preclinical workup using long-read amplicon sequencing provides families with de novo pathogenic variants access to universal preimplantation genetic testing. Hum Reprod 2023; 38:511-519. [PMID: 36625546 DOI: 10.1093/humrep/deac273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/16/2022] [Indexed: 01/11/2023] Open
Abstract
STUDY QUESTION Can long-read amplicon sequencing be beneficial for preclinical preimplantation genetic testing (PGT) workup in couples with a de novo pathogenic variant in one of the prospective parents? SUMMARY ANSWER Long-read amplicon sequencing represents a simple, rapid and cost-effective preclinical PGT workup strategy that provides couples with de novo pathogenic variants access to universal genome-wide haplotyping-based PGT programs. WHAT IS KNOWN ALREADY Universal PGT combines genome-wide haplotyping and copy number profiling to select embryos devoid of both familial pathogenic variants and aneuploidies. However, it cannot be directly applied in couples with a de novo pathogenic variant in one of the partners due to the absence of affected family members required for phasing the disease-associated haplotype. STUDY DESIGN, SIZE, DURATION This is a prospective study, which includes 32 families that were enrolled in the universal PGT program at the University Hospital of Leuven between 2018 and 2022. We implemented long-read amplicon sequencing during the preclinical PGT workup to deduce the parental origin of the disease-associated allele in the affected partner, which can then be traced in embryos during clinical universal PGT cycles. PARTICIPANTS/MATERIALS, SETTING, METHODS To identify the parental origin of the disease-associated allele, genomic DNA from the carrier of the de novo pathogenic variant and his/her parent(s) was used for preclinical PGT workup. Primers flanking the de novo variant upstream and downstream were designed for each family. Following long-range PCR, amplicons that ranged 5-10 kb in size, were sequenced using Pacific Bioscience and/or Oxford Nanopore platforms. Next, targeted variant calling and haplotyping were performed to identify parental informative single-nucleotide variants (iSNVs) linked to the de novo mutation. Following the preclinical PGT workup, universal PGT via genome-wide haplotyping was performed for couples who proceeded with clinical PGT cycle. In parallel, 13 trophectoderm (TE) biopsies from three families that were analyzed by universal PGT, were also used for long-read amplicon sequencing to explore this approach for embryo direct mutation detection coupled with targeted long-read haplotyping. MAIN RESULTS AND THE ROLE OF CHANCE The parental origin of the mutant allele was identified in 24/32 affected individuals during the preclinical PGT workup stage, resulting in a 75% success rate. On average, 5.95 iSNVs (SD = 4.5) were detected per locus of interest, and the average distance of closest iSNV to the de novo variant was ∼1750 bp. In 75% of those cases (18/24), the de novo mutation occurred on the paternal allele. In the remaining eight families, the risk haplotype could not be established due to the absence of iSNVs linked to the mutation or inability to successfully target the region of interest. During the time of the study, 12/24 successfully analyzed couples entered the universal PGT program, and three disease-free children have been born. In parallel to universal PGT analysis, long-read amplicon sequencing of 13 TE biopsies was also performed, confirming the segregation of parental alleles in the embryo and the results of the universal PGT. LIMITATIONS, REASONS FOR CAUTION The main limitation of this approach is that it remains targeted with the need to design locus-specific primers. Because of the restricted size of target amplicons, the region of interest may also remain non-informative in the absence of iSNVs. WIDER IMPLICATIONS OF THE FINDINGS Targeted haplotyping via long-read amplicon sequencing, particularly using Oxford Nanopore Technologies, provides a valuable alternative for couples with de novo pathogenic variants that allows access to universal PGT. Moreover, the same approach can be used for direct mutation analysis in embryos, as a second line confirmation of the preclinical PGT result or as a potential alternative PGT procedure in couples, where additional family members are not available. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by KU Leuven funding (no. C1/018 to J.R.V.) and Fonds Wetenschappelijk Onderzoek (1241121N to O.T.). J.R.V. is co-inventor of a patent ZL910050-PCT/EP2011/060211-WO/2011/157846 'Methods for haplotyping single-cells' and ZL913096-PCT/EP2014/068315-WO/2015/028576 'Haplotyping and copy number typing using polymorphic variant allelic frequencies' licensed to Agilent Technologies. All other authors have no conflict of interest to declare. TRIAL REGISTRATION NUMBER N/A.
Collapse
Affiliation(s)
- Olga Tsuiko
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Yasmine El Ayeb
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Tatjana Jatsenko
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Joke Allemeersch
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Cindy Melotte
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Jia Ding
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Sophie Debrock
- Leuven University Fertility Center, University Hospitals Leuven, Leuven, Belgium
| | - Karen Peeraer
- Leuven University Fertility Center, University Hospitals Leuven, Leuven, Belgium
| | - Arne Vanhie
- Leuven University Fertility Center, University Hospitals Leuven, Leuven, Belgium
| | - Anne De Leener
- Centre for Human Genetics, Cliniques Universitaires Saint Luc, UCLouvain, Brussels, Belgium
| | - Céline Pirard
- Department of Gynaecology, Cliniques Universitaires Saint Luc, UCLouvain, Brussels, Belgium
| | - Candice Kluyskens
- Department of Gynaecology, Cliniques Universitaires Saint Luc, UCLouvain, Brussels, Belgium
| | - Ellen Denayer
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Eric Legius
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Joris Robert Vermeesch
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Hilde Brems
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | |
Collapse
|
17
|
Al Kadi M, Okuzaki D. Unfolding the Bacterial Transcriptome Landscape Using Oxford Nanopore Technology Direct RNA Sequencing. Methods Mol Biol 2023; 2632:269-279. [PMID: 36781735 DOI: 10.1007/978-1-0716-2996-3_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Current genome annotation ignores important features of the transcriptome, such as untranslated regions and operon maps. RNA sequencing (RNA-seq) helps in identifying such features; however, the fragmentation step of classical RNA-seq makes this task challenging. Long-read sequencing methods, such as that of Oxford Nanopore Technologies (ONT), enable the sequencing of intact RNA molecules. Here, we present a method to annotate the full features of bacterial transcriptomes by combining a modified ONT direct RNA-seq method with our computational pipeline, UNAGI bacteria. The method reveals the full complexity of the bacterial transcriptome landscape, including transcription start sites, transcription termination sites, operon maps, and novel genes.
