Abstract
Noncoding RNAs were not only classified based on their structural variation but also on the basis of their regulatory roles in diverse cellular pathways. During the last two decades, several studies on noncoding RNAs have been reported and now it is well known that they regulate expression of genes involved in diverse biological functions. Therefore, in gene regulatory network, noncoding RNAs are considered as the important top-tier regulators. In Solanaceae plants, several studies on noncoding RNAs especially small noncoding RNAs are reported mostly in Tomato. However, in Capsicum (pepper), one of the most important vegetable crops, belonging to the same family Solanaceae as of Tomato, the identification and characterization of noncoding RNAs are still limited. Furthermore, recently the identification and characterization of long noncoding RNAs are being reported in plants including Solanaceae plants. Therefore, in this chapter, an attempt is being made to highlight the identification and characterization of noncoding RNAs in Capsicum species.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Allen E, Howell MD (2010) miRNAs in the biogenesis of trans-acting siRNAs in higher plants. Semin Cell Dev Biol 21:798–804. https://doi.org/10.1016/j.semcdb.2010.03.008
Allen E, Xie Z, Gustafson AM et al (2004) Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat Genet 36:1282
Backofen R, Bernhart SH, Flamm C et al (2006) RNAs everywhere: genome-wide annotation of structured RNAs. J Exp Zool Part B Mol Dev Evol 308B:1–25. https://doi.org/10.1002/jez.b.21130
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2):281–297
Bokszczanin KL, Krezdorn N, Fragkostefanakis S et al (2015) Identification of novel small ncRNAs in pollen of tomato. BMC Genom 16:714. https://doi.org/10.1186/s12864-015-1901-x
Brodersen P, Voinnet O (2006) The diversity of RNA silencing pathways in plants. Trends Genet 22:268–280. https://doi.org/10.1016/j.tig.2006.03.003
Brousse C, Liu Q, Beauclair L et al (2014) A non-canonical plant microRNA target site. Nucleic Acids Res 42:5270–5279
Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136:642–655. https://doi.org/10.1016/j.cell.2009.01.035
Castel SE, Martienssen RA (2013) RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat Rev Genet 14:100
Chekanova JA (2015) Long non-coding RNAs and their functions in plants. Curr Opin Plant Biol 27:207–216. https://doi.org/10.1016/j.pbi.2015.08.003
Chellappan P, Xia J, Zhou X et al (2010) siRNAs from miRNA sites mediate DNA methylation of target genes. Nucleic Acids Res 38:6883–6894. https://doi.org/10.1093/nar/gkq590
Chen X (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303:2022–2025. https://doi.org/10.1126/science.1088060
Chitra TR, Prakash HS, Albrechtsen SE et al (2002) Indexing of leaf and seed samples of tomato and bell pepper for tobamoviruses. Indian Phytopathol 55:84–86
Chou C-H, Shrestha S, Yang C-D et al (2018) miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. Nucleic Acids Res 46:D296–D302. https://doi.org/10.1093/nar/gkx1067
Crespi MD, Jurkevitch E, Poiret M et al (1994) enod40, a gene expressed during nodule organogenesis, codes for a non-translatable RNA involved in plant growth. EMBO J 13:5099–5112
Cruz de Carvalho MH, Sun H-X, Bowler C, Chua N-H (2015) Noncoding and coding transcriptome responses of a marine diatom to phosphate fluctuations. New Phytol 210:497–510. https://doi.org/10.1111/nph.13787
Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39:W155–W159. https://doi.org/10.1093/nar/gkr319
Delhaize E, Randall PJ (1995) Characterization of a phosphate-accumulator mutant of Arabidopsis thaliana. Plant Physiol 107:207–213
