Fig. 1

Schematic of the de novo transcriptome reconstruction and analysis pipeline. The pipeline consists of 5 steps. a Data generation: Multiple tissues are extracted from R. aegyptiacus and sequenced. b De novo Transcriptome assembly: Individual samples are first preprocessed to remove adapter sequences and assembled into contigs de novo. c MSA annotation: Once the set of contigs is generated, they are annotated using BLAST against three databases. In each step, unannotated contigs are iteratively annotated using the downstream databases. d Mering and Expression studies: A nonredundant contig set is obtained by merging the contig set of individual tissues two at a time. This pairwise merging is repeated until only one contig set is left. The subset of this contig can be obtained for the downstream analysis such as gene expression analysis by taking the transcripts with gene symbol and ORF sequence. See Fig. 2 for details. e Discovery of Novel Coding Transcripts: Novel coding transcripts can be identified by searching for contigs that failed annotation in the previous steps. Various metrics can be applied to generate high confidence novel coding transcript candidates