Collapse
Affiliation(s)
- Mohamad Al Kadi
- Single Cell Genomics, Human Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Daisuke Okuzaki
- Single Cell Genomics, Human Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan. .,Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan. .,Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan.
| |
Collapse
|
18
|
Weinmaier T, Conzemius R, Bergman Y, Lewis S, Jacobs EB, Tamma PD, Materna A, Weinberger J, Beisken S, Simner PJ. Validation and Application of Long-Read Whole-Genome Sequencing for Antimicrobial Resistance Gene Detection and Antimicrobial Susceptibility Testing. Antimicrob Agents Chemother 2023; 67:e0107222. [PMID: 36533931 DOI: 10.1128/aac.01072-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Next-generation sequencing applications are increasingly used for detection and characterization of antimicrobial-resistant pathogens in clinical settings. Oxford Nanopore Technologies (ONT) sequencing offers advantages for clinical use compared with other sequencing methodologies because it enables real-time basecalling, produces long sequencing reads that increase the ability to correctly assemble DNA fragments, provides short turnaround times, and requires relatively uncomplicated sample preparation. A drawback of ONT sequencing, however, is its lower per-read accuracy than short-read sequencing. We sought to identify best practices in ONT sequencing protocols. As some variability in sequencing results may be introduced by the DNA extraction methodology, we tested three DNA extraction kits across three independent laboratories using a representative set of six bacterial isolates to investigate accuracy and reproducibility of ONT technology. All DNA extraction techniques showed comparable performance; however, the DNeasy PowerSoil Pro kit had the highest sequencing yield. This kit was subsequently applied to 42 sequentially collected bacterial isolates from blood cultures to assess Ares Genetics's pipelines for predictive whole-genome sequencing antimicrobial susceptibility testing (WGS-AST) performance compared to phenotypic triplicate broth microdilution results. WGS-AST results ranged across the organisms and resulted in an overall categorical agreement of 95% for penicillins, 82.4% for cephalosporins, 76.7% for carbapenems, 86.9% for fluoroquinolones, and 96.2% for aminoglycosides. Very major errors/major errors were 0%/16.7% (penicillins), 11.7%/3.6% (cephalosporins), 0%/24.4% (carbapenems), 2.5%/7.7% (fluoroquinolones), and 0%/4.1% (aminoglycosides), respectively. This work showed that, although additional refinements are necessary, ONT sequencing demonstrates potential as a method to perform WGS-AST on cultured isolates for patient care.
Collapse
|
19
|
Bologa AM, Stoica I, Ratiu AC, Constantin ND, Ecovoiu AA. ONT-Based Alternative Assemblies Impact on the Annotations of Unique versus Repetitive Features in the Genome of a Romanian Strain of Drosophila melanogaster. Int J Mol Sci 2022; 23. [PMID: 36499217 DOI: 10.3390/ijms232314892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
To date, different strategies of whole-genome sequencing (WGS) have been developed in order to understand the genome structure and functions. However, the analysis of genomic sequences obtained from natural populations is challenging and the biological interpretation of sequencing data remains the main issue. The MinION device developed by Oxford Nanopore Technologies (ONT) is able to generate long reads with minimal costs and time requirements. These valuable assets qualify it as a suitable method for performing WGS, especially in small laboratories. The long reads resulted using this sequencing approach can cover large structural variants and repetitive sequences commonly present in the genomes of eukaryotes. Using MinION, we performed two WGS assessments of a Romanian local strain of Drosophila melanogaster, referred to as Horezu_LaPeri (Horezu). In total, 1,317,857 reads with a size of 8.9 gigabytes (Gb) were generated. Canu and Flye de novo assembly tools were employed to obtain four distinct assemblies with both unfiltered and filtered reads, achieving maximum reference genome coverages of 94.8% (Canu) and 91.4% (Flye). In order to test the quality of these assemblies, we performed a two-step evaluation. Firstly, we considered the BUSCO scores and inquired for a supplemental set of genes using BLAST. Subsequently, we appraised the total content of natural transposons (NTs) relative to the reference genome (ISO1 strain) and mapped the mdg1 retroelement as a resolution assayer. Our results reveal that filtered data provide only slightly enhanced results when considering genes identification, but the use of unfiltered data had a consistent positive impact on the global evaluation of the NTs content. Our comparative studies also revealed differences between Flye and Canu assemblies regarding the annotation of unique versus repetitive genomic features. In our hands, Flye proved to be moderately better for gene identification, while Canu clearly outperformed Flye for NTs analysis. Data concerning the NTs content were compared to those obtained with ONT for the D. melanogaster ISO1 strain, revealing that our strategy conducted to better results. Additionally, the parameters of our ONT reads and assemblies are similar to those reported for ONT experiments performed on various model organisms, revealing that our assembly data are appropriate for a proficient annotation of the Horezu genome.
Collapse
|
20
|
Hu QL, Ye YX, Zhuo JC, Huang HJ, Li JM, Zhang CX. Chromosome-level Assembly, Dosage Compensation and Sex-biased Gene Expression in the Small Brown Planthopper, Laodelphax striatellus. Genome Biol Evol 2022; 14:evac160. [PMID: 36317697 PMCID: PMC9651030 DOI: 10.1093/gbe/evac160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2022] [Indexed: 01/19/2024] Open
Abstract
In insects, sex chromosome differentiation often results in unequal gene dosages between sexes. Dosage compensation mechanisms evolve to balance gene expression, but the degree and mechanism of regulation often vary by insect species. In hemipteran species, the small brown planthopper (SBPH), Laodelphax striatellus, is an injurious crop pest, with a sex chromosome type XX in females and XO in males. This species offers the opportunity to study dosage compensation and sex-biased gene expression. In this study, we generated a chromosome-level genome of SBPH using Oxford Nanopore Technologies and high-throughput chromatin conformation capture (Hi-C) technology. We also sequenced RNA-seq data from 16 tissue samples to annotate the genome and analyze gene dosage compensation. We finally obtained a 510.2 megabases (Mb) genome with 99.12% of the scaffolds anchored on 15 chromosomes (14 autosomes and 1 X chromosome) and annotated 16,160 protein-coding genes based on full-length cDNA sequencing data. Furthermore, we found complete dosage compensation in all L. striatellus somatic tissues, but lack of dosage compensation in gonad tissue testis. We also found that female-biased genes were significantly enriched on the X chromosome in all tissues, whereas male-biased genes in gonad tissues were enriched on autosomes. This study not only provides a high-quality genome assembly but also lays a foundation for a better understanding of the sexual regulatory network in hemipteran insects.
Collapse
Affiliation(s)
- Qing-Ling Hu
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Yu-Xuan Ye
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
| | - Ji-Chong Zhuo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Hai-Jian Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Chuan-Xi Zhang
- Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| |
Collapse
|
21
|
Sharda SC, Bisht K, Sharma V, Lakku PR, Bhatia MS, Sharma N, Biswal M. Direct diagnosis of scrub typhus by full-length 16S ribosomal RNA gene analysis using Oxford Nanopore sequencing. Int J Infect Dis 2022; 125:132-4. [PMID: 36332903 DOI: 10.1016/j.ijid.2022.10.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/06/2022] [Accepted: 10/26/2022] [Indexed: 11/15/2022] Open
Abstract
Scrub typhus (caused by Orientia tsutsugamushi) is a neglected and underdiagnosed disease due to its non-specific clinical presentation and challenging diagnostics. We document the first study of direct diagnosis of scrub typhus from the blood sample of a patient by full-length 16S ribosomal RNA gene amplicon analysis using Oxford Nanopore sequencing.
