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ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages.
Nachtigall, Pedro G; Durham, Alan M; Rokyta, Darin R; Junqueira-de-Azevedo, Inácio L M.
Afiliação
  • Nachtigall PG; Laboratório de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, 05503-900 SP, Brazil.
  • Durham AM; Department of Biological Science, Florida State University, Tallahassee, 32306-4295 FL, USA.
  • Rokyta DR; Departamento de Ciência da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo (USP), São Paulo, 05508-090 SP, Brazil.
  • Junqueira-de-Azevedo ILM; Department of Biological Science, Florida State University, Tallahassee, 32306-4295 FL, USA.
Gigascience ; 132024 01 02.
Article em En | MEDLINE | ID: mdl-38241143
ABSTRACT

BACKGROUND:

The rapid development of sequencing technologies resulted in a wide expansion of genomics studies using venomous lineages. This facilitated research focusing on understanding the evolution of adaptive traits and the search for novel compounds that can be applied in agriculture and medicine. However, the toxin annotation of genomes is a laborious and time-consuming task, and no consensus pipeline is currently available. No computational tool currently exists to address the challenges specific to toxin annotation and to ensure the reproducibility of the process.

RESULTS:

Here, we present ToxCodAn-Genome, the first software designed to perform automated toxin annotation in genomes of venomous lineages. This pipeline was designed to retrieve the full-length coding sequences of toxins and to allow the detection of novel truncated paralogs and pseudogenes. We tested ToxCodAn-Genome using 12 genomes of venomous lineages and achieved high performance on recovering their current toxin annotations. This tool can be easily customized to allow improvements in the final toxin annotation set and can be expanded to virtually any venomous lineage. ToxCodAn-Genome is fast, allowing it to run on any personal computer, but it can also be executed in multicore mode, taking advantage of large high-performance servers. In addition, we provide a guide to direct future research in the venomics field to ensure a confident toxin annotation in the genome being studied. As a case study, we sequenced and annotated the toxin repertoire of Bothrops alternatus, which may facilitate future evolutionary and biomedical studies using vipers as models.

CONCLUSIONS:

ToxCodAn-Genome is suitable to perform toxin annotation in the genome of venomous species and may help to improve the reproducibility of further studies. ToxCodAn-Genome and the guide are freely available at https//github.com/pedronachtigall/ToxCodAn-Genome.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Peçonhas / Genoma / Bothrops / Serpentes Peçonhentas Tipo de estudo: Prognostic_studies Idioma: En Revista: Gigascience Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Brasil

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Peçonhas / Genoma / Bothrops / Serpentes Peçonhentas Tipo de estudo: Prognostic_studies Idioma: En Revista: Gigascience Ano de publicação: 2024 Tipo de documento: Article País de afiliação: Brasil