Abstract
In order to perform a well-balanced comparative transcriptomic analysis, the reference genome and annotations for all species included in the comparison must be of a similar quality and completeness. Frequently, comparative transcriptomic analyses include non-model organisms whose annotations are not as well curated; this inequality can lead to biases.
To avoid potential biases stemming from incomplete annotations, a comparative transcriptomic analysis can incorporate de novo transcriptome assemblies for each species, which reduces this disparity. This chapter covers all of the steps which are necessary to run a comparative transcriptomic analysis with de novo transcriptome assemblies, from the first step of the experimental design to the sequencing, and ultimately the bioinformatic analysis.
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Acknowledgments
This work was made possible by several grants including PGC2018- 094091-B-I00, BFU2015-65235-P, BFU2015-68351-P, BFU2016-80039-R, TIN2015-69175-C4-3-R, and RTI2018-094403-B-C33 from the Spanish Government FEDER (EU), as well as PT17/0009/0014 from the Instituto de Salud Carlos III. We also received support from grants 014SGR1121, 2014SGR0974, 2017SGR1054, and 2017SGR01020 from the Agència de Gestió d’Ajuts Universitaris i de Recerca Generalitat de Catalunya (AGAUR), and MDM-2014-0370 from the “Maria de Maeztu” Program for Units of Excellence in R&D.
We would like to thank Dr. Ksenia Pugach and the Verstrepen lab for donating cultures of several species of yeast. We also thank the sequencing facilities of the Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra (UPF) for their contributions.
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Blevins, W.R. (2022). Identification of Taxonomically Restricted Transcripts from Illumina RNA Sequencing Data. In: Devaux, F. (eds) Yeast Functional Genomics. Methods in Molecular Biology, vol 2477. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2257-5_7
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