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The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction.


ABSTRACT: The common toad Rhinella arenarum is widely distributed in Argentina, where it is utilised as an autochthonous model in ecotoxicological research and environmental toxicology. However, the lack of a reference genome makes molecular assays and gene expression studies difficult to carry out on this non-model species. To address this issue, we performed a genome-wide transcriptome analysis on R. arenarum larvae through massive RNA sequencing, followed by de novo assembly, annotation, and gene prediction. We obtained 57,407 well-annotated transcripts representing 99.4% of transcriptome completeness (available at http://rhinella.uncoma.edu.ar). We also defined a set of 52,800 high-confidence lncRNA transcripts and demonstrated the reliability of the transcriptome data to perform phylogenetic analysis. Our comprehensive transcriptome analysis of R. arenarum represents a valuable resource to perform functional genomic studies and to identify potential molecular biomarkers in ecotoxicological research.

SUBMITTER: Ceschin DG 

PROVIDER: S-EPMC6978513 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction.

Ceschin Danilo Guillermo DG   Pires Natalia Susana NS   Mardirosian Mariana Noelia MN   Lascano Cecilia Inés CI   Venturino Andrés A  

Scientific reports 20200123 1


The common toad Rhinella arenarum is widely distributed in Argentina, where it is utilised as an autochthonous model in ecotoxicological research and environmental toxicology. However, the lack of a reference genome makes molecular assays and gene expression studies difficult to carry out on this non-model species. To address this issue, we performed a genome-wide transcriptome analysis on R. arenarum larvae through massive RNA sequencing, followed by de novo assembly, annotation, and gene predi  ...[more]

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