Elucidating transcriptional regulation of the genes in exotic plant species using de novo transcriptome assembly

P. K. LIM & M. MUTWIL

School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore

Studying gene function and expression in plant species lacking genomes poses a significant challenge despite the abundance of transcriptomic data available. To address this issue, we developed the Large-Scale Transcriptome Assembly Pipeline for de novo assembled transcripts (LSTrAP-denovo) that automatically generates transcriptome atlases of eukaryotic species. LSTrAP-denovo filters undesirable RNA-seq accessions, selects RNA-seq accessions via unsupervised machine-learning to construct a sample-balanced dataset, assembles transcripts via over-assembly, functionally annotates coding sequences, and generates transcriptome atlases for downstream transcriptomic analyses. In this study, we applied this pipeline to exotic plant species and successfully generated the first-ever transcriptome atlases. By utilizing LSTrAP-denovo, we were able to gain functional insights and elucidate transcriptional regulation of the genes in these species, highlighting the power and versatility of our pipeline.