Sma3s: A Three-Step Modular Annotator for Large Sequence Datasets

Muñoz‐Mérida, Antonio; Viguera, Enrique; Claros, M. Gonzalo; Trelles, Oswaldo; Pérez-Pulido, Antonio J.

doi:10.1093/dnares/dsu001

Cited by 47 publications

(42 citation statements)

References 30 publications

(34 reference statements)

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“…The initial assignment of Gene Ontology (GO) terms for predicted proteins was performed using the UniProtKB/Swiss-Prot database (UniProt Consortium 2015) and the third module of the Sma3s program (Muñoz-Mérida et al. 2014), modified to accept only reciprocal BLAST hits for annotation.…”

Section: Methodsmentioning

confidence: 99%

Genomic survey of a hyperparasitic microsporidianAmphiamblyssp. (Metchnikovellidae)

2016

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Metchnikovellidae are a group of unusual microsporidians that lack some of the defining ultrastructural features characteristic of derived Microsporidia and are thought to be one of their earliest-branching lineages. The basal position of metchnikovellids was never confirmed by molecular phylogeny in published research, and thus far no genomic data for this group were available. In this work, we obtain a partial genome of metchnikovellid Amphiamblys sp. using multiple displacement amplification, next-generation sequencing, and metagenomic binning approaches. The partial genome, which we estimate to be close to 90% complete, displays genome compaction on par with gene-dense microsporidian genomes, but contains an unusual repertoire of unique repeat elements. Phylogenetic analyses of multigene datasets place Amphiamblys sp. as the first branch of the microsporidian lineage following the divergence of a mitochondriate microsporidian Mitosporidium. We find evidence for a mitochondrial remnant presumably functionally equivalent to a mitosome in Amphiamblys sp. and the common enzymatic complement for microsporidian anaerobic metabolism. Comparative genomic analyses identify the conservation of components for clathrin vesicle formation as one of the key features distinguishing the metchnikovellid from its highly derived relatives. The presented data confirm the notion of Metchnikovellidae as a less derived microsporidian group, and provide an additional stepping stone for reconstruction of an evolutionary transition from the early diverging parasitic fungi to derived Microsporidia.

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Section: Methodsmentioning

confidence: 99%

Genomic survey of a hyperparasitic microsporidianAmphiamblyssp. (Metchnikovellidae)

2016

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“…All the sequences were permuted to set the repA gene as the start position prior to annotation. Isolates genome annotation was complemented with the Sma3s tool v.2 (30) and by integrating data from conserved domains searches performed with InterProScan v.5.30-69.0 (31,32) . Integrons occuring in the Thai megaplasmids were identified using the Integron Finder package v.1.5.1 (33)(34)(35)(36) .…”

Section: Annotationmentioning

confidence: 99%

A megaplasmid family responsible for dissemination of multidrug resistance inPseudomonas

Cazares

Moore

Grimes

et al. 2019

Preprint

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Multidrug resistance (MDR) represents a global threat to health. Although plasmids can play an important role in the dissemination of MDR, they have not been commonly linked to the emergence of antimicrobial resistance in the pathogen Pseudomonas aeruginosa . We used whole genome sequencing to characterize a collection of P. aeruginosa clinical isolates from a hospital in Thailand. Using long-read sequence data we obtained complete sequences of two closely related megaplasmids (>420 kb) carrying large arrays of antibiotic resistance genes located in discrete, complex and dynamic resistance regions, and revealing evidence of extensive duplication and recombination events. A comprehensive pangenomic and phylogenomic analysis indicated that 1) these large plasmids comprise a family present in different members of the Pseudomonas genus and associated with multiple sources (geographical, clinical or environmental); 2) the megaplasmids encode diverse niche-adaptive accessory traits, including multidrug resistance; 3) the pangenome of the megaplasmid family is highly flexible and diverse, comprising a substantial core genome (average of 48% of plasmid genes), but with individual members carrying large numbers of unique genes. The history of the megaplasmid family, inferred from our analysis of the available database, suggests that members carrying multiple resistance genes date back to at least the 1970s.

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“…Transcripts were annotated using Sma3s (Muñoz-Mérida et al, 2014), AutoFact and Full-LengtherNext filtering for E < 10 −10 and a minimal identity of 30% as reported in Benzekri et al (2014). The homology identification analysis was performed using Blastx at NCBI database.…”

Section: Bioinformatic Analysismentioning

confidence: 99%

Characterization of Iodine-Related Molecular Processes in the Marine Microalga Tisochrysis lutea (Haptophyta)

et al. 2018

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Iodine metabolism is essential for the antioxidant defense of marine algae and in the biogeochemical cycle of iodine. Moreover, some microalgae can synthetize thyroid hormone-like compounds that are essential to sustain food webs. However, knowledge regarding iodine-related molecular processes in microalgae is still scarce. In this study, a de novo transcriptome of Tisochrysis lutea cultured under high iodide concentrations (5 mM) was assembled using both long and short reads. A database termed IsochrysisDB was established to host all genomic information. Gene expression analyses during microalgal growth showed that most of the antioxidant-(aryl, ccp, perox, sod1, sod2, sod3, apx3, ahp1) and iodide-specific deiodinase (dio) genes increased their mRNA abundance progressively until the stationary phase to cope with oxidative stress. Moreover, the increase of dio mRNA abundance in aging cultures indicated that this enzyme was also involved in senescence. Cell treatments with iodide modified the expression of perox whereas treatments with iodate changed the transcript levels of gpx1 and ccp. To test the dependence of perox on iodide, microalgae cells were treated with hydrogen peroxide (H 2 O 2 ) either in presence or absence of iodide observing that several genes related to reactive oxygen species (ROS) deactivation (perox, gpx1, apx2, apx3, ahp1, ahp2, sod1, sod3, and aryl) were transcriptionally activated although with some temporal differences. However, only the expression of perox was dependent on iodide levels indicating this enzyme, acquired by horizontal gene transfer (HGT), could act as a haloperoxidase. All these data indicate that T. lutea activates coordinately the expression of antioxidant genes to cope with oxidative stress. The identification of a phase-regulated deiodinase and a novel haloperoxidase provide new clues about the origin and evolution of thyroid signaling and the antioxidant role of iodine in the marine environment.

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Sma3s: A Three-Step Modular Annotator for Large Sequence Datasets

Cited by 47 publications

References 30 publications

Genomic survey of a hyperparasitic microsporidianAmphiamblyssp. (Metchnikovellidae)

Genomic survey of a hyperparasitic microsporidianAmphiamblyssp. (Metchnikovellidae)

A megaplasmid family responsible for dissemination of multidrug resistance inPseudomonas

Characterization of Iodine-Related Molecular Processes in the Marine Microalga Tisochrysis lutea (Haptophyta)

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