Collapse
|
22
|
Abstract
Actinobacillus pleuropneumoniae is a Gram-negative, rod-shaped bacterium of the family Pasteurellaceae causing pig pleuropneumonia associated with great economic losses worldwide. Nineteen serotypes with distinctive lipopolysaccharide (LPS) and capsular (CPS) compositions have been described so far, yet complete circular genomes are publicly available only for the reference strains of serotypes 1, 4 and 5b, and for field strains of serotypes 1, 3, 7 and 8. We aimed to complete this picture by sequencing the reference strains of 17 different serotypes with the MinION sequencer (Oxford Nanopore Technologies, ONT) and on an Illumina HiSeq (Illumina) platform. We also included two field isolates of serotypes 2 and 3 that were PacBio- and MinION-sequenced, respectively. Genome assemblies were performed following two different strategies, i.e. PacBio- or ONT-only de novo assemblies polished with Illumina reads or a hybrid assembly by directly combining ONT and Illumina reads. Both methods proved successful in obtaining accurate circular genomes with comparable qualities. blast-based genome comparisons and core-genome phylogeny based on core genes, SNP typing and multi-locus sequence typing (cgMLST) of the 26 circular genomes indicated well-conserved genomes across the 18 different serotypes, differing mainly in phage insertions, and CPS, LPS and RTX-toxin clusters, which, consistently, encode serotype-specific antigens. We also identified small antibiotic resistance plasmids, and complete subtype I-F and subtype II-C CRISPR-Cas systems. Of note, highly similar clusters encoding all those serotype-specific traits were also found in other pathogenic and commensal Actinobacillus species. Taken together with the presence of transposable elements surrounding these loci, we speculate a dynamic intra- and interspecies exchange of such virulence-related factors by horizontal gene transfer. In conclusion, our comprehensive genomics analysis provides useful information for diagnostic test and vaccine development, but also for whole-genome-based epidemiological studies, as well as for the surveillance of the evolution of antibiotic resistance and virulence genes in A. pleuropneumoniae.
Collapse
Affiliation(s)
- Valentina Donà
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| |
Collapse
|
23
|
Allemand E, Ango F. Analysis of Splicing Regulation by Third-Generation Sequencing. Methods Mol Biol 2022; 2537:81-95. [PMID: 35895260 DOI: 10.1007/978-1-0716-2521-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In Metazoa, the diversity of transcripts produced by the RNA Polymerase II is generated essentially through post-transcriptional processing of the nascent transcripts. The regulation of exon inclusion by alternative splicing is one of the main sources of this diversity, which leads to the expansion of the proteome. The portfolio of alternative transcripts remains largely underestimated. Improvement of the sequencing technologies has enhanced the characterization of RNA isoforms and led to the perpetual incrementation of gene expression diversity. Here, we describe a high throughput approach to assess in-depth the splicing regulation of target gene(s) using the third-generation sequencing (TGS) technologies.
Collapse
Affiliation(s)
- Eric Allemand
- Laboratory of cellular and molecular mechanisms of hematological disorders and therapeutic implications, Institut IMAGINE, INSERM, Paris, France.
| | - Fabrice Ango
- INM, University of Montpellier, INSERM, Montpellier, France
| |
Collapse
|
24
|
Vollrath P, Chawla HS, Alnajar D, Gabur I, Lee H, Weber S, Ehrig L, Koopmann B, Snowdon RJ, Obermeier C. Dissection of Quantitative Blackleg Resistance Reveals Novel Variants of Resistance Gene Rlm9 in Elite Brassica napus. Front Plant Sci 2021; 12:749491. [PMID: 34868134 PMCID: PMC8636856 DOI: 10.3389/fpls.2021.749491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/29/2021] [Indexed: 05/15/2023]
Abstract
Blackleg is one of the major fungal diseases in oilseed rape/canola worldwide. Most commercial cultivars carry R gene-mediated qualitative resistances that confer a high level of race-specific protection against Leptosphaeria maculans, the causal fungus of blackleg disease. However, monogenic resistances of this kind can potentially be rapidly overcome by mutations in the pathogen's avirulence genes. To counteract pathogen adaptation in this evolutionary arms race, there is a tremendous demand for quantitative background resistance to enhance durability and efficacy of blackleg resistance in oilseed rape. In this study, we characterized genomic regions contributing to quantitative L. maculans resistance by genome-wide association studies in a multiparental mapping population derived from six parental elite varieties exhibiting quantitative resistance, which were all crossed to one common susceptible parental elite variety. Resistance was screened using a fungal isolate with no corresponding avirulence (AvrLm) to major R genes present in the parents of the mapping population. Genome-wide association studies revealed eight significantly associated quantitative trait loci (QTL) on chromosomes A07 and A09, with small effects explaining 3-6% of the phenotypic variance. Unexpectedly, the qualitative blackleg resistance gene Rlm9 was found to be located within a resistance-associated haploblock on chromosome A07. Furthermore, long-range sequence data spanning this haploblock revealed high levels of single-nucleotide and structural variants within the Rlm9 coding sequence among the parents of the mapping population. The results suggest that novel variants of Rlm9 could play a previously unknown role in expression of quantitative disease resistance in oilseed rape.
