New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads

González-García, Laura; Guevara-Barrientos, David; Lozano‐Arce, Daniela; Gil, Juanita; Díaz-Riaño, Jorge Iván; Duarte, Erick; Andrade, Germán I.; Bojacá, Juan Camilo; Hoyos-Sanchez, Maria Camila; Chavarro, Christian; Guayazan, Natalia; Chica, Luis Alberto; Acosta, Maria Camila Buitrago; Bautista, Edwin; Trujillo, Miller; Duitama, Jorge

doi:10.26508/lsa.202201719

Cited by 3 publications

(2 citation statements)

References 41 publications

(78 reference statements)

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“…The reads were error-corrected using NECAT v0.0.1 correction step ( 29 ) with default parameters. Corrected reads were assembled, and the resulting assemblies were circularized using NGSEP Assembler v4.3.1 with default parameters ( 30 ). The genes used for circularization were rpoB for chromosome I and oriC for chromosome II.…”

Section: Methodsmentioning

confidence: 99%

Unveiling potential virulence determinants in Vibrio isolates from Anadara tuberculosa through whole genome analyses

Restrepo-Benavides,

Lozano-Arce,

Gonzalez-Garcia

et al. 2024

Microbiol Spectr

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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. IMPORTANCE This 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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Section: Methodsmentioning

confidence: 99%

Unveiling potential virulence determinants in Vibrio isolates from Anadara tuberculosa through whole genome analyses

Restrepo-Benavides,

Lozano-Arce,

Gonzalez-Garcia

et al. 2024

Microbiol Spectr

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“…Hifiasm v0.12(r304) 80 was executed with the parameter “-n-hap” equal to 2 to assemble a diploid genome. The Assembler command of the Next Generation Sequencing Experience Platform (NGSEP) v4.3.1 was also executed using as parameters a k-mer length (-k) of 25, window length (-w) 40 and ploidy (-ploidy) of 2 81 . Contigs were aligned to the publicly available haploid genome assembly of the TcI Brazil A4 strain using Minimap2 v2.22 82 .…”

Section: Methodsmentioning

confidence: 99%

A phased genome assembly of a Colombian Trypanosoma cruzi TcI strain and the evolution of gene families

Hoyos Sanchez,

Ospina Zapata,

Suarez

et al. 2024

Sci Rep

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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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Efficient data reconstruction: The bottleneck of large-scale application of DNA storage

Cao,

Zheng,

Shao

et al. 2024

Cell Reports

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New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads

Cited by 3 publications

References 41 publications

Unveiling potential virulence determinants in Vibrio isolates from Anadara tuberculosa through whole genome analyses

Unveiling potential virulence determinants in Vibrio isolates from Anadara tuberculosa through whole genome analyses

A phased genome assembly of a Colombian Trypanosoma cruzi TcI strain and the evolution of gene families

Efficient data reconstruction: The bottleneck of large-scale application of DNA storage

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