Delpu Y, Larrieu D, Gayral M, et al (2016) Noncoding RNAs: clinical and therapeutic applications (Chapter 12). In: Egger G (ed) Arimondo PBT-DD in CE. Academic Press, Boston, pp 305–326
Di C, Yuan J, Wu Y et al (2014) Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features. Plant J 80:848–861. https://doi.org/10.1111/tpj.12679
Din M, Barozai MYK, Baloch IA (2016) Profiling and annotation of microRNAs and their putative target genes in chilli (Capsicum annuum L.) using ESTs. Gene Reports 5:62–69. https://doi.org/10.1016/j.genrep.2016.08.010
Ding J, Lu Q, Ouyang Y et al (2012) A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proc Natl Acad Sci USA 109:2654–2659. https://doi.org/10.1073/pnas.1121374109
Fire A, Xu S, Montgomery MK et al (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806
Franco-Zorrilla JM, Valli A, Todesco M et al (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39:1033
Gong L, Kakrana A, Arikit S et al (2013) Composition and expression of conserved microRNA genes in diploid cotton (Gossypium) species. Genome Biol Evol 5:2449–2459. https://doi.org/10.1093/gbe/evt196
Gonzalez-Ballester D, Grossman AR (2009) Chapter 5—Sulfur: from acquisition to assimilation. In: Harris EH, Stern DB, Witman GBBT-TCS (eds) The chlamydomonas sourcebook, 2nd edn. Academic Press, London, pp 159–187
Guleria P, Goswami D, Mahajan M et al (2012) MicroRNAs and their role in plants during abiotic stresses BT. In: Ahmad P, Prasad MNV (eds) Environmental adaptations and stress tolerance of plants in the era of climate change. Springer, New York, pp 265–278
Heo JB, Sung S (2011) Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331(80):76–79
Herbig A, Nieselt K (2011) nocoRNAc: characterization of non-coding RNAs in prokaryotes. BMC Bioinform 12:40. https://doi.org/10.1186/1471-2105-12-40
Hou X, Du Y, Liu X et al (2017) Genome-wide analysis of long non-coding RNAs in potato and their potential role in tuber sprouting process. Int J Mol Sci 19:101. https://doi.org/10.3390/ijms19010101
Hwang D-G, Park JH, Lim JY et al (2013) The hot pepper (Capsicum annuum) microRNA transcriptome reveals novel and conserved targets: a foundation for understanding microRNA functional roles in hot pepper. PLoS ONE 8:e64238–e64238. https://doi.org/10.1371/journal.pone.0064238
Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14:787–799. https://doi.org/10.1016/j.molcel.2004.05.027
Jorgensen R (1990) Altered gene expression in plants due totrans interactions between homologous genes. Trends Biotechnol 8:340–344. https://doi.org/10.1016/0167-7799(90)90220-R
Kalvari I, Argasinska J, Olvera NQ, Nawrocki EP, Rivas E, Eddy ES, Bateman A, Finn RD, Petrov AI (2017) Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res. https://doi.org/10.1093/nar/gkx1038
Kang C, Liu Z (2015) Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development. BMC Genom 16:815. https://doi.org/10.1186/s12864-015-2014-2
Kasschau KD, Fahlgren N, Chapman EJ et al (2007) Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol 5:e57–e57. https://doi.org/10.1371/journal.pbio.0050057
Kawashima CG, Yoshimoto N, Maruyama-Nakashita A et al (2009) Sulphur starvation induces the expression of microRNA-395 and one of its target genes but in different cell types. Plant J 57:313–321. https://doi.org/10.1111/j.1365-313X.2008.03690.x
Kim H-J, Kwang-Hyun Baek, Bong-Woo Lee et al (2011) In silico identification and characterization of microRNAs and their putative target genes in Solanaceae plants. Genome 54:91–98. https://doi.org/10.1139/G10-104
Kong L, Zhang Y, Ye Z-Q et al (2007) CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 35:W345–W349. https://doi.org/10.1093/nar/gkm391
Kozomara A, Griffiths-Jones S (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42(1):D68–D73