Collapse
Affiliation(s)
- Paul Vollrath
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Harmeet S. Chawla
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Dima Alnajar
- Plant Pathology and Crop Protection Division, Department of Crop Sciences, Georg August University of Göttingen, Göttingen, Germany
| | - Iulian Gabur
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
- Department of Plant Sciences, Faculty of Agriculture, Iasi University of Life Sciences, Iaşi, Romania
| | - HueyTyng Lee
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Sven Weber
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Lennard Ehrig
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Birger Koopmann
- Plant Pathology and Crop Protection Division, Department of Crop Sciences, Georg August University of Göttingen, Göttingen, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| |
Collapse
|
25
|
Lu W, Lan X, Zhang T, Sun H, Ma S, Xia Q. Precise Characterization of Bombyx mori Fibroin Heavy Chain Gene Using Cpf1-Based Enrichment and Oxford Nanopore Technologies. Insects 2021; 12:insects12090832. [PMID: 34564273 PMCID: PMC8467315 DOI: 10.3390/insects12090832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Bombyx mori (B. mori), an important economic insect, is famous for its silk. B. mori silk is mainly composed of silk fibroin coated with sericin. Among them, the silk fibroin heavy chain protein has the highest content and the largest molecular weight, which is encoded by the silk fibroin heavy chain (FibH) gene. At present, apart from the complete sequence of the FibH of the B. mori strain p50T, there are no other reports regarding this protein. This is mainly because the special structure formed by the GC-rich repetitive sequence in FibH hinders the amplification of polymerase and the application of Sanger sequencing. Here, the FibH sequence of Dazao, which has 99.98% similarity to that of p50T, was obtained by means of CEO. As far as we know, this is the first complete FibH sequence of the Chinese B. mori strain. Additionally, the methylated CG sites in the FibH repeat unit were identified. Abstract To study the evolution of gene function and a species, it is essential to characterize the tandem repetitive sequences distributed across the genome. Cas9-based enrichment combined with nanopore sequencing is an important technique for targeting repetitive sequences. Cpf1 has low molecular weight, low off-target efficiency, and the same editing efficiency as Cas9. There are numerous studies on enrichment sequencing using Cas9 combined with nanopore, while there are only a few studies on the enrichment sequencing of long and highly repetitive genes using Cpf1. We developed Cpf1-based enrichment combined with ONT sequencing (CEO) to characterize the B. mori FibH gene, which is composed of many repeat units with a long and GC-rich sequence up to 17 kb and is not easily amplified by means of a polymerase chain reaction (PCR). CEO has four steps: the dephosphorylation of genomic DNA, the Cpf1 targeted cleavage of FibH, adapter ligation, and ONT sequencing. Using CEO, we determined the fine structure of B. moriFibH, which is 16,845 bp long and includes 12 repetitive domains separated by amorphous regions. Except for the difference of three bases in the intron from the reference gene, the other sequences are identical. Surprisingly, many methylated CG sites were found and distributed unevenly on the FibH repeat unit. The CEO we established is an available means to depict highly repetitive genes, but also a supplement to the enrichment method based on Cas9.
Collapse
Affiliation(s)
- Wei Lu
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing 400715, China
| | - Xinhui Lan
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
| | - Tong Zhang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing 400715, China
| | - Hao Sun
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing 400715, China
| | - Sanyuan Ma
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing 400715, China
- Correspondence: (S.M.); (Q.X.)
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing 400715, China
- Correspondence: (S.M.); (Q.X.)
| |
Collapse
|
26
|
Ammer-Herrmenau C, Pfisterer N, van den Berg T, Gavrilova I, Amanzada A, Singh SK, Khalil A, Alili R, Belda E, Clement K, Abd El Wahed A, Gady EE, Haubrock M, Beißbarth T, Ellenrieder V, Neesse A. Comprehensive Wet-Bench and Bioinformatics Workflow for Complex Microbiota Using Oxford Nanopore Technologies. mSystems 2021; 6:e0075021. [PMID: 34427527 DOI: 10.1128/mSystems.00750-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The advent of high-throughput sequencing techniques has recently provided an astonishing insight into the composition and function of the human microbiome. Next-generation sequencing (NGS) has become the gold standard for advanced microbiome analysis; however, 3rd generation real-time sequencing, such as Oxford Nanopore Technologies (ONT), enables rapid sequencing from several kilobases to >2 Mb with high resolution. Despite the wide availability and the enormous potential for clinical and translational applications, ONT is poorly standardized in terms of sampling and storage conditions, DNA extraction, library creation, and bioinformatic classification. Here, we present a comprehensive analysis pipeline with sampling, storage, DNA extraction, library preparation, and bioinformatic evaluation for complex microbiomes sequenced with ONT. Our findings from buccal and rectal swabs and DNA extraction experiments indicate that methods that were approved for NGS microbiome analysis cannot be simply adapted to ONT. We recommend using swabs and DNA extractions protocols with extended washing steps. Both 16S rRNA and metagenomic sequencing achieved reliable and reproducible results. Our benchmarking experiments reveal thresholds for analysis parameters that achieved excellent precision, recall, and area under the precision recall values and is superior to existing classifiers (Kraken2, Kaiju, and MetaMaps). Hence, our workflow provides an experimental and bioinformatic pipeline to perform a highly accurate analysis of complex microbial structures from buccal and rectal swabs. IMPORTANCE Advanced microbiome analysis relies on sequencing of short DNA fragments from microorganisms like bacteria, fungi, and viruses. More recently, long fragment DNA sequencing of 3rd generation sequencing has gained increasing importance and can be rapidly conducted within a few hours due to its potential real-time sequencing. However, the analysis and correct identification of the microbiome relies on a multitude of factors, such as the method of sampling, DNA extraction, sequencing, and bioinformatic analysis. Scientists have used different protocols in the past that do not allow us to compare results across different studies and research fields. Here, we provide a comprehensive workflow from DNA extraction, sequencing, and bioinformatic workflow that allows rapid and accurate analysis of human buccal and rectal swabs with reproducible protocols. This workflow can be readily applied by many scientists from various research fields that aim to use long-fragment microbiome sequencing.
Collapse
|
27
|
Chalapati S, Crosbie CA, Limbachiya D, Pinnamaneni N. Direct oligonucleotide sequencing with nanopores. Open Res Eur 2021; 1:47. [PMID: 37645114 PMCID: PMC10445935 DOI: 10.12688/openreseurope.13578.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/13/2021] [Indexed: 08/31/2023]
Abstract
Third-generation DNA sequencing has enabled sequencing of long, unamplified DNA fragments with minimal steps. Direct sequencing of ssDNA or RNA gives valuable insights like base-level modifications, phosphoramidite synthesis yield estimates and strand quality analysis, without the need to add the complimentary strand. Direct sequencing of single-stranded nucleic acid species is challenging as they are non-compatible to the double-stranded sequencing adapters used by manufacturers. The MinION platform from Oxford Nanopore Technologies performs sequencing by passing single-strands of DNA through a layer of biological nanopore sensors; although sequencing is performed on single-strands, the recommended template by the manufacturer is double-stranded. We have identified that the MinION platform can perform sequencing of short, single-strand oligonucleotides directly without amplification or second-strand synthesis by performing a single annealing step before library preparation. Short 5' phosphorylated oligos when annealed to an adapter sequence can be directly sequenced in the 5' to 3' direction via nanopores. Adapter sequences were designed to bind to the 5' end of the oligos and to leave a 3' adenosine overhang after binding to their target. The 3' adenosine overhang of the adapter and the terminal phosphate makes the 5' end of the oligo analogous to an end-prepared dsDNA, rendering it compatible with ligation-based library preparation for sequencing. An oligo-pool containing 42,000, 120 nt orthogonal sequences was phosphorylated and sequenced using this method and ~90% of these sequences were recovered with high accuracy using BLAST. In the nanopore raw data, we have identified that empty signals can be wrongly identified as a valid read by the MinION platform and sometimes multiple signals containing several strands can be fused into a single raw sequence file due to segmentation faults in the software. This direct oligonucleotide sequencing method enables novel applications in DNA data storage systems where short oligonucleotides are the primary information carriers.
