Small RNAs in Botrytis
cinerea were analyzed via high-throughput sequencing on BGISEQ-500
platform. A total of 8 novel miRNAs and 110 novel siRNAs were predicted.
Sequence information, construction, length distribution, base bias and
expression levels of miRNAs and siRNAs were determined as well. Through GO and
KEGG enrichment analysis, the miRNA target genes are mostly located in membrane
and organelle, possessed binding and catalytic activities, and involved in
signal transduction and carbohydrate metabolism. The results will provide a
theoretical foundation for understanding the developmental and pathogenic
mechanisms of B. cinereaat the transcriptional level.
References
[1]
Cheung, N., Tian, L., Liu, X.R. and Li, X. (2020) The Destructive Fungal Pathogen Botrytis cinerea—Insights from Genes Studied with Mutant Analysis. Pathogens, 9, 923. https://doi.org/10.3390/pathogens9110923
[2]
Leroux, P., Fritz, R., Debieu, D., Albertini, C., Lanen, C., Bach, J., Gredt, M. and Chapeland, F. (2002) Mechanisms of Resistance to Fungicides in Field Strains of Botrytis cinerea. Pest Management Science, 58, 876-888.
https://doi.org/10.1002/ps.566
[3]
González-Domínguez, E., Fedele, G., Caffi, T., Delière L., Sauris, P., Gramajie, D., De Ojier, J.L.R., Díaz-Losada, E., Díez-Navajas, A.M., Bengoa, P. and Rossi, V. (2019) A Network Meta-Analysis Provides New Insight into Fungicide Scheduling for the Control of Botrytis cinerea in Vineyards. Pest Management Science, 75, 324-332. https://doi.org/10.1002/ps.5116
[4]
Van Kan, J.A.L., Stassen, J.H.M., Mosbach, A., Van Der Lee, T.A.J., Faino, L., Farmer, A.D., Papasotiriou, D.G., Zhou, S.G., Seidl, M.F., Cottam, E., Edel, D., Hahn, M., Schwartz, D.C., Dietrich, R.A., Widdison, S. and Scalliet, G. (2017) A Gapless Genome Sequence of the Gungus Botrytis cinerea. Molecular Plant Pathology, 18, 75-89. https://doi.org/10.1111/mpp.12384
[5]
Nkajima, M. and Akutsu, K. (2014) Virulence Factors of Botrytis cinerea. Journal of General Plant Pathology, 80, 15-23. https://doi.org/10.1007/s10327-013-0492-0
[6]
González-Fernández, R., Valero-Galván, J., Gómez-Gálvez, F.J. and Jorrin-Novo, J.V. (2015) Unraveling the in Vitro Secretome of the Phytopathogen Botrytis cinerea to Understand the Interaction with Its Hosts. Frontiers in Plant Science, 6, Article No. 839. https://doi.org/10.3389/fpls.2015.00839
[7]
Li, H., Chen, Y., Zhang, Z.Q., Li, B.Q., Qin, G.Z. and Tian, S.P. (2018) Pathogenic Mechanisms and Control Strategies of Botrytis cinerea Causing Post-harvest Decay in Fruits and Vegetables. Food Quality and Safety, 3, 111-119.
https://doi.org/10.1093/fqsafe/fyy016
[8]
Nguyen, T.C., Zaleta-Rivera, K., Huang, X.R., Dai, X.F. and Zhong, S. (2018) RNA, Action through Interactions. Trends in Genetics, 34, 867-882.
https://doi.org/10.1016/j.tig.2018.08.001
[9]
Qian, X.Y., Zhao, J.Y., Yeung, P.Y., Zhang, Q.F.C. and Kwok, C.K. (2019) Revealing LncRNA Structures and Interactions by Sequencing Based Approaches. Trends in Genetics, 44, 33-52. https://doi.org/10.1016/j.tibs.2018.09.012
[10]
Achkar, N.P., Cambiagno, D.A. and Manavella, P.A. (2016) miRNA Biogenesis: A Dynamic Pathway. Trends in Genetics, 21, 1034-1044.
https://doi.org/10.1016/j.tplants.2016.09.003
[11]
Neumeier, J. and Meister, G. (2021) siRNA Specificity: RNAi Mechanisms and Strategies to Reduce Off-Target Effects. Frontiers in Plant Science, 11, Article ID: 526455. https://doi.org/10.3389/fpls.2020.526455
[12]
Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and Memory-Efficient Alignment of Short DNA Sequences to the Human Genome. Genome Biology, 10, R23. https://doi.org/10.1186/gb-2009-10-3-r25
Friedländer, M.R., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S. and Rajewsky, N. (2008) Discovering MicroRNAs from Deep Sequencing Data Using MiRDeep. Nature Biotechnology, 26, 407-415. https://doi.org/10.1038/nbt1394
[15]
Evers, M., Huttner, M., Dueck, A., Meister, G. and Engelmann, J.C. (2015) MiRA: Adaptable Novel MiRNA Identification in Plants Using Small RNA Sequencing Data. BMC Bioinformatics, 16, Article No. 370.
https://doi.org/10.1186/s12859-015-0798-3
[16]
Jagla, B., Aulner, N., Kelly, P.D., Song, D., Volchuk, A., Zatorski, A., Shum, D., Mayer, T., De Angelis, D.A., Ouerfelli, O., Rutishauser, U. and Rothman, J.E. (2005) Sequence Characteristics of Functional SiRNAs. RNA, 11, 864-872.
