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 difcult to carry out on this non-...

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Autores principales: Ceschin, Danilo Guillermo, Pires, Natalia Susana, Mardirosian, Mariana Noelia, Lascano, Cecilia Inés, Venturino, Andres
Formato: Artículo article acceptedVersion
Lenguaje:Inglés
Publicado: Nature Research 2020
Materias:
Rhinella arenarum
Ecotoxicology
Gene prediction
Transcriptome
Ciencias Puras
Acceso en línea:http://rdi.uncoma.edu.ar/handle/uncomaid/17000
Aporte de:
Repositorio Institucional UNCo de Universidad Nacional del Comahue
id I22-R178-uncomaid-17000
record_format dspace
spelling I22-R178-uncomaid-170002023-10-06T16:08:55Z The Rhinella arenarum transcriptome : de novo assembly, annotation and gene prediction Ceschin, Danilo Guillermo Pires, Natalia Susana Mardirosian, Mariana Noelia Lascano, Cecilia Inés Venturino, Andres Rhinella arenarum Ecotoxicology Gene prediction Transcriptome Ciencias Puras 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 difcult 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 defned a set of 52,800 highconfdence 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. Fil: Ceschin, Danilo Guillermo. Universidad Nacional del Comahue. Facultad de Ciencias Agrarias; Argentina. Fil: Ceschin, Danilo Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue. Instituto de Biotecnología Agropecuaria del Comahue; Argentina. Fil: Ceschin, Danilo Guillermo. Instituto Universitario de Ciencias Biomédicas de Córdoba; Argentina. Fil: Pires, Natalia Susana. Universidad Nacional del Comahue. Facultad de Ciencias Agrarias; Argentina. Fil: Pires, Natalia Susana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue. Instituto de Biotecnología Agropecuaria del Comahue; Argentina. Fil: Mardirosian, Mariana Noelia. Universidad Nacional del Comahue. Facultad de Ciencias Agrarias; Argentina. Fil: Mardirosian, Mariana Noelia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue. Instituto de Biotecnología Agropecuaria del Comahue; Argentina. Fil: Lascano, Cecilia Inés. Universidad Nacional del Comahue. Facultad de Ciencias Agrarias; Argentina. Fil: Lascano, Cecilia Inés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue. Instituto de Biotecnología Agropecuaria del Comahue; Argentina. Fil: Venturino, Andres. Universidad Nacional del Comahue. Facultad de Ciencias Agrarias; Argentina. Fil: Venturino, Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue. Instituto de Biotecnología Agropecuaria del Comahue; Argentina. 2020-12 2023-03-06T13:50:17Z 2023-03-06T13:50:17Z Artículo article acceptedVersion 2045-2322 http://rdi.uncoma.edu.ar/handle/uncomaid/17000 eng https://www.nature.com/articles/s41598-020-57961-4 https://ri.conicet.gov.ar/bitstream/handle/11336/114350/CONICET_Digital_Nro.4c35a576-7e65-4b06-b437-84a7fe869419_A.pdf?sequence=2&isAllowed=y Atribución-NoComercial-CompartirIgual 2.5 Argentina https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ application/pdf pp. 1-8 application/pdf Nature Research Scientific Reports. Vol. 10 Núm. 1053 (2020)
institution Universidad Nacional del Comahue
institution_str I-22
repository_str R-178
collection Repositorio Institucional UNCo
language Inglés
topic Rhinella arenarum
Ecotoxicology
Gene prediction
Transcriptome
Ciencias Puras
spellingShingle Rhinella arenarum
Ecotoxicology
Gene prediction
Transcriptome
Ciencias Puras
Ceschin, Danilo Guillermo
Pires, Natalia Susana
Mardirosian, Mariana Noelia
Lascano, Cecilia Inés
Venturino, Andres
The Rhinella arenarum transcriptome : de novo assembly, annotation and gene prediction
topic_facet Rhinella arenarum
Ecotoxicology
Gene prediction
Transcriptome
Ciencias Puras
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 difcult 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 defned a set of 52,800 highconfdence 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 Artículo
article
acceptedVersion
author Ceschin, Danilo Guillermo
Pires, Natalia Susana
Mardirosian, Mariana Noelia
Lascano, Cecilia Inés
Venturino, Andres
author_facet Ceschin, Danilo Guillermo
Pires, Natalia Susana
Mardirosian, Mariana Noelia
Lascano, Cecilia Inés
Venturino, Andres
author_sort Ceschin, Danilo Guillermo
title 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_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_sort rhinella arenarum transcriptome : de novo assembly, annotation and gene prediction
publisher Nature Research
publishDate 2020
url http://rdi.uncoma.edu.ar/handle/uncomaid/17000
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