Collapse
Affiliation(s)
- Sachin Chalapati
- Helixworks Technologies, Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
| | - Conor A Crosbie
- Helixworks Technologies, Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
| | - Dixita Limbachiya
- Helixworks Technologies, Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
| | - Nimesh Pinnamaneni
- Helixworks Technologies, Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
| |
Collapse
|
28
|
Abstract
Third-generation DNA sequencing has enabled sequencing of long, unamplified DNA fragments with minimal steps. Direct sequencing of ssDNA or RNA gives valuable insights like base-level modifications, phosphoramidite synthesis yield estimates and strand quality analysis, without the need to add the complimentary strand. Direct sequencing of single-stranded nucleic acid species is challenging as they are non-compatible to the double-stranded sequencing adapters used by manufacturers. The MinION platform from Oxford Nanopore Technologies performs sequencing by passing single-strands of DNA through a layer of biological nanopore sensors; although sequencing is performed on single-strands, the recommended template by the manufacturer is double-stranded. We have identified that the MinION platform can perform sequencing of short, single-strand oligonucleotides directly without amplification or second-strand synthesis by performing a single annealing step before library preparation. Short 5' phosphorylated oligos when annealed to an adapter sequence can be directly sequenced in the 5' to 3' direction via nanopores. Adapter sequences were designed to bind to the 5' end of the oligos and to leave a 3' adenosine overhang after binding to their target. The 3' adenosine overhang of the adapter and the terminal phosphate makes the 5' end of the oligo analogous to an end-prepared dsDNA, rendering it compatible with ligation-based library preparation for sequencing. An oligo-pool containing 42,000, 120 nt orthogonal sequences was phosphorylated and sequenced using this method and ~90% of these sequences were recovered with high accuracy using BLAST. In the nanopore raw data, we have identified that empty signals can be wrongly identified as a valid read by the MinION platform and sometimes multiple signals containing several strands can be fused into a single raw sequence file due to segmentation faults in the software. This direct oligonucleotide sequencing method enables novel applications in DNA data storage systems where short oligonucleotides are the primary information carriers.
Collapse
Affiliation(s)
- Sachin Chalapati
- Helixworks Technologies, Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
| | - Conor A Crosbie
- Helixworks Technologies, Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
| | - Dixita Limbachiya
- Helixworks Technologies, Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
| | - Nimesh Pinnamaneni
- Helixworks Technologies, Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
| |
Collapse
|
29
|
Ammer-Herrmenau C, Asendorf T, Beyer G, Buchholz SM, Cameron S, Damm M, Frost F, Henker R, Jaster R, Phillip V, Placzek M, Ratei C, Sirtl S, van den Berg T, Weingarten MJ, Woitalla J, Mayerle J, Ellenrieder V, Neesse A. Study protocol P-MAPS: microbiome as predictor of severity in acute pancreatitis-a prospective multicentre translational study. BMC Gastroenterol 2021; 21:304. [PMID: 34332533 PMCID: PMC8325304 DOI: 10.1186/s12876-021-01885-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022] Open
Abstract
Background Acute pancreatitis (AP) is an inflammatory disorder that causes a considerable economic health burden. While the overall mortality is low, around 20% of patients have a complicated course of disease resulting in increased morbidity and mortality. There is an emerging body of evidence that the microbiome exerts a crucial impact on the pathophysiology and course of AP. For several decades multiple clinical and laboratory parameters have been evaluated, and complex scoring systems were developed to predict the clinical course of AP upon admission. However, the majority of scoring systems are determined after several days and achieve a sensitivity around 70% for early prediction of severe AP. Thus, continued efforts are required to investigate reliable biomarkers for the early prediction of severity in order to guide early clinical management of AP patients.
Methods We designed a multi-center, prospective clinical-translational study to test whether the orointestinal microbiome may serve as novel early predictor of the course, severity and outcome of patients with AP. We will recruit 400 AP patients and obtain buccal and rectal swabs within 72 h of admission to the hospital. Following DNA extraction, microbiome analysis will be performed using 3rd generation sequencing Oxford Nanopore Technologies (ONT) for 16S rRNA and metagenomic sequencing. Alpha- and beta-diversity will be determined and correlated to the revised Atlanta classification and additional clinical outcome parameters such as the length of hospital stay, number and type of complications, number of interventions and 30-day mortality. Discussion If AP patients show a distinct orointestinal microbiome dependent on the severity and course of the disease, microbiome sequencing could rapidly be implemented in the early clinical management of AP patients in the future. Trial registration: ClinicalTrials.gov Identifier: NCT04777812
Collapse
Affiliation(s)
- C Ammer-Herrmenau
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Robert-Kochsstraße 40, 37075, Göttingen, Germany
| | - T Asendorf
- Department of Medical Statistics, University Medical Center, Göttingen, Germany
| | - G Beyer
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - S M Buchholz
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Robert-Kochsstraße 40, 37075, Göttingen, Germany
| | - S Cameron
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Robert-Kochsstraße 40, 37075, Göttingen, Germany
| | - M Damm
- Department of Medicine I, University Hospital Halle, Halle, Germany
| | - F Frost
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - R Henker
- Division of Gastroenterology, Medical Department II, University Hospital of Leipzig, Leipzig, Germany
| | - R Jaster
- Department of Medicine II, University Hospital Rostock, Rostock, Germany
| | - V Phillip
- Department of Medicine II, University Hospital rechts der Isar, Technical University Munich, Munich, Germany
| | - M Placzek
- Department of Medical Statistics, University Medical Center, Göttingen, Germany
| | - C Ratei
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Robert-Kochsstraße 40, 37075, Göttingen, Germany
| | - S Sirtl
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - T van den Berg
- Department of Medical Bioinformatics, University Medical Center, Göttingen, Germany
| | - M J Weingarten
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Robert-Kochsstraße 40, 37075, Göttingen, Germany
| | - J Woitalla
- Department of Medicine II, University Hospital Rostock, Rostock, Germany
| | - J Mayerle
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - V Ellenrieder
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Robert-Kochsstraße 40, 37075, Göttingen, Germany
| | - A Neesse
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center, Robert-Kochsstraße 40, 37075, Göttingen, Germany.
| |
Collapse
|
30
|
Liefting LW, Waite DW, Thompson JR. Application of Oxford Nanopore Technology to Plant Virus Detection. Viruses 2021; 13:v13081424. [PMID: 34452290 PMCID: PMC8402922 DOI: 10.3390/v13081424] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/15/2021] [Accepted: 07/20/2021] [Indexed: 12/13/2022] Open
Abstract
The adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior amplification. The portability of the MinION and Flongle platforms combined with lowering costs and continued improvements in read accuracy make ONT an attractive method for both low- and high-scale virus diagnostics. Here, we provide a detailed step-by-step protocol using the ONT Flongle platform that we have developed for the routine application on a range of symptomatic post-entry quarantine and domestic surveillance plant samples. The aim of this methods paper is to highlight ONT’s feasibility as a valuable component to the diagnostician’s toolkit and to hopefully stimulate other laboratories towards the eventual goal of integrating high-throughput sequencing technologies as validated plant virus diagnostic methods in their own right.
