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Article

Evaluation of Seven Different RNA-Seq Alignment Tools Based on Experimental Data from the Model Plant Arabidopsis thaliana

Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
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Int. J. Mol. Sci. 2020, 21(5), 1720; https://doi.org/10.3390/ijms21051720
Received: 30 January 2020 / Revised: 28 February 2020 / Accepted: 29 February 2020 / Published: 3 March 2020
(This article belongs to the Section Molecular Informatics)
Quantification of gene expression is crucial to connect genome sequences with phenotypic and physiological data. RNA-Sequencing (RNA-Seq) has taken a prominent role in the study of transcriptomic reactions of plants to various environmental and genetic perturbations. However, comparative tests of different tools for RNA-Seq read mapping and quantification have been mainly performed on data from animals or humans, which necessarily neglect, for example, the large genetic variability among natural accessions within plant species. Here, we compared seven computational tools for their ability to map and quantify Illumina single-end reads from the Arabidopsis thaliana accessions Columbia-0 (Col-0) and N14. Between 92.4% and 99.5% of all reads were mapped to the reference genome or transcriptome and the raw count distributions obtained from the different mappers were highly correlated. Using the software DESeq2 to determine differential gene expression (DGE) between plants exposed to 20 °C or 4 °C from these read counts showed a large pairwise overlap between the mappers. Interestingly, when the commercial CLC software was used with its own DGE module instead of DESeq2, strongly diverging results were obtained. All tested mappers provided highly similar results for mapping Illumina reads of two polymorphic Arabidopsis accessions to the reference genome or transcriptome and for the determination of DGE when the same software was used for processing. View Full-Text
Keywords: Arabidopsis thaliana; differential gene expression; natural genetic variation; read mapping tools; RNA-Seq Arabidopsis thaliana; differential gene expression; natural genetic variation; read mapping tools; RNA-Seq
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MDPI and ACS Style

Schaarschmidt, S.; Fischer, A.; Zuther, E.; Hincha, D.K. Evaluation of Seven Different RNA-Seq Alignment Tools Based on Experimental Data from the Model Plant Arabidopsis thaliana. Int. J. Mol. Sci. 2020, 21, 1720. https://doi.org/10.3390/ijms21051720

AMA Style

Schaarschmidt S, Fischer A, Zuther E, Hincha DK. Evaluation of Seven Different RNA-Seq Alignment Tools Based on Experimental Data from the Model Plant Arabidopsis thaliana. International Journal of Molecular Sciences. 2020; 21(5):1720. https://doi.org/10.3390/ijms21051720

Chicago/Turabian Style

Schaarschmidt, Stephanie; Fischer, Axel; Zuther, Ellen; Hincha, Dirk K. 2020. "Evaluation of Seven Different RNA-Seq Alignment Tools Based on Experimental Data from the Model Plant Arabidopsis thaliana" Int. J. Mol. Sci. 21, no. 5: 1720. https://doi.org/10.3390/ijms21051720

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