ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages

Autor(es)

Nachtigall, Pedro G. ; Durham, Alan M. ; Rokyta, Darin R. ; Junqueira-de-Azevedo, Inacio L. M.

• Tipo de documento: Artigo Científico
• Fonte: GIGASCIENCE; v. 13, p. 17-pg., 2024-01-18.

Resumo

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. (AU)

• Processo FAPESP: 18/26520-4 - Caracterização da inter-relação entre transcriptomas, miRNomas e proteomas de glândulas de veneno de Bothrops fonsecai e Bothrops cotiara
• Beneficiário: Pedro Gabriel Nachtigall
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 13/07467-1 - CeTICS - Centro de Toxinas, Imuno-Resposta e Sinalização Celular
• Beneficiário: Hugo Aguirre Armelin
• Modalidade de apoio: Auxílio à Pesquisa - Centros de Pesquisa, Inovação e Difusão - CEPIDs
• Processo FAPESP: 22/04988-0 - Caracterização e comparação de regiões promotoras e acentuadoras de genes de toxinas entre duas populações de Agkistrodon piscivorus usando os métodos de sequenciamento RNA-seq, ATAC-seq e CUT&RUN
• Beneficiário: Pedro Gabriel Nachtigall
• Modalidade de apoio: Bolsas no Exterior - Estágio de Pesquisa - Pós-Doutorado
• Processo FAPESP: 16/50127-5 - Dimensions US-BIOTA São Paulo: scales of biodiversity: integrated studies of snake venom evolution and function across multiple levels of diversity
• Beneficiário: Inácio de Loiola Meirelles Junqueira de Azevedo
• Modalidade de apoio: Auxílio à Pesquisa - Programa BIOTA - Temático