Collapse
|
31
|
Dai Q, Zheng M, Chen Q, Zheng H, Li B. The Preoperative Diagnostic Value of MRI and Otoneural Tests in Acoustic Neuroma. Front Oncol 2021; 11:626485. [PMID: 34268105 PMCID: PMC8276692 DOI: 10.3389/fonc.2021.626485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 06/07/2021] [Indexed: 02/05/2023] Open
Abstract
Objectives To determine the preoperative diagnostic accuracy of MRI and otoneural tests (ONT) for acoustic neuroma (AN) in a cohort of unselected patients with pontocerebellar angle tumors. To find a convenient way to screening out the potential asymptomatic AN patient earlier. Design This diagnostic accuracy study was performed in a central hospital and included a consecutive sample of unilateral incipient pontocerebellar angle tumor patients referred for MRI and ONT before surgery. Different AN features of MRI and ONT were collected and concluded into preoperative diagnostic variables or variable combinations. Those of MRI and ONT are analyzed and compared with biopsy results by multivariable receiver operating characteristic (ROC) analysis. The early-stage group, the course of which is 1 year or less, was separately computed and compared. Results Eighty-three subjects were collected from June 2013 to June 2019; 62 were confirmed AN postoperatively by biopsy, whereas others are not AN. The area under the curve (AUC) of MRI was 0.611, whereas the AUC of ONT was 0.708. In the early-stage group, the AUC of MRI was 0.539, and the AUC of ONT was 0.744. Conclusions ONT was able to identify more subjects affected by unilateral incipient AN than MRI preoperatively. Given that ONT is a functional test for internal auditory canal nerves, it is an optimal screening test for AN patients because it provides more information than MRI for the further clinical plan. It is particularly noteworthy for identifying asymptomatic AN patients and for early stage. Therefore, it may help more patients from unnessesary surgery. Furthermore, an MRI follow-up is suggested if the patient was found alert in ONT.
Collapse
Affiliation(s)
- Qingqing Dai
- Department of Otolaryngology, West China Hospital of Sichuan University, Chengdu, China
| | - Meijun Zheng
- Department of Otolaryngology, West China Hospital of Sichuan University, Chengdu, China
| | - Qiurong Chen
- Department of Otolaryngology, West China Hospital of Sichuan University, Chengdu, China
| | - Hong Zheng
- Department of Otolaryngology, West China Hospital of Sichuan University, Chengdu, China
| | - Bilan Li
- Department of Otolaryngology-Head and Neck Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| |
Collapse
|
32
|
Murigneux V, Roberts LW, Forde BM, Phan MD, Nhu NTK, Irwin AD, Harris PNA, Paterson DL, Schembri MA, Whiley DM, Beatson SA. MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction. BMC Genomics 2021; 22:474. [PMID: 34172000 PMCID: PMC8235852 DOI: 10.1186/s12864-021-07767-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/03/2021] [Indexed: 11/23/2022] Open
Abstract
Background Oxford Nanopore Technology (ONT) long-read sequencing has become a popular platform for microbial researchers due to the accessibility and affordability of its devices. However, easy and automated construction of high-quality bacterial genomes using nanopore reads remains challenging. Here we aimed to create a reproducible end-to-end bacterial genome assembly pipeline using ONT in combination with Illumina sequencing. Results We evaluated the performance of several popular tools used during genome reconstruction, including base-calling, filtering, assembly, and polishing. We also assessed overall genome accuracy using ONT both natively and with Illumina. All steps were validated using the high-quality complete reference genome for the Escherichia coli sequence type (ST)131 strain EC958. Software chosen at each stage were incorporated into our final pipeline, MicroPIPE. Further validation of MicroPIPE was carried out using 11 additional ST131 E. coli isolates, which demonstrated that complete circularised chromosomes and plasmids could be achieved without manual intervention. Twelve publicly available Gram-negative and Gram-positive bacterial genomes (with available raw ONT data and matched complete genomes) were also assembled using MicroPIPE. We found that revised basecalling and updated assembly of the majority of these genomes resulted in improved accuracy compared to the current publicly available complete genomes. Conclusions MicroPIPE is built in modules using Singularity container images and the bioinformatics workflow manager Nextflow, allowing changes and adjustments to be made in response to future tool development. Overall, MicroPIPE provides an easy-access, end-to-end solution for attaining high-quality bacterial genomes. MicroPIPE is available at https://github.com/BeatsonLab-MicrobialGenomics/micropipe. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07767-z.
Collapse
Affiliation(s)
- Valentine Murigneux
- QCIF Facility for Advanced Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Leah W Roberts
- University of Queensland Centre for Clinical Research, Brisbane, Queensland, Australia. .,Queensland Children's Hospital, Brisbane, Queensland, Australia. .,European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL), Hinxton, Cambridge, UK.
| | - Brian M Forde
- University of Queensland Centre for Clinical Research, Brisbane, Queensland, Australia
| | - Minh-Duy Phan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Nguyen Thi Khanh Nhu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Adam D Irwin
- University of Queensland Centre for Clinical Research, Brisbane, Queensland, Australia.,Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - Patrick N A Harris
- University of Queensland Centre for Clinical Research, Brisbane, Queensland, Australia.,Central Microbiology, Pathology Queensland, Royal Brisbane & Women's Hospital, Brisbane, Queensland, Australia
| | - David L Paterson
- University of Queensland Centre for Clinical Research, Brisbane, Queensland, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - David M Whiley
- University of Queensland Centre for Clinical Research, Brisbane, Queensland, Australia.,Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia.
| |
Collapse
|
33
|
Hallgren MB, Overballe-Petersen S, Lund O, Hasman H, Clausen PTLC. MINTyper: an outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads. Biol Methods Protoc 2021; 6:bpab008. [PMID: 33981853 PMCID: PMC8106442 DOI: 10.1093/biomethods/bpab008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/09/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022] Open
Abstract
For detection of clonal outbreaks in clinical settings, we present a complete pipeline that generates a single-nucleotide polymorphisms-distance matrix from a set of sequencing reads. Importantly, the program is able to handle a separate mix of both short reads from the Illumina sequencing platforms and long reads from Oxford Nanopore Technologies’ (ONT) platforms as input. MINTyper performs automated reference identification, alignment, alignment trimming, optional methylation masking, and pairwise distance calculations. With this approach, we could rapidly and accurately cluster a set of DNA sequenced isolates, with a known epidemiological relationship to confirm the clustering. Functions were built to allow for both high-accuracy methylation-aware base-called MinION reads (hac_m Q10) and fast generated lower-quality reads (fast Q8) to be used, also in combination with Illumina data. With fast Q8 reads a higher number of base pairs were excluded from the calculated distance matrix, compared with the high-accuracy methylation-aware Q10 base-calling of ONT data. Nonetheless, when using different qualities of ONT data with corresponding input parameters, the clustering of isolates were nearly identical.
