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

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The Rhinella arenarum transcriptome: de novo assembly, annotation and gene prediction.
Scientific Reports ( IF 3.8 ) Pub Date : 2020-01-23 , DOI: 10.1038/s41598-020-57961-4
Danilo Guillermo Ceschin _{1,

2} , Natalia Susana Pires ₁ , Mariana Noelia Mardirosian ₁ , Cecilia Inés Lascano ₁ , Andrés Venturino ₁

Affiliation

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.

中文翻译：

Rhinella arenarum 转录组：从头组装、注释和基因预测。

普通蟾蜍Rhinella arenarum广泛分布于阿根廷，被用作生态毒理学研究和环境毒理学的本土模型。然而，缺乏参考基因组使得分子测定和基因表达研究难以在这种非模式物种上进行。为了解决这个问题，我们通过大规模 RNA 测序对沙蚕幼虫进行了全基因组转录组分析，然后进行从头组装、注释和基因预测。我们获得了 57,407 个注释良好的转录本，代表了 99.4% 的转录组完整性（可在 http://rhinella.uncoma.edu.ar 获取）。我们还定义了一组 52,800 个高可信度 lncRNA 转录本，并证明了转录组数据进行系统发育分析的可靠性。我们对沙粒菌的全面转录组分析是进行功能基因组研究和识别生态毒理学研究中潜在分子生物标志物的宝贵资源。

更新日期：2020-01-23

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