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Molecular Genetics and Genomics (2018) 293:1017–1033
https://doi.org/10.1007/s00438-018-1456-z
ORIGINAL ARTICLE
Widespread antisense transcription of Populus genome under drought
Yinan Yuan
1
· Su Chen
1
Received: 1 November 2017 / Accepted: 31 May 2018 / Published online: 6 June 2018
© Springer-Verlag GmbH Germany, part of Springer Nature 2018
Abstract
Antisense transcription is widespread in many genomes and plays important regulatory roles in gene expression. The objec-
tive of our study was to investigate the extent and functional relevance of antisense transcription in forest trees. We employed
Populus, a model tree species, to probe the antisense transcriptional response of tree genome under drought, through stranded
RNA-seq analysis. We detected nearly 48% of annotated Populus gene loci with antisense transcripts and 44% of them with
co-transcription from both DNA strands. Global distribution of reads pattern across annotated gene regions uncovered that
antisense transcription was enriched in untranslated regions while sense reads were predominantly mapped in coding exons.
We further detected 1185 drought-responsive sense and antisense gene loci and identified a strong positive correlation
between the expression of antisense and sense transcripts. Additionally, we assessed the antisense expression in introns and
found a strong correlation between intronic expression and exonic expression, confirming antisense transcription of introns
contributes to transcriptional activity of Populus genome under drought. Finally, we functionally characterized drought-
responsive sense–antisense transcript pairs through gene ontology analysis and discovered that functional groups including
transcription factors and histones were concordantly regulated at both sense and antisense transcriptional level. Overall, our
study demonstrated the extensive occurrence of antisense transcripts of Populus genes under drought and provided insights
into genome structure, regulation pattern and functional significance of drought-responsive antisense genes in forest trees.
Datasets generated in this study serve as a foundation for future genetic analysis to improve our understanding of gene
regulation by antisense transcription.
Keywords Stranded RNA-seq analysis · Populus genome · Antisense transcripts · Functional characterization · Drought
Introduction
Drought is a major environmental constraint affecting the
growth and productivity of plants including forest trees.
The frequent and high intensity of drought worldwide in
recent years has strained forests, and in worst scenario,
led to massive tree death in numerous regions (Allen et al.
2010; Peng et al. 2011). Trees have evolved various response
mechanisms including molecular changes at genome-wide
level to cope with drought (Ryan 2011; Brunner et al. 2015;
Viger et al. 2016). In response to stress tree genomes tran-
scribe large quantity of drought-inducible gene products
including transcription factors, to initiate stress response
through transcriptional regulation mechanisms and even-
tually establish drought tolerance at cellular level (Street
et al. 2006; Chen et al. 2013). To understand the molecular
mechanism of trees responding to drought, it is essential
to characterize drought-induced transcriptome and identify
drought-responsive gene loci for further genetic manipula-
tion to improve the drought tolerance of forest trees.
Tree genus of Populus is a model organism to study the
transcriptional response of forest trees under drought, own-
ing to its sequenced genome and the availability of rich
genetic resources (Tuskan et al. 2006; Hamanishi et al.
2010; Viger et al. 2016). Poplar trees are grown world-
wide largely for wood-based products and in recent years
are also grown extensively as bioenergy crops for biofuel
Communicated by S. Hohmann.
Electronic supplementary material The online version of this
article (https ://doi.org/10.1007/s0043 8-018-1456-z) contains
supplementary material, which is available to authorized users.
* Yinan Yuan
yinyuan@mtu.edu
1
School of Forest Resources and Environmental Science,
Michigan Technological University, Houghton, MI 49931,
USA
@Phil_Robichaud
@deepthiw
@JoseServera