Collapse
Affiliation(s)
- Malte B Hallgren
- National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kgs. Lyngby, Denmark
| | | | - Ole Lund
- National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kgs. Lyngby, Denmark
| | - Henrik Hasman
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark
| | - Philip T L C Clausen
- National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kgs. Lyngby, Denmark
| |
Collapse
|
34
|
Siregar IZ, Dwiyanti FG, Pratama R, Matra DD, Majiidu M. Generating long-read sequences using Oxford Nanopore Technology from Diospyros celebica genomic DNA. BMC Res Notes 2021; 14:75. [PMID: 33640010 PMCID: PMC7913452 DOI: 10.1186/s13104-021-05484-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/12/2021] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Development of sequencing technology has opened up vast opportunities for tree genomic research in the tropics. One of the aforesaid technologies named ONT (Oxford Nanopore Technology) has attracted researchers in undertaking testings and experiments due to its affordability and accessibility. To the best of our knowledge, there has been no published reports on the use of ONT for genomic analysis of Indonesian tree species. This progress is promising for further improvement in order to acquire more genomic data for research purposes. Therefore, the present study was carried out to determine the effectiveness of ONT in generating long-read DNA sequences using DNA isolated from leaves and wood cores of Macassar ebony (Diospyros celebica Bakh.). DATA DESCRIPTION Long-read sequences data of leaves and wood cores of Macassar ebony were generated by using the MinION device and MinKnow v3.6.5 (ONT). The obtained data, as the first long-read sequence dataset for Macassar ebony, is of great importance to conserve the genetic diversity, understanding the molecular mechanism, and sustainable use of plant genetic resources for downstream applications.
Collapse
Affiliation(s)
- Iskandar Zulkarnaen Siregar
- Department of Silviculture, Faculty of Forestry and Environment, IPB University (Bogor Agricultural University), Bogor, Indonesia
- Molecular Science Research Group, Advanced Research Laboratory, IPB University (Bogor Agricultural University), Bogor, Indonesia
| | - Fifi Gus Dwiyanti
- Department of Silviculture, Faculty of Forestry and Environment, IPB University (Bogor Agricultural University), Bogor, Indonesia
- Molecular Science Research Group, Advanced Research Laboratory, IPB University (Bogor Agricultural University), Bogor, Indonesia
| | - Rahadian Pratama
- Molecular Science Research Group, Advanced Research Laboratory, IPB University (Bogor Agricultural University), Bogor, Indonesia
- Department of Biochemistry, Faculty of Mathematic and Natural Science, IPB University (Bogor Agricultural University), Bogor, Indonesia
| | - Deden Derajat Matra
- Molecular Science Research Group, Advanced Research Laboratory, IPB University (Bogor Agricultural University), Bogor, Indonesia
- Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University (Bogor Agricultural University), Bogor, Indonesia
| | - Muhammad Majiidu
- Molecular Science Research Group, Advanced Research Laboratory, IPB University (Bogor Agricultural University), Bogor, Indonesia
| |
Collapse
|
35
|
Murigneux V, Rai SK, Furtado A, Bruxner TJC, Tian W, Harliwong I, Wei H, Yang B, Ye Q, Anderson E, Mao Q, Drmanac R, Wang O, Peters BA, Xu M, Wu P, Topp B, Coin LJM, Henry RJ. Comparison of long-read methods for sequencing and assembly of a plant genome. Gigascience 2020; 9:giaa146. [PMID: 33347571 PMCID: PMC7751402 DOI: 10.1093/gigascience/giaa146] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/07/2020] [Accepted: 11/22/2020] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Sequencing technologies have advanced to the point where it is possible to generate high-accuracy, haplotype-resolved, chromosome-scale assemblies. Several long-read sequencing technologies are available, and a growing number of algorithms have been developed to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology, as well as the most appropriate software for assembly and polishing. It is thus important to benchmark different approaches applied to the same sample. RESULTS Here, we report a comparison of 3 long-read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION), and BGI (single-tube Long Fragment Read) technologies for the same sample. Several assemblers were benchmarked in the assembly of Pacific Biosciences and Nanopore reads. Results obtained from combining long-read technologies or short-read and long-read technologies are also presented. The assemblies were compared for contiguity, base accuracy, and completeness, as well as sequencing costs and DNA material requirements. CONCLUSIONS The 3 long-read technologies produced highly contiguous and complete genome assemblies of M. jansenii. At the time of sequencing, the cost associated with each method was significantly different, but continuous improvements in technologies have resulted in greater accuracy, increased throughput, and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.
Collapse
Affiliation(s)
- Valentine Murigneux
- Genome Innovation Hub, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Subash Kumar Rai
- Genome Innovation Hub, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Timothy J C Bruxner
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Wei Tian
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Australia, 300 Herston Road, Herston, QLD 4006, Australia
| | - Ivon Harliwong
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Australia, 300 Herston Road, Herston, QLD 4006, Australia
| | - Hanmin Wei
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Bicheng Yang
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Australia, 300 Herston Road, Herston, QLD 4006, Australia
| | - Qianyu Ye
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Australia, 300 Herston Road, Herston, QLD 4006, Australia
| | - Ellis Anderson
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
| | - Qing Mao
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
| | - Radoje Drmanac
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
| | - Ou Wang
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Brock A Peters
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
| | - Mengyang Xu
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Qingdao, Building 2, No. 2 Hengyunshan Road, Qingdao 266555, China
| | - Pei Wu
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Tianjin, Airport Business Park, Building E3, Airport Economics Area, Tianjin 300308, China
| | - Bruce Topp
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lachlan J M Coin
- Genome Innovation Hub, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC 3004, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
36
|
Murigneux V, Rai SK, Furtado A, Bruxner TJC, Tian W, Harliwong I, Wei H, Yang B, Ye Q, Anderson E, Mao Q, Drmanac R, Wang O, Peters BA, Xu M, Wu P, Topp B, Coin LJM, Henry RJ. Comparison of long-read methods for sequencing and assembly of a plant genome. Gigascience 2020; 9:6042729. [PMID: 33347571 DOI: 10.1101/2020.03.16.992933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/07/2020] [Accepted: 11/22/2020] [Indexed: 05/23/2023] Open
Abstract
BACKGROUND Sequencing technologies have advanced to the point where it is possible to generate high-accuracy, haplotype-resolved, chromosome-scale assemblies. Several long-read sequencing technologies are available, and a growing number of algorithms have been developed to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology, as well as the most appropriate software for assembly and polishing. It is thus important to benchmark different approaches applied to the same sample. RESULTS Here, we report a comparison of 3 long-read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION), and BGI (single-tube Long Fragment Read) technologies for the same sample. Several assemblers were benchmarked in the assembly of Pacific Biosciences and Nanopore reads. Results obtained from combining long-read technologies or short-read and long-read technologies are also presented. The assemblies were compared for contiguity, base accuracy, and completeness, as well as sequencing costs and DNA material requirements. CONCLUSIONS The 3 long-read technologies produced highly contiguous and complete genome assemblies of M. jansenii. At the time of sequencing, the cost associated with each method was significantly different, but continuous improvements in technologies have resulted in greater accuracy, increased throughput, and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.
