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

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Abstract

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 cytokinin-responsive 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.

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Abbreviations

QTLs:

Quantitative trait loci

ESTs:

Expressed sequence tags

PEG:

Polyethylene glycol

TF:

Transcription factor

Gb:

Gigabases

RPKM:

Reads per kilobase of exon region per million mapped reads

ARFs:

Auxin responsive factors

LOB:

Lateral organ boundaries

AS:

Alternative splicing

ES:

Exon skipping

IR:

Intron retention

A5SS:

Alternative 5′ splicing site

A3SS:

Alternative 3′ splice site

GO:

Gene ontology

ddCt:

Delta–delta Ct

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Acknowledgments

This work was supported by the Key Project from the Ministry of Agriculture (Grant Nos. 2011ZX08001–003) and the National Natural Science Foundation of China (Grant No. U0836605).

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The authors declare that they have no competing interests.

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Authors and Affiliations

  1. Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun St., Beijing, 100081, China

    Ting Zhang, Xiuqin Zhao, Wensheng Wang, Liyu Huang, Xiaoyue Liu, Ying Zong, Linghua Zhu, Binying Fu & Zhikang Li

  2. State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China

    Ting Zhang & Daichang Yang

Authors
  1. Ting Zhang
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  2. Xiuqin Zhao
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  3. Wensheng Wang
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  4. Liyu Huang
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  5. Xiaoyue Liu
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  6. Ying Zong
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  7. Linghua Zhu
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  8. Daichang Yang
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  9. Binying Fu
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  10. Zhikang Li
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Corresponding authors

Correspondence to Binying Fu or Zhikang Li.

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Ting Zhang and Xiuqin Zhao have contributed equally to this work.

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Zhang, T., Zhao, X., Wang, W. et al. Deep transcriptome sequencing of rhizome and aerial-shoot in Sorghum propinquum . Plant Mol Biol 84, 315–327 (2014). https://doi.org/10.1007/s11103-013-0135-z

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  • DOI: https://doi.org/10.1007/s11103-013-0135-z

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