Plant Molecular Biology

, Volume 84, Issue 3, pp 315–327 | Cite as

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

  • Ting Zhang
  • Xiuqin Zhao
  • Wensheng Wang
  • Liyu Huang
  • Xiaoyue Liu
  • Ying Zong
  • Linghua Zhu
  • Daichang Yang
  • Binying Fu
  • Zhikang Li
Article
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Accepted:

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.

Keywords

Sorghum propinquum Transcriptome Illumina sequencing Aerial-shoot Rhizome 

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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Notes

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).

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Ting Zhang
    • 1
    • 2
  • Xiuqin Zhao
    • 1
  • Wensheng Wang
    • 1
  • Liyu Huang
    • 1
  • Xiaoyue Liu
    • 1
  • Ying Zong
    • 1
  • Linghua Zhu
    • 1
  • Daichang Yang
    • 2
  • Binying Fu
    • 1
  • Zhikang Li
    • 1
  1. 1.Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic ImprovementChinese Academy of Agricultural SciencesBeijingChina
  2. 2.State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina

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