Data from: 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.