| Description |
Genes have the ability to produce transcript variants that perform specific cellular functions. However, accurately detecting all transcript variants remains a long-standing challenge, especially when working with poorly annotated genomes or without a known genome. To address this issue, we have developed a new computational method, TransIntegrator, that enables transcriptome-wide detection of novel transcript variants. In this study, we utilized TransIntegrator to integrate ten Illumina sequencing transcriptomes and one PacBio sequencing transcriptome to compile an integrative transcript variant library for the amphioxus, an evolutionarily significant species with a draft genome. The resulting iTrancriptome contained 91,915 distinct transcript variants, with an average of 2.4 variants per gene. This substantially improved the current amphioxus genome annotation by expanding the number of genes from 21,954 to 38,777. Moreover, we demonstrated that the iTrancriptome can serve as a reliable alternative genomic reference for aiding accurate transcriptome assembly. For user convenience, we have deposited the source codes of TransIntegrator on GitHub and made the iTrancriptome for the amphioxus available at http://www.bio-add.org/InTrans/. In summary, this study proposes a comprehensive method to capture all transcript variants for a given species and provides an efficient and cost-effective solution for reliable transcriptomic research in most species. |
