Cotton Genomics and Genetics 2016, Vol.7, No.2, 1-23
1
Research Article Open Access
Comparative miRNAome Analysis Revealed Numerous Conserved and Novel
Drought Responsive miRNAs in Cotton (
Gossypium
spp.)
Boopathi M.N.
1,2
Sathish S.
1
Kavitha P.
1
Dachinamoorthy P.
1
Ravikesavan R.
3
1 Department of Plant Molecular Biology and Bioinformatics, Center for Plant Molecular Biology and Biotechnology, India
2 Department of Fruit Crops, Horticultural College and Research Institute, TNAU, Periyakulam, 625604, India
3 Department of Millets, CPBG, Tamil Nadu Agricultural University (TNAU), Coimbatore, 641003, India
Corresponding Author
Cotton Genomics and Genetics, 2016, Vol.7, No.2
doi
Received: 15 Apr., 2016
Accepted: 15 May, 2016
Published: 19 May, 2016
Copyright © 2016 Boopathi et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:
Boopathi M.N., Sathish S., Kavitha P., Dachinamoorthy P, and Ravikesavan R., 2016, Comparative miRNAome Analysis Revealed Numerous Conserved and
Novel Drought Responsive miRNAs in Cotton (
Gossypium
spp.), Cotton Genomics and Genetics, 7(2): 1-23 (doi
Abstract
Negative regulations of gene expression by endogenous, non-coding miRNAs have been shown to play important role in
abiotic stress responses in plants. However, limited knowledge is available on water stress responsive miRNAs in cotton. In this
study, differentially expressed drought responsive miRNAs and their targets were identified under natural field conditions th rough
high-throughput small RNA sequencing by comparing leaf samples of drought tolerant
Gossypium hirsutum
cv. KC3 and drought
susceptible
G.
barbadense
cv. Suvin. Totally four small RNA libraries were constructed and sequenced by employing ion proton
TM
technology. Altogether, there were 39 407 089 reads with a mean read length of 22 nt. In KC3, there were 5 138 unique miRNA
reads that were differentially expressed with at least two folds under water stressed conditions. In contrast, Suvin have shown 8 469
unique miRNA reads that were differentially expressed with minimum of two folds under water stressed conditions. Comparison of
miRNAs expressed under water stressed conditions between KC3 and Suvin, have resulted 7 494 miRNA reads and interestingly
majority of them were down regulated with at least two folds. Besides identify ing large numbers of novel miRNAs, several abiotic
stress responsive conserved miRNAs were also noticed. Of particular interest were miR750, miR2, miR14, miR276, miR279, miR-
bantam and miR5176 that were highly down regulated in KC3 under water stress conditions. Strikingly, miR2 and miR-bantam were
previously shown to target pre-apoptotic genes in biological systems. Further, the identified miRNAs were also targeting different
classes of dehydrogenases, protein kinases and transcription factors. Our results revealed for the first time that there were large
numbers of water stress related miRNAs that might be sequentially and/or complexly involved in gene regulation that confers
drought tolerance in cotton under field conditions and they have enormous potential in elucidating the molecular mechanism of
miRNA based gene regulation and more importantly in genetic improvement of drought tolerance in cotton. Further, this is the first
report on experimentally identifying miRNAs in
G. barbadense
.
Keywords
Cotton; Drought tolerance; MicroRNAs; Next generation sequencing; Transcriptomics
Introduction
Diverse types of ribonucleic acids (RNA) with various functions such as coding, noncoding/non-messenger,
structural, enzymatic and regulatory functions were reported so far. Among them, RNAs with regulatory activities
are termed as micro-RNAs (miRNAs). They are about 22-24 nucleotide (nt) in length and found in all the living
organisms including crop plants (Ambros, 2004). As negative regulators of plant gene expression, miRNAs can
function by means of minimum two ways: 1) miRNAs base pair with mRNA targets by precise or nearly precise
complementarity and cleave / destruct the target mRNA through the RNA interference machinery and 2) they
inhibit protein synthesis through an unknown mechanism (Tang et al., 2003). Some known miRNA genic loci
form clusters in the genome and these miRNA clusters and the miRNAs in a given cluster are often expressed
simultaneously (Wei et al., 2013). Confirmations for the role of miRNA in cell growth and proliferation,
developmental timing and phase switch such as vegetative to reproductive growth and response to biotic and
abiotic stresses are increasing endlessly and now it is largely deliberated that their regulatory role is more
persistent than what was assumed earlier.
