Year: 2021
Type: article
Abstract: MOTIVATION: Next-generation sequencing has become exceedingly common and has transformed our ability to explore nonmodel systems. In particular, transcriptomics has facilitated the study of venom and evolution of toxins in venomous lineages; however, many challenges remain. Primarily, annotation of toxins in the transcriptome is a laborious and time-consuming task. Current annotation software often fails to predict the correct coding sequence and overestimates the number of toxins present in the transcriptome. Here, we present ToxCodAn, a python script designed to perform precise annotation of snake venom gland transcriptomes. We test ToxCodAn with a set of previously curated transcriptomes and compare the results to other annotators. In addition, we provide a guide for venom gland transcriptomics to facilitate future research and use Bothrops alternatus as a case study for ToxCodAn and our guide. RESULTS: Our analysis reveals that ToxCodAn provides precise annotation of toxins present in the transcriptome of venom glands of snakes. Comparison with other annotators demonstrates that ToxCodAn has better performance with regard to run time ($>20x$ faster), coding sequence prediction ($>3x$ more accurate) and the number of toxins predicted (generating $>4x$ less false positives). In this sense, ToxCodAn is a valuable resource for toxin annotation. The ToxCodAn framework can be expanded in the future to work with other venomous lineages and detect novel toxins.
Source: Briefings in Bioinformatics
DOI: 10.1093/bib/bbab095
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: bronze
Awards: Collaborative Research: Dimensions US-BIOTA-Sao Paulo: Scales of biodiversity - Integrated studies of snake venom evolution and function across multiple levels of diversity, G1669410935, G4290916013, Collaborative Research: Dimensions US-BIOTA-Sao Paulo: Scales of biodiversity - Integrated studies of snake venom evolution and function across multiple levels of diversity, Dimensions US-BIOTA São Paulo: scales of biodiversity: integrated studies of snake venom evolution and function across multiple levels of diversity, Collaborative Research: ABI Development: Development and Application of Graphical User Interfaces for System Building and Analysis of Membrane Simulations, G7104835510, Collaborative Research: Dimensions US-BIOTA-Sao Paulo: Scales of biodiversity-Integrated studies of snake venom evolution and function across multiple levels of diversity, G7822383032, G8140016130
OpenAlex ID: W3155550370