Here, we employed single-molecule long-read sequencing of cDNA libraries from five tissues of the teosinte inbred line TIL11 and identified 70,044 non-redundant transcript isoforms. 23,527 predicted genes were identified using our state-of-the-art, machine learning-based bioinformatics pipeline DenovoAS_Finder without a complete reference genome. Additionally, we constructed a draft TIL11 genome based on a Nanopore sequencing dataset with 16,633 high-quality contigs and a N50 of 112 kb.