Genome-wide annotation of genes and noncoding RNAs of foxtail
millet in response to simulated drought stress by deep sequencing
Xin Qi
•
Shaojun Xie
•
Yuwei Liu
•
Fei Yi
•
Jingjuan Yu
Received: 22 February 2013 / Accepted: 2 July 2013 / Published online: 17 July 2013
Ó Springer Science+Business Media Dordrecht 2013
Abstract Drought is a major abiotic stress that affects
plant growth, production, and survival. Plants have evolved
sophisticated and highly complex reactions to drought
stress, including large-scale transcriptome reconfiguration.
Foxtail millet (Setaria italica) is a member of the Poaceae
family. Because of its outstanding tolerance to drought
stress foxtail millet has the potential to become a new
model organism. To enrich our knowledge of the processes
that contribute to drought resistance, we have used a deep
sequencing approach to generate a genome-wide tran-
scriptome of foxtail millet after exposure to simulated
drought stress. A large number of differentially expressed
genes were characterized; in particular, we examined the
roles of small interfering RNAs (siRNAs) and long
noncoding RNAs (lncRNAs) in response to a water-deficit
condition. These RNAs have remained largely unexplored
in previous studies of stress-induced transcriptomes. We
found that the reduced levels of 24-nt siRNA flanking
genes were associated, for the most part, with proximal up-
regulated genes, indicating a potential effect of 24-nt siR-
NAs on drought-regulated gene expression. Several lncR-
NAs that responded to the simulated drought stress were
also identified, and we found that one of them shared
sequence conservation and colinearity with its counterpart
in sorghum (Sorghum bicolor). Our findings provide new
insights into drought-induced changes in the foxtail millet
transcriptome.
Keywords Drought stress Á Foxtail millet Á
Transcriptome Á siRNA Á Long noncoding RNA
Introduction
Plants are sessile organisms that are constantly challenged
by a wide range of environmental stresses. Drought is one
of the most severe abiotic stresses that adversely affect
crop growth and productivity (Boyer 1982). Crops respond
and adapt to these stresses through complex but integrated
biochemical and physiological processes (Shinozaki et al.
2003) that include altered gene expression levels, cellular
metabolic rate, and regulation pathways, thus acquiring
resistance. To improve crop performance and productivity
in water-limited regions of the world, numerous studies
have been conducted to investigate the drought-responsive
transcriptome and regulatory networks in several plant
species, including Arabidopsis (Seki et al. 2002; Zeller
et al. 2009; Wilkins et al. 2010), rice (Zhou et al. 2007;
Lenka et al. 2011), sorghum (Dugas et al. 2011), wheat
Accession numbers of sequence data: SRA062640, SRA062827.
Xin Qi, Shaojun Xie and Yuwei Liu have contributed equally to this
work.
Electronic supplementary material The online version of this
article (doi:10.1007/s11103-013-0104-6) contains supplementary
material, which is available to authorized users.
X. Qi Á S. Xie Á Y. Liu Á F. Yi Á J. Yu (&)
State Key Laboratory for Agrobiotechnology, College of
Biological Sciences, China Agricultural University,
No. 2 Yuanmingyuan West Road, Beijing 100193, China
e-mail: yujj@cau.edu.cn
X. Qi
e-mail: qixin@cau.edu.cn
S. Xie
e-mail: xieshaojun0621@cau.edu.cn
Y. Liu
e-mail: liuyw@cau.edu.cn
F. Yi
e-mail: yifei56@cau.edu.cn
123
Plant Mol Biol (2013) 83:459–473
DOI 10.1007/s11103-013-0104-6