Technological innovations in transcriptome sequencing, such as single-cell and spatial transcriptomics, have been progressing rapidly. These emerging techniques allow us to comprehensively characterize omics states, including gene expression patterns in cells under diverse conditions. During these analyses, the obtained transcript sequences are mapped to a reference genome that contains detailed functional information on gene structures, potential splice variants and other elements, which aids in the interpretation of data.

The foundations of transcriptome analysis can be traced back to full-length cDNA analysis in the early 2000s, which was driven by the development of specific methods that enabled full-length cDNA sequencing and the transcript and gene structure reference catalogues that these methods helped build. Earlier cDNA projects generated shorter cDNA sequences. However, to assign functional annotations to the reference genome, it was necessary to identify full-length RNA transcripts produced from the genome and infer the proteins they encoded.