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Cao B, Zheng Y, Shao Q, Liu Z, Xie L, Zhao Y, Wang B, Zhang Q, Wei X. Efficient data reconstruction: The bottleneck of large-scale application of DNA storage. Cell Rep 2024; 43:113699. [PMID: 38517891 DOI: 10.1016/j.celrep.2024.113699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/15/2023] [Accepted: 01/05/2024] [Indexed: 03/24/2024] Open
Abstract
Over the past decade, the rapid development of DNA synthesis and sequencing technologies has enabled preliminary use of DNA molecules for digital data storage, overcoming the capacity and persistence bottlenecks of silicon-based storage media. DNA storage has now been fully accomplished in the laboratory through existing biotechnology, which again demonstrates the viability of carbon-based storage media. However, the high cost and latency of data reconstruction pose challenges that hinder the practical implementation of DNA storage beyond the laboratory. In this article, we review existing advanced DNA storage methods, analyze the characteristics and performance of biotechnological approaches at various stages of data writing and reading, and discuss potential factors influencing DNA storage from the perspective of data reconstruction.
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Affiliation(s)
- Ben Cao
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, Dalian, Liaoning 116024, China; Centre for Frontier AI Research, Agency for Science, Technology, and Research (A(∗)STAR), 1 Fusionopolis Way, Singapore 138632, Singapore
| | - Yanfen Zheng
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, Dalian, Liaoning 116024, China
| | - Qi Shao
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Zhenlu Liu
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Lei Xie
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Yunzhu Zhao
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, Dalian, Liaoning 116024, China.
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, Dalian, Liaoning 116024, China
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Restrepo-Benavides M, Lozano-Arce D, Gonzalez-Garcia LN, Báez-Aguirre F, Ariza-Aranguren G, Faccini D, Zambrano MM, Jiménez P, Fernández-Bravo A, Restrepo S, Guevara-Suarez M. Unveiling potential virulence determinants in Vibrio isolates from Anadara tuberculosa through whole genome analyses. Microbiol Spectr 2024; 12:e0292823. [PMID: 38189292 PMCID: PMC10846245 DOI: 10.1128/spectrum.02928-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/14/2023] [Indexed: 01/09/2024] Open
Abstract
The genus Vibrio includes pathogenic bacteria able to cause disease in humans and aquatic organisms, leading to disease outbreaks and significant economic losses in the fishery industry. Despite much work on Vibrio in several marine organisms, no specific studies have been conducted on Anadara tuberculosa. This is a commercially important bivalve species, known as "piangua hembra," along Colombia's Pacific coast. Therefore, this study aimed to identify and characterize the genomes of Vibrio isolates obtained from A. tuberculosa. Bacterial isolates were obtained from 14 A. tuberculosa specimens collected from two locations along the Colombian Pacific coast, of which 17 strains were identified as Vibrio: V. parahaemolyticus (n = 12), V. alginolyticus (n = 3), V. fluvialis (n = 1), and V. natriegens (n = 1). Whole genome sequence of these isolates was done using Oxford Nanopore Technologies (ONT). The analysis revealed the presence of genes conferring resistance to β-lactams, tetracyclines, chloramphenicol, and macrolides, indicating potential resistance to these antimicrobial agents. Genes associated with virulence were also found, suggesting the potential pathogenicity of these Vibrio isolates, as well as genes for Type III Secretion Systems (T3SS) and Type VI Secretion Systems (T6SS), which play crucial roles in delivering virulence factors and in interbacterial competition. This study represents the first genomic analysis of bacteria within A. tuberculosa, shedding light on Vibrio genetic factors and contributing to a comprehensive understanding of the pathogenic potential of these Vibrio isolates.IMPORTANCEThis study presents the first comprehensive report on the whole genome analysis of Vibrio isolates obtained from Anadara tuberculosa, a bivalve species of great significance for social and economic matters on the Pacific coast of Colombia. Research findings have significant implications for the field, as they provide crucial information on the genetic factors and possible pathogenicity of Vibrio isolates associated with A. tuberculosa. The identification of antimicrobial resistance genes and virulence factors within these isolates emphasizes the potential risks they pose to both human and animal health. Furthermore, the presence of genes associated with Type III and Type VI Secretion Systems suggests their critical role in virulence and interbacterial competition. Understanding the genetic factors that contribute to Vibrio bacterial virulence and survival strategies within their ecological niche is of utmost importance for the effective prevention and management of diseases in aquaculture practices.