https://doi.org/10.1261/rna.7275905
[17]
Hoen, P.A.C., Ariyurek, Y., Thygesen, H.H., Vreugdenhil, E., Vossen, R.H.A.M., De Menezes, R.X., Boer, J.M., Van Ommen, G.B. and Den Dunnen, J.T. (2008) Deep Sequencing-Based Expression Analysis Shows Major Advances in Robustness, Resolution and Inter-Lab Portability over Five Microarray Plat Forms. Nucleic Acids Research, 36, e141. https://doi.org/10.1093/nar/gkn705
[18]
Bonnet, E., He, Y., Billiau, K. and De Peer, Y.V. (2010) TAPIR, a Web Werver for the Prediction of Plant MicroRNA Targets, Including Target Mimics. Bioinformatics, 26, 1566-1568. https://doi.org/10.1093/bioinformatics/btq233
[19]
Yadav, A., Sanyal, I., Rai, S.P. and Lata, C. (2021) An Overview on MiRNA-Encoded Peptides in Plant Biology Research. Genomics, 113, 2385-2391.
https://doi.org/10.1016/j.ygeno.2021.05.013
[20]
Jonas, S. and Izaurralde, E. (2015) Towards a Molecular Understanding of MicroRNA-Mediated Gene Silencing. Nature Review Genetics, 16, 421-433.
https://doi.org/10.1038/nrg3965
[21]
Iwakawa, H.O. and Tomari, Y. (2015) The Functions of MicroRNAs: mRNA Decay and Translational Repression. Trends in Cell Biology, 25, 651-665.
https://doi.org/10.1016/j.tcb.2015.07.011
[22]
Lee, H.C., Li, L.D., GU, W.F., Xue, Z.H., Crosthwaite, S.K., Pertsemlidis, A., Lewis, Z.A., Freitag, M., Selker, E.U., Mello, C.C. and Liu, Y. (2010) Divers Ppathways Generate MicroRNA-Like RNAs and Dicer-Independent Small Interfering RNAs in Fungi. Molecular Cell, 38, 803-814. https://doi.org/10.1016/j.molcel.2010.04.005
[23]
Lin, Y.L., Ma L.T., Lee, Y.R., Lin, S.S., Wang, S.Y., Chang, T.T., Shaw, J.F., Li, W.H. and Chu, F.H. (2015) MicroRNA-Like Small RNAs Prediction in the Development of Antrodia cinnamomea. PLoS ONE, 10, e0123245.
https://doi.org/10.1371/journal.pone.0123245
[24]
Wang, B., Sun, Y.F., Song, N., Zhao, M.X., Liu, R., Feng, H., Wang, X.J. and Kang, Z.S. (2017) Puccinia striiformis f. sp. tritici MicroRNA-Like RNA 1 (Pst-milR1), an Important Pathogenicity Factor of Pst, Impairs Wheat Resistance to Pst by Suppressing the Wheat Pathogenesis-Related 2 Gene. New Phytologist, 215, 338-350.
https://doi.org/10.1111/nph.14577
[25]
Jin, Y., Zhao, J.H., Zhao, P., Zhang, T., Wang, S. and Guo, H.S. (2018) A Fungal MilRNA Mediates Epigenetic Repression of a Virulence Gene in Verticillium dahlia. Philosophical Transactions B of the Royal Society, 4, Article ID: 20180309.
https://doi.org/10.1098/rstb.2018.0309
[26]
Hu, X.Y., Hoden, K.P., Liao, Z., Asman, A. and Dixelius, C. (2022) Phytophthora infestans Ago1-Associated MiRNA Promotes Potato Late Blight Disease. New Phytologist, 233, 443-457. https://doi.org/10.1111/nph.17758
[27]
Meister, G. and Tuschl, M. (2004) Mechanisms of Gene Silencing by Double-Stranded RNA. Nature, 431, 343-349. https://doi.org/10.1038/nature02873
[28]
Jinek, M. and Doudna, J.A. (2009) A Three-Dimensional View of the Molecular Machinery of RNA Interference. Nature, 457, 405-412.
https://doi.org/10.1038/nature07755
[29]
Meister, G. (2013) Argonaute Proteins: Functional Insights and Emerging Roles. Nature, 14, 864-872. https://doi.org/10.1038/nrg3462
[30]
Khatri, M. and Rajam, M.V. (2007) Targeting Polyamines of Aspergillus nidulans by SiRNA Specific to Fungal Ornithine Decarboxylase Gene. Medical Mycology, 45, 211-220. https://doi.org/10.1080/13693780601158779
[31]
Hammond, T.M., Xiao, H., Boone, E.C., Decker, L.M., Lee, S.A., Perdue, T.D., Pukkila, P.J. and Shiu, P.K.T. (2013) Novel Proteins Required for Meiotic Silencing by Unpaired DNA and SiRNA Generation in Neurospora crassa. Genetics, 194, 91-100.
https://doi.org/10.1534/genetics.112.148999
[32]
Deshmukh, R. and Purohi, H.J. (2014) SiRNA Mediated Gene Silencing in Fusarium sp. HKF15 for Overproduction of Bikaverin. Bioresource Technology, 157, 368-371.
https://doi.org/10.1016/j.biortech.2014.02.057
[33]
Yu, R., Jih, G., Iglesias, N. and Moazed, D. (2014) Determinants of Heterochromatic SiRNA Biogenesis and Function. Molecular Cell, 53, 262-276.
https://doi.org/10.1016/j.molcel.2013.11.014
[34]
Yu, H., Tsuchida, M., Ando, M., Hashizaki, T., Shimada, A., Takahata, S. and Murakami, Y. (2021) Trimethylguanosine Synthase 1 (TGS1) Is Involved in Swi6/HP1-Independent SiRNA Production and Establishment of Heterochromatin in Fission Yeast. Genes to Cells, 26, 203-218. https://doi.org/10.1111/gtc.12833