Collapse
Affiliation(s)
- Valentine Murigneux
- Genome Innovation Hub, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Subash Kumar Rai
- Genome Innovation Hub, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Timothy J C Bruxner
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Wei Tian
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Australia, 300 Herston Road, Herston, QLD 4006, Australia
| | - Ivon Harliwong
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Australia, 300 Herston Road, Herston, QLD 4006, Australia
| | - Hanmin Wei
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Bicheng Yang
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Australia, 300 Herston Road, Herston, QLD 4006, Australia
| | - Qianyu Ye
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Australia, 300 Herston Road, Herston, QLD 4006, Australia
| | - Ellis Anderson
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
| | - Qing Mao
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
| | - Radoje Drmanac
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
| | - Ou Wang
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
| | - Brock A Peters
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- MGI, BGI-Shenzhen, Building 11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA
| | - Mengyang Xu
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Qingdao, Building 2, No. 2 Hengyunshan Road, Qingdao 266555, China
| | - Pei Wu
- BGI-Shenzhen, No.21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China
- BGI-Tianjin, Airport Business Park, Building E3, Airport Economics Area, Tianjin 300308, China
| | - Bruce Topp
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lachlan J M Coin
- Genome Innovation Hub, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, VIC 3004, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
37
|
Mohamed M, Dang NTM, Ogyama Y, Burlet N, Mugat B, Boulesteix M, Mérel V, Veber P, Salces-Ortiz J, Severac D, Pélisson A, Vieira C, Sabot F, Fablet M, Chambeyron S. A Transposon Story: From TE C ontent to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore. Cells 2020; 9:E1776. [PMID: 32722451 PMCID: PMC7465170 DOI: 10.3390/cells9081776] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/17/2020] [Accepted: 07/23/2020] [Indexed: 11/17/2022] Open
Abstract
Transposable elements (TEs) are the main components of genomes. However, due to their repetitive nature, they are very difficult to study using data obtained with short-read sequencing technologies. Here, we describe an efficient pipeline to accurately recover TE insertion (TEI) sites and sequences from long reads obtained by Oxford Nanopore Technology (ONT) sequencing. With this pipeline, we could precisely describe the landscapes of the most recent TEIs in wild-type strains of Drosophila melanogaster and Drosophila simulans. Their comparison suggests that this subset of TE sequences is more similar than previously thought in these two species. The chromosome assemblies obtained using this pipeline also allowed recovering piRNA cluster sequences, which was impossible using short-read sequencing. Finally, we used our pipeline to analyze ONT sequencing data from a D. melanogaster unstable line in which LTR transposition was derepressed for 73 successive generations. We could rely on single reads to identify new insertions with intact target site duplications. Moreover, the detailed analysis of TEIs in the wild-type strains and the unstable line did not support the trap model claiming that piRNA clusters are hotspots of TE insertions.
Collapse
Affiliation(s)
- Mourdas Mohamed
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
| | - Nguyet Thi-Minh Dang
- IRD/UM UMR DIADE, 911 avenue Agropolis BP64501, 34394 Montpellier, France; (N.T.-M.D.); (F.S.)
| | - Yuki Ogyama
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
| | - Nelly Burlet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Bruno Mugat
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
| | - Matthieu Boulesteix
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Vincent Mérel
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Philippe Veber
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Judit Salces-Ortiz
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Dany Severac
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, 34094 Montpellier, France;
| | - Alain Pélisson
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
| | - Cristina Vieira
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - François Sabot
- IRD/UM UMR DIADE, 911 avenue Agropolis BP64501, 34394 Montpellier, France; (N.T.-M.D.); (F.S.)
| | - Marie Fablet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Séverine Chambeyron
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
| |
Collapse
|
38
|
Byrne A, Supple MA, Volden R, Laidre KL, Shapiro B, Vollmers C. Depletion of Hemoglobin Transcripts and Long-Read Sequencing Improves the Transcriptome Annotation of the Polar Bear ( Ursus maritimus). Front Genet 2019; 10:643. [PMID: 31379921 PMCID: PMC6658610 DOI: 10.3389/fgene.2019.00643] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/18/2019] [Indexed: 11/26/2022] Open
Abstract
Transcriptome studies evaluating whole blood and tissues are often confounded by overrepresentation of highly abundant transcripts. These abundant transcripts are problematic, as they compete with and prevent the detection of rare RNA transcripts, obscuring their biological importance. This issue is more pronounced when using long-read sequencing technologies for isoform-level transcriptome analysis, as they have relatively lower throughput compared to short-read sequencers. As a result, long-read based transcriptome analysis is prohibitively expensive for non-model organisms. While there are off-the-shelf kits available for select model organisms capable of depleting highly abundant transcripts for alpha (HBA) and beta (HBB) hemoglobin, they are unsuitable for non-model organisms. To address this, we have adapted the recent CRISPR/Cas9-based depletion method (depletion of abundant sequences by hybridization) for long-read full-length cDNA sequencing approaches that we call Long-DASH. Using a recombinant Cas9 protein with appropriate guide RNAs, full-length hemoglobin transcripts can be depleted in vitro prior to performing any short- and long-read sequencing library preparations. Using this method, we sequenced depleted full-length cDNA in parallel using both our Oxford Nanopore Technology (ONT) based R2C2 long-read approach, as well as the Illumina short-read based Smart-seq2 approach. To showcase this, we have applied our methods to create an isoform-level transcriptome from whole blood samples derived from three polar bears (Ursus maritimus). Using Long-DASH, we succeeded in depleting hemoglobin transcripts and generated deep Smart-seq2 Illumina datasets and 3.8 million R2C2 full-length cDNA consensus reads. Applying Long-DASH with our isoform identification pipeline, Mandalorion, we discovered ∼6,000 high-confidence isoforms and a number of novel genes. This indicates that there is a high diversity of gene isoforms within U. maritimus not yet reported. This reproducible and straightforward approach has not only improved the polar bear transcriptome annotations but will serve as the foundation for future efforts to investigate transcriptional dynamics within the 19 polar bear subpopulations around the Arctic.
Collapse
Affiliation(s)
- Ashley Byrne
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA, United States
- Genomics Institute, University of California, Santa Cruz, CA, United States
| | - Megan A. Supple
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Roger Volden
- Genomics Institute, University of California, Santa Cruz, CA, United States
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Kristin L. Laidre
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA, United States
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Christopher Vollmers
- Genomics Institute, University of California, Santa Cruz, CA, United States
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| |
Collapse
|