Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds
Wilhelmsson PKI, Chandler JO, Fernandez-Pozo N, Graeber K, Ullrich KK, Arshad W, Khan S, Hofberger JA, Buchta K, Edger PP, Pires JC, Schranz ME, Leubner-Metzger G, Rensing SA.
BMC Genomics. 2019 Jan 30;20(1):95.
RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. A de novo transcriptome assembly was generated using sequences from M+ and NM Ae. arabicum dry seed morphs and contrasted with genomic data. Whilst there was only modest overlap of DEGs identified in reference-free versus -dependent approaches, the resulting GO analysis was concordant in both approaches.