Kumar S, Dubey AK, Karmakar R et al (2012) Inhibition of TMV multiplication by siRNA constructs against TOM1 and TOM3 genes of Capsicum annuum. J Virol Methods 186:78–85. https://doi.org/10.1016/j.jviromet.2012.07.014
Li L, Eichten SR, Shimizu R et al (2014) Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biol 15:R40. https://doi.org/10.1186/gb-2014-15-2-r40
Lippman Z, Martienssen R (2004) The role of RNA interference in heterochromatic silencing. Nature 431:364
Liu C, Muchhal US, Raghothama KG (1997) Differential expression of TPS11, a phosphate starvation-induced gene in tomato. Plant Mol Biol 33:867–874. https://doi.org/10.1023/A:1005729309569
Liu J, Jung C, Xu J et al (2012) Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 24:4333–4345. https://doi.org/10.1105/tpc.112.102855
Liu Z, Zhang Y, Ou L et al (2017) Identification and characterization of novel microRNAs for fruit development and quality in hot pepper (Capsicum annuum L.). Gene 608:66–72. https://doi.org/10.1016/j.gene.2017.01.020
Lv D-K, Bai X, Li Y et al (2010) Profiling of cold-stress-responsive miRNAs in rice by microarrays. Gene 459:39–47. https://doi.org/10.1016/j.gene.2010.03.011
Manila T M, Riju A, Lakshmi Priya Darshini, K, Chandrasekar A. Eapen SJ (2009) In silico microRNA identification from paprika (Capsicum annuum) ESTs. Available from Nature Precedings. http://hdl.handle.net/10101/npre.2009.3737.1
Mello CC, Conte D (2004) Revealing the world of RNA interference. Nature 31:338–342
Meng Y, Gou L, Chen D, Mao C, Jin Y, Wu P, Chen M (2011) PmiRKB: a plant microRNA knowledge base. Nucleic Acids Res. https://doi.org/10.1093/nar/gkq721
Mhuantong W, Wichadakul D (2009) MicroPC (µPC): comprehensive resource for predicting and comparing plant microRNAs, BMC Genom 10:366
Mosher RA, Melnyk CW, Kelly KA et al (2009) Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 460:283
Omidvar V, Mohorianu I, Dalmay T, Fellner M (2015) MicroRNA regulation of abiotic stress response in male-sterile tomato mutant. Plant Genome 8:13. https://doi.org/10.3835/plantgenome2015.02.0008
Ou L, Liu Z, Zhang Z et al (2017) Noncoding and coding transcriptome analysis reveals the regulation roles of long noncoding RNAs in fruit development of hot pepper (Capsicum annuum L.). Plant Growth Regul 83:141–156. https://doi.org/10.1007/s10725-017-0290-3
Park W, Li J, Song R et al (2002) Carpel factory, a dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol 12:1484–1495
Ponting CP, Oliver PL, Reik W (2009) Evolution and functions of long noncoding RNAs. Cell 136:629–641. https://doi.org/10.1016/j.cell.2009.02.006
Qin C, Yu C, Shen Y, et al (2014) Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci 111:5135–5140
Riffo-Campos ÁL, Riquelme I, Brebi-Mieville P (2016) Tools for sequence-based miRNA target prediction: what to choose? Int J Mol Sci 17:1987. https://doi.org/10.3390/ijms17121987
Schachtman DP, Reid RJ, Ayling SM (1998) Phosphorus uptake by plants: from soil to cell. Plant Physiol 116:447–453
Seo E, Kim T, Park JH, et al (2018) Genome-wide comparative analysis in Solanaceous species reveals evolution of microRNAs targeting defense genes in Capsicum spp. DNA Res dsy025–dsy025
Shin S-Y, Shin C (2016) Regulatory non-coding RNAs in plants: potential gene resources for the improvement of agricultural traits. Plant Biotechnol Rep 10:35–47. https://doi.org/10.1007/s11816-016-0389-4
Shuai P, Liang D, Tang S et al (2014) Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa. J Exp Bot 65:4975–4983. https://doi.org/10.1093/jxb/eru256
Sun L, Luo H, Bu D et al (2013) Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res 41:e166–e166. https://doi.org/10.1093/nar/gkt646
