Deep transcriptome sequencing of rhizome and aerial-shoot
in Sorghum propinquum
Received: 21 March 2013 / Accepted: 23 September 2013 / Published online: 9 October 2013
Ó Springer Science+Business Media Dordrecht 2013
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 tran-
scriptome 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 ROOT-
MOTIFTAPOX1 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 rhi-
zome-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 tran-
scriptome 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 Á Transcriptome Á
Illumina sequencing Á Aerial-shoot Á Rhizome
QTLs Quantitative trait loci
ESTs Expressed sequence tags
PEG Polyethylene glycol
TF Transcription factor
RPKM Reads per kilobase of exon region per million
ARFs Auxin responsive factors
LOB Lateral organ boundaries
AS Alternative splicing
ES Exon skipping
IR Intron retention
A5SS Alternative 5
A3SS Alternative 3
GO Gene ontology
ddCt Delta–delta Ct
Ting Zhang and Xiuqin Zhao have contributed equally to this work.
Electronic supplementary material The online version of this
article (doi:10.1007/s11103-013-0135-z) contains supplementary
material, which is available to authorized users.
T. Zhang Á X. Zhao Á W. Wang Á L. Huang Á X. Liu Á Y. Zong Á
L. Zhu Á B. Fu (&) Á Z. Li (&)
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
T. Zhang Á D. Yang
State Key Laboratory of Hybrid Rice, College of Life Sciences,
Wuhan University, Wuhan 430072, China
Plant Mol Biol (2014) 84:315–327