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ISSN (Print): 1570-1646
ISSN (Online): 1875-6247

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Research Article

RNA-Seq Data Analysis Unveils Potential Conserved Micro-RNAs in Agave Deserti

Author(s): Basit Jabbar, Batcho Agossa Anicet, Muhammad Bilal Sarwar, Bushra Rashid*, Sameera Hassan and Tayyab Husnain

Volume 18, Issue 2, 2021

Published on: 29 May, 2020

Page: [248 - 263] Pages: 16

DOI: 10.2174/1570164617999200529122637

Price: $65

Abstract

Aims: Exploring molecular mechanism of abiotic stress tolerance in plants is needed to overcome the deterioration of yield and quality of crop plants to meet the food security challenges of the growing population.

Background: MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate target gene expression for modulating plant growth, development, and response to different stresses. Agave belonging to CAM plants’ has remarkable tolerance to extreme conditions of drought and heat; however, molecular mechanisms underlying this excellence are yet to explore.

Objective: This study applies comparative genomics approach on available Transcriptome (RNA- Seq) data of Agave deserti to identify potential miRNAs, and miRNA targets.

Methods: Transcriptome datasets consisting of 128,869 Agave contigs was processed to create local database, for nucleotide homology analysis with 6,028 non-redundant plant miRNAs as query sequences. Protein coding sequences were removed, and potential pre-miRNA sequences were tested for stability analysis based on a variety of factors, including but not limited to %G+C content and minimum free energy (-ΔG), as a filter to remove pseudo pre-miRNAs.

Results: This study identified 30 unique miRNAs of Agave deserti harboring 14 different categories of precursors. Phylogenetic analysis revealed evolutionary relationship between newly identified pre-miRNAs with corresponding pre-miRNA homologues. Target genes of miRNAs were predicted subsequently, and possible functions were defined by functional annotation analysis.

Conclusion: The results of this study will pave the way for further research, exploring the molecular mechanisms in Agave deserti and the role of miRNAs in gene regulation under abiotic stresses.

Keywords: Micro-RNA, Agave deserti, gene homology, minimum free energy, precursors, target gene.