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Affiliation(s)
- Mariana Restrepo-Benavides
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
- Unit of Microbiology, Department of Basic Health Sciences, Faculty of Medicine and Health Sciences, IISPV, University Rovira i Virgili, Reus, Spain
| | - Daniela Lozano-Arce
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
| | - Laura Natalia Gonzalez-Garcia
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
- Systems and Computing Engineering Department, Universidad de Los Andes, Bogotá, Colombia
- UMR DIADE, Institut de Recherche pour le Développement, Université de Montpellier, Montpellier, France
| | - Felipe Báez-Aguirre
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
| | - Gabriela Ariza-Aranguren
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
| | - Daniel Faccini
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
| | | | - Pedro Jiménez
- Laboratorio de Fitopatología, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá, Colombia
| | - Ana Fernández-Bravo
- Unit of Microbiology, Department of Basic Health Sciences, Faculty of Medicine and Health Sciences, IISPV, University Rovira i Virgili, Reus, Spain
| | - Silvia Restrepo
- Departamento de Ingeniería Química y de Alimentos, Laboratorio de Micología y Fitopatología, Universidad de los Andes, Bogotá, Colombia
| | - Marcela Guevara-Suarez
- Applied Genomics Research Group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
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Hoyos Sanchez MC, Ospina Zapata HS, Suarez BD, Ospina C, Barbosa HJ, Carranza Martinez JC, Vallejo GA, Urrea Montes D, Duitama J. A phased genome assembly of a Colombian Trypanosoma cruzi TcI strain and the evolution of gene families. Sci Rep 2024; 14:2054. [PMID: 38267502 PMCID: PMC10808112 DOI: 10.1038/s41598-024-52449-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/18/2024] [Indexed: 01/26/2024] Open
Abstract
Chagas is an endemic disease in tropical regions of Latin America, caused by the parasite Trypanosoma cruzi. High intraspecies variability and genome complexity have been challenges to assemble high quality genomes needed for studies in evolution, population genomics, diagnosis and drug development. Here we present a chromosome-level phased assembly of a TcI T. cruzi strain (Dm25). While 29 chromosomes show a large collinearity with the assembly of the Brazil A4 strain, three chromosomes show both large heterozygosity and large divergence, compared to previous assemblies of TcI T. cruzi strains. Nucleotide and protein evolution statistics indicate that T. cruzi Marinkellei separated before the diversification of T. cruzi in the known DTUs. Interchromosomal paralogs of dispersed gene families and histones appeared before but at the same time have a more strict purifying selection, compared to other repeat families. Previously unreported large tandem arrays of protein kinases and histones were identified in this assembly. Over one million variants obtained from Illumina reads aligned to the primary assembly clearly separate the main DTUs. We expect that this new assembly will be a valuable resource for further studies on evolution and functional genomics of Trypanosomatids.
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Affiliation(s)
- Maria Camila Hoyos Sanchez
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, 79106, USA
| | | | - Brayhan Dario Suarez
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Universidad del Tolima, Ibagué, Colombia
| | - Carlos Ospina
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Universidad del Tolima, Ibagué, Colombia
| | - Hamilton Julian Barbosa
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Universidad del Tolima, Ibagué, Colombia
| | | | - Gustavo Adolfo Vallejo
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Universidad del Tolima, Ibagué, Colombia
| | - Daniel Urrea Montes
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Universidad del Tolima, Ibagué, Colombia
| | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
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