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The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction
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 no...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6978513/ https://www.ncbi.nlm.nih.gov/pubmed/31974515 http://dx.doi.org/10.1038/s41598-020-57961-4 |
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author | Ceschin, Danilo Guillermo Pires, Natalia Susana Mardirosian, Mariana Noelia Lascano, Cecilia Inés Venturino, Andrés |
author_facet | Ceschin, Danilo Guillermo Pires, Natalia Susana Mardirosian, Mariana Noelia Lascano, Cecilia Inés Venturino, Andrés |
author_sort | Ceschin, Danilo Guillermo |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6978513 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-69785132020-01-30 The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction Ceschin, Danilo Guillermo Pires, Natalia Susana Mardirosian, Mariana Noelia Lascano, Cecilia Inés Venturino, Andrés Sci Rep Article 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. Nature Publishing Group UK 2020-01-23 /pmc/articles/PMC6978513/ /pubmed/31974515 http://dx.doi.org/10.1038/s41598-020-57961-4 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Ceschin, Danilo Guillermo Pires, Natalia Susana Mardirosian, Mariana Noelia Lascano, Cecilia Inés Venturino, Andrés The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction |
title | The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction |
title_full | The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction |
title_fullStr | The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction |
title_full_unstemmed | The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction |
title_short | The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction |
title_sort | rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6978513/ https://www.ncbi.nlm.nih.gov/pubmed/31974515 http://dx.doi.org/10.1038/s41598-020-57961-4 |
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