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[1]
Iwakawa, H.O.; Tomari, Y. The functions of microRNAs: mRNA decay and translational repression. Trends Cell Biol., 2015, 25(11), 651-665.
[http://dx.doi.org/10.1016/j.tcb.2015.07.011] [PMID: 26437588]
[2]
Beauclair, L.; Yu, A.; Bouché, N. microRNA-directed cleavage and translational repression of the copper chaperone for superoxide dismutase mRNA in Arabidopsis. Plant J., 2010, 62(3), 454-462.
[http://dx.doi.org/10.1111/j.1365-313X.2010.04162.x] [PMID: 20128885]
[3]
Park, W.; Li, J.; Song, R.; Messing, J.; Chen, X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol., 2002, 12(17), 1484-1495.
[http://dx.doi.org/10.1016/S0960-9822(02)01017-5] [PMID: 12225663]
[4]
Bartel, D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. cell, 2004, 2(116), 281-297.
[5]
He, L.; Hannon, G.J. MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet., 2004, 5(7), 522-531.
[http://dx.doi.org/10.1038/nrg1379] [PMID: 15211354]
[6]
Jeong, D-H.; Park, S.; Zhai, J.; Gurazada, S.G.R.; De Paoli, E.; Meyers, B.C.; Green, P.J. Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage. Plant Cell, 2011, 23(12), 4185-4207.
[http://dx.doi.org/10.1105/tpc.111.089045] [PMID: 22158467]
[7]
Guo, H-S.; Xie, Q.; Fei, J-F.; Chua, N-H. MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development. Plant Cell, 2005, 17(5), 1376-1386.
[http://dx.doi.org/10.1105/tpc.105.030841] [PMID: 15829603]
[8]
Ling, L-Z.; Zhang, S-D.; Zhao, F.; Yang, J-L.; Song, W-H.; Guan, S-M.; Li, X-S.; Huang, Z-J.; Cheng, L. Transcriptome-wide identification and prediction of mirnas and their targets in paris polyphylla var. Yunnanensis by high-throughput sequencing analysis. Int. J. Mol. Sci., 2017, 18(1), 219.
[http://dx.doi.org/10.3390/ijms18010219] [PMID: 28117746]
[9]
Zhang, B.; Pan, X.; Cobb, G.P.; Anderson, T.A. Plant microRNA: a small regulatory molecule with big impact. Dev. Biol., 2006, 289(1), 3-16.
[http://dx.doi.org/10.1016/j.ydbio.2005.10.036] [PMID: 16325172]
[10]
Lee, R.C.; Feinbaum, R.L.; Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. cell, 1993, 75(5), 843-854.
[11]
Reinhart, B.J.; Slack, F.J.; Basson, M.; Pasquinelli, A.E.; Bettinger, J.C.; Rougvie, A.E.; Horvitz, H.R.; Ruvkun, G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. nature, 2000, 403(6772), 901.
[12]
Berezikov, E.; Cuppen, E.; Plasterk, R.H. Approaches to microRNA discovery. Nat. Genet., 2006, 38(Suppl.), S2-S7.
[http://dx.doi.org/10.1038/ng1794] [PMID: 16736019]
[13]
Wu, F.; Shu, J.; Jin, W. Identification and validation of miRNAs associated with the resistance of maize (Zea mays L.) to Exserohilum turcicum. PLoS One, 2014, 9(1), e87251.
[http://dx.doi.org/10.1371/journal.pone.0087251] [PMID: 24489881]
[14]
Luis Lauro, E-T. Potential of plants from the genus Agave as bioenergy crops. BioEnergy Res., 2012, 5(1), 1-9.
[15]
Sarwar, M.B.; Ahmad, Z.; Rashid, B.; Hassan, S.; Gregersen, P.L.; Leyva, M.O.; Nagy, I.; Asp, T.; Husnain, T. De novo assembly of Agave sisalana transcriptome in response to drought stress provides insight into the tolerance mechanisms. Sci. Rep., 2019, 9(1), 396.
[http://dx.doi.org/10.1038/s41598-018-35891-6] [PMID: 30674899]
[16]
Gross, S.M.; Martin, J.A.; Simpson, J.; Abraham-Juarez, M.J.; Wang, Z.; Visel, A. De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. BMC Genomics, 2013, 14(1), 563.
[http://dx.doi.org/10.1186/1471-2164-14-563] [PMID: 23957668]
[17]
Martin, J.; Bruno, V.M.; Fang, Z.; Meng, X.; Blow, M.; Zhang, T.; Sherlock, G.; Snyder, M.; Wang, Z. Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. BMC Genomics, 2010, 11(1), 663.
[http://dx.doi.org/10.1186/1471-2164-11-663] [PMID: 21106091]
[18]
Kimura, M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol., 1980, 16(2), 111-120.
[http://dx.doi.org/10.1007/BF01731581] [PMID: 7463489]
[19]
Kumar, S.; Stecher, G.; Li, M.; Knyaz, C.; Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol., 2018, 35(6), 1547-1549.
[http://dx.doi.org/10.1093/molbev/msy096] [PMID: 29722887]
[20]
Dai, X.; Zhao, P.X. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res., 2011, 39(suppl_2), W155-W159.
[21]
Binns, D.; Dimmer, E.; Huntley, R.; Barrell, D.; O’Donovan, C.; Apweiler, R.; Quick, G.O. QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics, 2009, 25(22), 3045-3046.
[http://dx.doi.org/10.1093/bioinformatics/btp536] [PMID: 19744993]
[22]
Apweiler, R.; Bairoch, A.; Wu, C.H.; Barker, W.C.; Boeckmann, B.; Ferro, S.; Gasteiger, E.; Huang, H.; Lopez, R.; Magrane, M. UniProt: the universal protein knowledgebase. Nucleic acids research, 2004, 32(suppl_1), D115-D119.
