Identification of conserved miRNA molecules in einkorn wheat ( Triticum monococcum subsp. monococcum ) by using small RNA sequencing analysis
Triticum monococcum subsp. monococcum as a first cultivated diploid wheat species possesses desirable agronomic and quality
characteristics. Drought and salinity are the most dramatic environmental stress factors that have serious impact on yield and quality
of crops; however, plants can use alternative defense mechanisms against these stresses. The posttranscriptional alteration of gene
expression by microRNAs (miRNAs) is one of the most conserved mechanisms. In plant species including wheat genomes, miRNAs
have been implicated in the management of salt and drought stress; however, studies on einkorn wheat (Triticum monococcum subsp.
monococcum) are not yet available. In this study, we aimed to identify conserved miRNAs in einkorn wheat using next generation
sequencing technology and bioinformatics analysis. In order to include a larger set of miRNAs, small RNA molecules from pooled
plant samples grown under normal, drought, and salinity conditions were used for the library preparation and sequence analysis.
After bioinformatics analysis, we identified 167 putative mature miRNA sequences belonging to 140 distinct miRNA families. We also
presented a comparative analysis to propose that miRNAs and their target genes were involved in salt and drought stress control in
addition to a comprehensive analysis of the scanned target genes in the T. aestivum genome.
___
- Akdogan G, Tufekci ED, Uranbey S, Unver T (2016). miRNA-based
drought regulation in wheat. Funct Integr Genomics 16: 221-
233.
- Alptekin B, Budak H (2016). Wheat miRNA ancestors: evident by
transcriptome analysis of A, B, and D genome donors. Funct
Integr Genomics 17: 171-187.
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990). Basic
local alignment search tool. J Mol Biol 215: 403-410.
- Barrera-Figueroa BE, Gao L, Wu Z, Zhou X, Zhu J, Jin H, Liu R,
Zhu JK (2012). High throughput sequencing reveals novel and
abiotic stress-regulated microRNAs in the inflorescences of
rice. BMC Plant Biol 12: 132.
- Bartel DP (2004). MicroRNAs: genomics, biogenesis, mechanism,
and function. Cell 116: 281-297.
- Briggle L (1963). Classification of Triticum species and of wheat
varieties grown in the United States. 1st ed. Washington, D.C.,
USA: United States Department of Agriculture.
- Budak H, Akpinar BA (2015). Plant miRNAs: biogenesis, organization
and origins. Funct Integr Genomics 15: 523-531.
- Carthew RW, Sontheimer EJ (2009). Origins and mechanisms of
miRNAs and siRNAs. Cell 136: 642-655.
- Curwen-McAdams C, Arterburn M, Murphy K, Cai X, Jones SS
(2016). Toward a taxonomic definition of perennial wheat: a
new species ×Tritipyrum aaseae described. Genet Resour Crop
Evol 64: 1651-1659.
- Dai X, Zhao PX (2011). psRNATarget: a plant small RNA target
analysis server. Nucleic Acids Res 39: W155-9.
- Datta R, Paul S (2015). Plant microRNAs: master regulator of gene
expression mechanism. Cell Biol Int 39: 1185-1190.
- Deng P, Wang L, Cui L, Feng K, Liu F, Du X, Tong W, Nie X, Ji W,
Weining S (2015). Global identification of microRNAs and
their targets in barley under salinity stress. PLoS One 10:
e0137990.
- Ding D, Zhang L, Wang H, Liu Z, Zhang Z, Zheng Y (2009).
Differential expression of miRNAs in response to salt stress in
maize roots. Ann Bot 103: 29-38.
- Eren H, Pekmezci MY, Okay S, Turktas M, Inal B, Ilhan E, Atak
M, Erayman M, Unver T (2015). Hexaploid wheat (
Triticum
aestivum
) root miRNome analysis in response to salt stress.
Ann Appl Biol 167: 208-216.
- Ge X, Zhang Y, Jiang J, Zhong Y, Yang X, Li Z, Huang Y, Tan A
(2013). Identification of microRNAs in
Helicoverpa armigera
and
Spodoptera litura
based on deep sequencing and homology
analysis. Int J Biol Sci 9: 1-15.
- Griffiths-Jones S, Saini HK, Dongen S van, Enright AJ (2008).
miRBase: tools for microRNA genomics. Nucleic Acids Res 36:
D154-8.
