DOI: 10.5061/dryad.87r18
title: Data from: Characterization of the teosinte transcriptome reveals adaptive sequence divergence during maize domestication

description: 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 &gt;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.
description: Teosinte unigenes'
 sequencesDue to the lack of
 available reference genome, clean reads from Zea may ssp. parviglumis and
 Zea mays ssp. mexicana were first de novo assembled into contigs using
 Trans-ABySS, which can use a multiple K-mer strategy to assemble the
 transcriptome. After that, transcriptome from different samples were
 pooled to reconstruct the transcriptome using CD-HIT-EST with a word
 length of 8 and an identity threshold ≥ 0.98.Sequentially, CAP3 was used
 to discard the redundancy transcripts, and the resulting contigs and
 singlets were combined to represent transcriptome of
 teosinte.Teosinte.fastaZea mays ssp. parviglumis unigenes' sequencesDue to lack of available reference genome, clean reads from 3 Zea mays ssp. parviglumis were first de novo assembled into contigs using Trans-ABySS. After discarding the contigs &lt;200 bp, the remaing contigs were then assembled into unigenes, whcih represented the individual transcriptome at the seedling stage. To obtain the transcriptomes from Zea mays ssp. parviglumis, individual transcriptomes were pooled to reconstruct the transcriptome using CD-HIT-EST with a word length of 8 and an identity threshold ≥ 0.98. Sequentially, CAP3 was used to discard the redundancy transcripts, and the resulting contigs and singlets were combined to represent Zea mays ssp. parviglumis transcriptome.Zea_mays_parviglumis.fastaZea mays ssp. mexicana unigenes'sequencesDue to lack of available reference genome, clean reads from 3 Zea mays ssp. mexicana were first de novo assembled into contigs using Trans-ABySS. After discarding the contigs &lt;200 bp, the remaing contigs were then assembled into unigenes, whcih represented the individual transcriptome at the seedling stage. To obtain the transcriptomes from Zea mays ssp. mexicana, individual transcriptomes were pooled to reconstruct the transcriptome using CD-HIT-EST with a word length of 8 and an identity threshold ≥ 0.98. Sequentially, CAP3 was used to discard the redundancy transcripts, and the resulting contigs and singlets were combined to represent Zea mays ssp. mexicana transcriptome.Zea_mays_mexicana.fastaAnnotation information of teosinte unigenesFunctional annnotation was conducted using InterProScan against Pfam database.Teosinte_annotation.txt