Metagenome-Assembled Genome of
            <i>Acidibrevibacterium fodinaquatile</i>
            FLA01 from Fumarole Sediments from the Los Azufres Geothermal Field

Bolivar-Torres, Hermes H; Marín-Paredes, Roberto; Ramos-Madrigal, Cristal; Servín-Garcidueñas, Luis E.

doi:10.1128/mra.00823-22

Cited by 2 publications

(2 citation statements)

References 14 publications

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“…Third Generation Sequencing (TGS) technology is expected to resolve the repeat problem if its long reads can span the repeat regions. Nevertheless, many genomes have been or are still sequenced, partially or fully, by Second Generation Sequencing (SGS) technology [ 2 – 5 ], due to its high accuracy, low cost, and wide availability. It is desirable to reconstruct, at least some, regions of repetitive elements by the SGS reads.…”

Section: Introductionmentioning

confidence: 99%

RegCloser: a robust regression approach to closing genome gaps

Cao

2023

BMC Bioinformatics

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Background Closing gaps in draft genomes leads to more complete and continuous genome assemblies. The ubiquitous genomic repeats are challenges to the existing gap-closing methods, based on either the k-mer representation by the de Bruijn graph or the overlap-layout-consensus paradigm. Besides, chimeric reads will cause erroneous k-mers in the former and false overlaps of reads in the latter. Results We propose a novel local assembly approach to gap closing, called RegCloser. It represents read coordinates and their overlaps respectively by parameters and observations in a linear regression model. The optimal overlap is searched only in the restricted range consistent with insert sizes. Under this linear regression framework, the local DNA assembly becomes a robust parameter estimation problem. We solved the problem by a customized robust regression procedure that resists the influence of false overlaps by optimizing a convex global Huber loss function. The global optimum is obtained by iteratively solving the sparse system of linear equations. On both simulated and real datasets, RegCloser outperformed other popular methods in accurately resolving the copy number of tandem repeats, and achieved superior completeness and contiguity. Applying RegCloser to a plateau zokor draft genome that had been improved by long reads further increased contig N50 to 3-fold long. We also tested the robust regression approach on layout generation of long reads. Conclusions RegCloser is a competitive gap-closing tool. The software is available at https://github.com/csh3/RegCloser. The robust regression approach has a prospect to be incorporated into the layout module of long read assemblers.

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Section: Introductionmentioning

confidence: 99%

RegCloser: a robust regression approach to closing genome gaps

Cao

2023

BMC Bioinformatics

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“…In the last three years, two metagenomes have been sequenced from green sediments around a hot spring and around a fumarole. At the moment, only one genome of Acidibrevibacterium has been recovered from the green sediments around a fumarole [19].…”

Section: Introductionmentioning

confidence: 99%

A Metagenome from a Steam Vent in Los Azufres Geothermal Field Shows an Abundance of Thermoplasmatales archaea and Bacteria from the Phyla Actinomycetota and Pseudomonadota

Marín-Paredes,

Bolívar-Torres,

Coronel-Gaytán

et al. 2023

CIMB

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Los Azufres National Park is a geothermal field that has a wide number of thermal manifestations; nevertheless, the microbial communities in many of these environments remain unknown. In this study, a metagenome from a sediment sample from Los Azufres National Park was sequenced. In this metagenome, we found that the microbial diversity corresponds to bacteria (Actinomycetota, Pseudomonadota), archaea (Thermoplasmatales and Candidatus Micrarchaeota and Candidatus Parvarchaeota), eukarya (Cyanidiaceae), and viruses (Fussellovirus and Caudoviricetes). The functional annotation showed genes related to the carbon fixation pathway, sulfur metabolism, genes involved in heat and cold shock, and heavy-metal resistance. From the sediment, it was possible to recover two metagenome-assembled genomes from Ferrimicrobium and Cuniculiplasma. Our results showed that there are a large number of microorganisms in Los Azufres that deserve to be studied.

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Metagenome-Assembled Genome of Acidibrevibacterium fodinaquatile FLA01 from Fumarole Sediments from the Los Azufres Geothermal Field

Cited by 2 publications

References 14 publications

RegCloser: a robust regression approach to closing genome gaps

RegCloser: a robust regression approach to closing genome gaps

A Metagenome from a Steam Vent in Los Azufres Geothermal Field Shows an Abundance of Thermoplasmatales archaea and Bacteria from the Phyla Actinomycetota and Pseudomonadota

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