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.

一年生大刍草（teosinte）是栽培玉米（Zea mays ssp. mays）的祖先物种，是提升玉米遗传多样性并增强其对各类环境刺激适应性的宝贵种质资源。然而，目前公共数据库中尚未收录完整的大刍草转录组与基因组资源，这极大阻碍了对大刍草中优良基因或等位变异的挖掘与利用。本研究通过Illumina双端测序技术，对6份大刍草材料的转录组进行了全局测序。我们从头组装获得了高质量的大刍草转录组，其平均序列长度为770 bp，注释单基因簇（unigene）的比例达63.99%。研究发现，约75%的基因在玉米与大刍草之间呈现高度保守性。此外，我们还鉴定出1516个大刍草特异性表达的单基因簇，其中84个单基因簇得到4种植物基因模型的支持，另有571个单基因簇定位于玉米基因组的基因间区，这表明存在基于实验证据的表达型存在/缺失变异（ePAVs）。进一步地，我们还鉴定出99个携带强选择信号的单基因簇，以及57个Ka/Ks比值大于1的单基因簇，这表明这些基因可能在玉米驯化与遗传改良过程中受到了强烈的正向选择。此外，本研究还开发了11286个大刍草单基因簇来源的引物对，用于扩增简单序列重复（simple sequence repeat, SSR）位点。本研究构建了完整的大刍草转录组资源，筛选得到了在玉米驯化与改良过程中呈现高度保守或显著分化的基因子集，并提供了大量可用的SSR引物对。本研究结果将有助于推动大刍草比较基因组学与分子驯化机制研究，同时为利用大刍草种质资源开展玉米遗传改良提供重要支撑。