[http://dx.doi.org/10.1093/nar/gkh131]
[23]
Hunter, S.; Apweiler, R.; Attwood, T.K.; Bairoch, A.; Bateman, A.; Binns, D.; Bork, P.; Das, U.; Daugherty, L.; Duquenne, L. InterPro: the integrative protein signature database. Nucleic acids research, 2008, 37(suppl_1), D211-D215.
[24]
Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 2003, 31(13), 3406-3415.
[http://dx.doi.org/10.1093/nar/gkg595] [PMID: 12824337]
[25]
Zhang, B.H.; Pan, X.P.; Cox, S.B.; Cobb, G.P.; Anderson, T.A. Evidence that miRNAs are different from other RNAs. Cell. Mol. Life Sci., 2006, 63(2), 246-254.
[http://dx.doi.org/10.1007/s00018-005-5467-7] [PMID: 16395542]
[26]
Yang, H.; Zhang, H.; Zhu, L.; Zhang, C.; Li, D. Identification and characterization of microRNAs in Macaca fascicularis by EST analysis. Comparative Funct. Genom., 2012, 2012
[27]
Zhang, B.H.; Pan, X.P.; Wang, Q.L.; Cobb, G.P.; Anderson, T.A. Identification and characterization of new plant microRNAs using EST analysis. Cell Res., 2005, 15(5), 336-360.
[http://dx.doi.org/10.1038/sj.cr.7290302] [PMID: 15916721]
[28]
Panda, D.; Dehury, B.; Sahu, J.; Barooah, M.; Sen, P.; Modi, M.K. Computational identification and characterization of conserved miRNAs and their target genes in garlic (Allium sativum L.) expressed sequence tags. Gene, 2014, 537(2), 333-342.
[http://dx.doi.org/10.1016/j.gene.2014.01.010] [PMID: 24434367]
[29]
Nodine, M.D.; Bartel, D.P. MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis. Genes Dev., 2010, 24(23), 2678-2692.
[http://dx.doi.org/10.1101/gad.1986710] [PMID: 21123653]
[30]
Chen, X.; Zhang, Z.; Liu, D.; Zhang, K.; Li, A.; Mao, L. SQUAMOSA promoter-binding protein-like transcription factors: star players for plant growth and development. J. Integr. Plant Biol., 2010, 52(11), 946-951.
[http://dx.doi.org/10.1111/j.1744-7909.2010.00987.x] [PMID: 20977652]
[31]
Huijser, P.; Schmid, M. The control of developmental phase transitions in plants. Development, 2011, 138(19), 4117-4129.
[http://dx.doi.org/10.1242/dev.063511] [PMID: 21896627]
[32]
Zhu, Q-H.; Fan, L.; Liu, Y.; Xu, H.; Llewellyn, D.; Wilson, I. miR482 regulation of NBS-LRR defense genes during fungal pathogen infection in cotton. PLoS One, 2013, 8(12), e84390.
[http://dx.doi.org/10.1371/journal.pone.0084390] [PMID: 24391949]
[33]
Stief, A.; Altmann, S.; Hoffmann, K.; Pant, B.D.; Scheible, W-R.; Bäurle, I. Arabidopsis miR156 regulates tolerance to recurring environmental stress through SPL transcription factors. Plant Cell, 2014, 26(4), 1792-1807.
[http://dx.doi.org/10.1105/tpc.114.123851] [PMID: 24769482]
[34]
Linder, P.; Jankowsky, E. From unwinding to clamping - the DEAD box RNA helicase family. Nat. Rev. Mol. Cell Biol., 2011, 12(8), 505-516.
[http://dx.doi.org/10.1038/nrm3154] [PMID: 21779027]
[35]
Ransom-Hodgkins, W.D. The application of expression analysis in elucidating the eukaryotic elongation factor one alpha gene family in Arabidopsis thaliana. Mol. Genet. Genomics, 2009, 281(4), 391-405.
[http://dx.doi.org/10.1007/s00438-008-0418-2] [PMID: 19132394]
[36]
Shi, L-X.; Lorković, Z.J.; Oelmüller, R.; Schröder, W.P. The low molecular mass PsbW protein is involved in the stabilization of the dimeric photosystem II complex in Arabidopsis thaliana. J. Biol. Chem., 2000, 275(48), 37945-37950.
[http://dx.doi.org/10.1074/jbc.M006300200] [PMID: 10950961]
[37]
Hagman, A.; Shi, L-X.; Rintamäki, E.; Andersson, B.; Schröder, W.P. The nuclear-encoded PsbW protein subunit of photosystem II undergoes light-induced proteolysis. Biochemistry, 1997, 36(42), 12666-12671.
[http://dx.doi.org/10.1021/bi970685o] [PMID: 9335523]
[38]
Amann, K.; Lezhneva, L.; Wanner, G.; Herrmann, R.G.; Meurer, J. Accumulation of photosystem one1, a member of a novel gene family, is required for accumulation of [4Fe-4S] cluster-containing chloroplast complexes and antenna proteins. Plant Cell, 2004, 16(11), 3084-3097.
[http://dx.doi.org/10.1105/tpc.104.024935] [PMID: 15494558]
[39]
Jung, J-H.; Lee, S.; Yun, J.; Lee, M.; Park, C-M. The miR172 target TOE3 represses AGAMOUS expression during Arabidopsis floral patterning. Plant Sci., 2014, 215-216, 29-38.
[http://dx.doi.org/10.1016/j.plantsci.2013.10.010] [PMID: 24388512]
[40]
Aukerman, M.J.; Sakai, H. Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell, 2003, 15(11), 2730-2741.
[http://dx.doi.org/10.1105/tpc.016238] [PMID: 14555699]

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