| Full text | |
| Author(s): |
Nachtigall, Pedro G.
;
Durham, Alan M.
;
Rokyta, Darin R.
;
Junqueira-de-Azevedo, Inacio L. M.
Total Authors: 4
|
| Document type: | Journal article |
| Source: | GIGASCIENCE; v. 13, p. 17-pg., 2024-01-18. |
| 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. (AU) | |
| FAPESP's process: | 18/26520-4 - Characterization of the interrelationship between transcriptomes, miRNomes and proteomes from the venom glands of Bothrops fonsecai and Bothrops cotiara |
| Grantee: | Pedro Gabriel Nachtigall |
| Support Opportunities: | Scholarships in Brazil - Post-Doctoral |
| FAPESP's process: | 13/07467-1 - CeTICS - Center of Toxins, Immune-Response and Cell Signaling |
| Grantee: | Hugo Aguirre Armelin |
| Support Opportunities: | Research Grants - Research, Innovation and Dissemination Centers - RIDC |
| FAPESP's process: | 22/04988-0 - Characterization and comparison of promoter and enhancer regions of toxin genes between two populations of Agkistrodon piscivorus using RNA-seq, ATAC-seq, and CUT&RUN sequencing methods |
| Grantee: | Pedro Gabriel Nachtigall |
| Support Opportunities: | Scholarships abroad - Research Internship - Post-doctor |
| FAPESP's process: | 16/50127-5 - Dimensions US-BIOTA São Paulo: scales of biodiversity: integrated studies of snake venom evolution and function across multiple levels of diversity |
| Grantee: | Inácio de Loiola Meirelles Junqueira de Azevedo |
| Support Opportunities: | BIOTA-FAPESP Program - Thematic Grants |