Usability of reference-free transcriptome assemblies for detection of 
differential expression: a case study on Aethionema arabicum dimorphic seeds

Wilhelmsson, Per K. I.; Chandler, Jake O.; Fernandez-Pozo, Noe; Graeber, Kai; Ullrich, Kristian K.; Arshad, Waheed; Khan, Safina; Hofberger, Johannes A.; Buchta, Karl; Edger, Patrick P.; Pires, J. Chris; Schranz, M. Eric; Leubner-Metzger, Gerhard; Rensing, Stefan A.

doi:10.1186/s12864-019-5452-4

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Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds

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Ullrich, Kristian K.
Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Citation

Wilhelmsson, P. K. I., Chandler, J. O., Fernandez-Pozo, N., Graeber, K., Ullrich, K. K., Arshad, W., et al. (2019). Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds. BMC Genomics, 20: 95. doi:10.1186/s12864-019-5452-4.

Cite as: https://hdl.handle.net/21.11116/0000-0002-F579-2

Abstract

RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy – producing both a less dormant mucilaginous (M+) seed morph and a more dormant non-mucilaginous (NM) seed morph. Here, we compared de novo and reference-genome based transcriptome assemblies to investigate Ae. arabicum seed dimorphism and to evaluate the reference-free versus -dependent approach for identifying differentially expressed genes (DEGs).