Sunkar R, Zhu J-K (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001–2019
Swiezewski S, Liu F, Magusin A, Dean C (2009) Cold-induced silencing by long antisense transcripts of an Arabidopsis polycomb target. Nature 462:799
Szcześniak MW, Rosikiewicz W, Makałowska I (2016) CANTATAdb: a collection of plant long non-coding RNAs. Plant Cell Physiol 57:e8–e8. https://doi.org/10.1093/pcp/pcv201
Taller D, Bálint J, Gyula P et al (2018) Expansion of Capsicum annum fruit is linked to dynamic tissue-specific differential expression of miRNA and siRNA profiles. PLoS ONE 13:e0200207
Trapnell C, Roberts A, Goff L et al (2012) Differential gene and transcript expression analysis of RNA-seq experiments with tophat and cufflinks. Nat Protoc 7:562
Tuteja N, Sopory SK (2008) Chemical signaling under abiotic stress environment in plants. Plant Signal Behav 3:525–536
Ulitsky I, Bartel DP (2013) lincRNAs: genomics, evolution, and mechanisms. Cell 154:26–46. https://doi.org/10.1016/j.cell.2013.06.020
Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136:669–687. https://doi.org/10.1016/j.cell.2009.01.046
Wang M, Yuan D, Tu L et al (2015) Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.). New Phytol 207:1181–1197. https://doi.org/10.1111/nph.13429
Wang W, Vinocur B, Altman A (2003) Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta 218:1–14. https://doi.org/10.1007/s00425-003-1105-5
Wang Z-W, Wu Z, Raitskin O et al (2014) Antisense-mediated FLC transcriptional repression requires the P-TEFb transcription elongation factor. Proc Natl Acad Sci USA 111:7468–7473. https://doi.org/10.1073/pnas.1406635111
Wasaki J, Yonetani R, Shinano T, et al (2003) Expression of the OsPI1 gene, cloned from rice roots using cDNA microarray, rapidly responds to phosphorus status. New Phytol 158:239–248. https://doi.org/10.1046/j.1469-8137.2003.00748.x
Wu H-J, Wang Z-M, Wang M, Wang X-J (2013) Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants. Plant Physiol 161:1875–1884. https://doi.org/10.1104/pp.113.215962
Yang W-C, Katinakis P, Hendriks P et al (2018) Characterization of GmENOD40, a gene showing novel patterns of cell-specific expression during soybean nodule development. Plant J 3:573–585. https://doi.org/10.1046/j.1365-313X.1993.03040573.x
Zhang B (2015) MicroRNA: a new target for improving plant tolerance to abiotic stress. J Exp Bot 66:1749–1761. https://doi.org/10.1093/jxb/erv013
Zhang L, Qin C, Mei J, et al (2017) Identification of microRNA targets of Capsicum spp. using mirtrans—a trans-omics approach. Front Plant Sci 8:495. https://doi.org/10.3389/fpls.2017.00495
Zhu Q-H, Wang M-B (2012) Molecular functions of long non-coding RNAs in plants. Genes (Basel) 3:176–190. https://doi.org/10.3390/genes3010176
Zuo J, Wang Y, Zhu B et al (2018) Analysis of the coding and non-coding RNA transcriptomes in response to bell pepper chilling. Int J Mol Sci 19:2001. https://doi.org/10.3390/ijms19072001
Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z (2010) PMRD: plant microRNA database. Nucleic Acids Res 38:D806–D813
Acknowledgements
This work was supported under Special Assistance Programme (SAP) by the University Grant Commission (UGC), India, to Jawaharlal Nehru University, New Delhi, India.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Ahmad, I., Nitin, M., Rawoof, A., Dubey, M., Ramchiary, N. (2019). Noncoding RNAs in Capsicum Genome. In: Ramchiary, N., Kole, C. (eds) The Capsicum Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-97217-6_10
Download citation
DOI: https://doi.org/10.1007/978-3-319-97217-6_10
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-97216-9
Online ISBN: 978-3-319-97217-6
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)