Characterization of the teosinte transcriptome reveals adaptive sequence divergence during maize domestication

Annual teosinte, the ancestor of cultivated maize (Zea mays ssp. mays), is a valuable germplasm for enhancing the genetic diversity and adaptability of maize to various environment stimuli. However, comprehensive transcriptomic and genomic resources are unavailable in public databases, which significantly impede the identification and utilization of favourable genes or alleles in teosinte. In this study, we globally sequenced the transcriptomes of six teosinte accessions by Illumina paired-end sequencing. A high-quality teosinte transcriptome was de novo assembled with an average length of 770 bp and 63.99% of annotated unigenes. We found approximately 75% of the genes were highly conserved between maize and teosinte. Moreover, we also found 1516 unigenes were specifically expressed in teosinte, of which 84 unigenes were supported by gene models of four plant species, and 571 unigenes were located in the intergenic regions of maize genome, showing evidence-based expressed presence/absence variations (ePAVs). Furthermore, we also identified 99 unigenes with strong selection signals and 57 unigenes with >1 Ka/Ks ratios, suggesting that these genes might be under strong selection during maize domestication and improvement. Additionally, 11 286 teosinte unigene-derived primer pairs were developed for amplifying simple sequence repeat (SSR) loci. This study provides a comprehensive transcriptome of teosinte, a subset of genes that are highly conserved or diverged during maize domestication and improvement, and a massive set of available SSR primer pairs. These results facilitate the investigation of the comparative genomics and molecular domestication of teosinte and the utilization of teosinte germplasm for maize improvement.