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

Huang J, Youjun G, Haitao J, Zhang Z

Date Published: March 1, 2016

DOI: http://dx.doi.org/10.5061/dryad.87r18

 

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Title Teosinte unigenes' sequences
Downloaded 22 times
Description Due 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.
Download Teosinte.fasta (79.37 Mb)
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Title Zea mays ssp. parviglumis unigenes' sequences
Downloaded 12 times
Description Due 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 <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.
Download Zea_mays_parviglumis.fasta (50.68 Mb)
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Title Zea mays ssp. mexicana unigenes'sequences
Downloaded 16 times
Description Due 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 <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.
Download Zea_mays_mexicana.fasta (57.50 Mb)
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Title Annotation information of teosinte unigenes
Downloaded 51 times
Description Functional annnotation was conducted using InterProScan against Pfam database.
Download Teosinte_annotation.txt (2.876 Mb)
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When using this data, please cite the original publication:

Huang J, Youjun G, Haitao J, Zhang Z (2016) Characterization of the teosinte transcriptome reveals adaptive sequence divergence during maize domestication. Molecular Ecology Resources 16(6): 1465–1477. http://dx.doi.org/10.1111/1755-0998.12526

Additionally, please cite the Dryad data package:

Huang J, Youjun G, Haitao J, Zhang Z (2016) Data from: Characterization of the teosinte transcriptome reveals adaptive sequence divergence during maize domestication. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.87r18
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