Deep transcriptome sequencing of rhizome and aerial-shoot in Sorghum propinquum

文献类型： 外文期刊

第一作者： Zhang, Ting

作者： Zhang, Ting;Zhao, Xiuqin;Wang, Wensheng;Huang, Liyu;Liu, Xiaoyue;Zong, Ying;Zhu, Linghua;Fu, Binying;Li, Zhikang;Zhang, Ting;Yang, Daichang

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关键词： Sorghum propinquum;Transcriptome;Illumina sequencing;Aerial-shoot;Rhizome

期刊名称：PLANT MOLECULAR BIOLOGY （ 影响因子：4.076； 五年影响因子：4.89 ）

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收录情况： SCI

摘要： Transcriptomic data for Sorghum propinquum, the wild-type sorghum, are limited in public databases. S. propinquum has a subterranean rhizome and transcriptome data will help in understanding the molecular mechanisms underlying rhizome formation. We sequenced the transcriptome of S. propinquum aerial-shoot and rhizome using an Illumina platform. More than 70 % of the genes in the S. propinquum genome were expressed in aerial-shoot and rhizome. The expression patterns of 1963 and 599 genes, including transcription factors, were specific or enriched in aerial-shoot and rhizome respectively, indicating their possible roles in physiological processes in these tissues. Comparative analysis revealed several cis-elements, ACGT box, GCCAC, GATC and TGACG box, which showed significantly higher abundance in aerial-shoot-specific genes. In rhizome-specific genes MYB and ROOTMOTIFTAPOX1 motifs, and 10 promoter and cytokininresponsive elements were highly enriched. Of the S. propinquum genes, 27.9 % were identified as alternatively spliced and about 60 % of the alternative splicing (AS) events were tissue-specific, suggesting that AS played a crucial role in determining tissue-specific cellular function. The transcriptome data, especially the co-localized rhizome- enriched expressed transcripts that mapped to the publicly available rhizome-related quantitative trait loci, will contribute to gene discovery in S. propinquum and to functional studies of the sorghum genome. Deep transcriptome sequencing revealed a clear difference in the expression patterns of genes between aerial-shoot and rhizome in S. propinquum. This data set provides essential information for future studies into the molecular genetic mechanisms involved in rhizome formation.

分类号： Q946

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