- Hackenberg M, Gustafson P, Langridge P, Shi BJ (2015). Differential
expression of microRNAs and other small RNAs in barley
between water and drought conditions. Plant Biotechnol J 13:
2-13.
- Jiang H, Lei R, Ding SW, Zhu S (2014). Skewer: a fast and accurate
adapter trimmer for next-generation sequencing paired-end
reads. BMC Bioinformatics 15: 182.
- Jones-Rhoades MW, Bartel DP, Bartel B (2006). MicroRNAs and
their regulatory roles in plants. Annu Rev Plant Biol 57: 19-53.
- Karagöz A, Zencirci N (2005). Variation in wheat (
Tr iti c um
spp.)
landraces from different altitudes of three regions of Turkey.
Genet Resour Crop Evol 52: 775-785.
- Kersey PJ, Allen JE, Armean I, Boddu S, Bolt BJ, Carvalho-Silva D,
Christensen M, Davis P, Falin LJ, Grabmueller C et al (2016).
Ensembl Genomes 2016: more genomes, more complexity.
Nucleic Acids Res 44: D574-D580.
- Kozomara A, Griffiths-Jones S (2011). miRBase: integrating
microRNA annotation and deep-sequencing data. Nucleic
Acids Res 39: D152-D157.
- Langmead B, Trapnell C, Pop M, Salzberg SL (2009). Ultrafast and
memory-efficient alignment of short DNA sequences to the
human genome. Genome Biol 10: R25.
- Lau NC, Lim LP, Weinstein EG, Bartel DP (2001). An abundant class
of tiny RNAs with probable regulatory roles in
Caenorhabditis
elegans
. Science 294: 858-862.
- Liu HH, Tian X, Li YJ, Wu CA, Zheng CC (2008). Microarray-
based analysis of stress-regulated microRNAs in
Arabidopsis
thaliana
. RNA 14: 836-843.
- Mahmood I, Razzaq A, Hafiz I, Kaleem S, Khan A, Qayyum A,
Ahmad M (2002). Interaction of callus selection media and
stress duration for in vitro selection of drought tolerant callus
of wheat. African J Biotechnol 11: 4000-4006.
- Mathews DH, Sabina J, Zuker M, Turner DH (1999). Expanded
sequence dependence of thermodynamic parameters improves
prediction of RNA secondary structure. J Mol Biol 288: 911-
940.
- Mayer KF, Rogers J, Doležel J, Pozniak C, Eversole K, Feuillet C,
Gill B, Friebe B, Lukaszewski AJ, Sourdille P et al (2014). A
chromosome-based draft sequence of the hexaploid bread
wheat (
Triticum aestivum
) genome. Science 345: 1251788.
- Peters L, Meister G (2007). Argonaute proteins: mediators of RNA
silencing. Mol Cell 26: 611-623.
- Ritchie W, Legendre M, Gautheret D (2007). RNA stem-loops: to be
or not to be cleaved by RNAse III. RNA 13: 457-462.
- Serpen A, G
ökmen V, Karag
öz A, K
öksel H (2008). Phytochemical
quantification and total antioxidant capacities of emmer
(
Triticum dicoccon
Schrank) and einkorn (
Triticum
monococcum
L.) wheat landraces. J Agric Food Chem 56: 7285-
7292.
- Ünlü ES, Gordon DM, Telli M (2015). Small RNA sequencing based
identification of miRNAs in
Daphnia magna
. PLoS One 10:
e0137617.
- Vaucheret H (2009). AGO1 homeostasis involves differential
production of 21-nt and 22-nt miR168 species by MIR168a
and MIR168b. PLoS One 4: e6442.
- Wei L, Zhang D, Xiang F, Zhang Z (2009). Differentially expressed
miRNAs potentially involved in the regulation of defense
mechanism to drought stress in maize seedlings. Int J Plant Sci
170: 979-989.
- Zhang B, Pan X, Cobb GP, Anderson TA (2006). Plant microRNA: a
small regulatory molecule with big impact. Dev Biol 289: 3-16.
- Zhou L, Liu Y, Liu Z, Kong D, Duan M, Luo L (2010). Genome-wide
identification and analysis of drought-responsive microRNAs
in
Oryza sativa
. J Exp Bot 61: 4157-4168.
- Zuker M (2003). Mfold web server for nucleic acid folding and
hybridization prediction. Nucleic Acids Res 31: 3406-3415.