Identification of miRNAs in sweet potato by Solexa sequencing

详细信息    查看全文

• 作者：X. Bian ; Z. E ; P. Ma ; Z. Jia ; X. Guo ; Y. Xie
• 关键词：Ipomoea batatas ; microRNAs ; deep sequencing ; conserved miRNA ; target
• 刊名：Russian Journal of Plant Physiology
• 出版年：2016
• 出版时间：March 2016
• 年：2016
• 卷：63
• 期：2
• 页码：283-292
• 全文大小：764 KB
• 参考文献：1.Pashkovskiy, P.P. and Ryazansky, S.S., Biogenesis, evolution, and functions of plant microRNAs, Biochemistry (Moscow), 2013, vol. 78, pp. 627–637.CrossRef
  2.Jones-Rhoades, M.W., Bartel, D.P., and Bartel, B., MicroRNAs and their regulatory roles in plants, Annu. Rev. Plant Biol., 2006, vol. 57, pp. 19–53.CrossRef PubMed
  3.Zhang, B., Wang, Q., and Pan, X., MicroRNAs and their regulatory roles in animals and plants, J. Cell Physiol., 2007, vol. 210, pp. 279–289.CrossRef PubMed
  4.Kozomara, A. and Griffiths-Jones, S., MiRBase: annotating high confidence microRNAs using deep sequencing data, Nucleic Acids Res., 2013, vol. 42: D68–73. doi 10.1093/nar/gkt1181CrossRef PubMed PubMedCentral
  5.Sunkar, R., Zhou, X., Zheng, Y., Zhang, W., and Zhu, J.K., Identification of novel and candidate miRNAs in rice by high throughput sequencing, BMC Plant Biol., 2008, vol. 8, p. 25.CrossRef PubMed PubMedCentral
  6.Song, C., Wang, C., Zhang, C., Korir, N.K., Yu, H., Ma, Z., and Fang, J., Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliate), BMC Genomics, 2010, vol. 11, p. 431.CrossRef PubMed PubMedCentral
  7.Zhao, C.Z., Xia, H., Frazier, T.P., Yao, Y.Y., Bi, Y.P., Li, A.Q., Li, M.J., Li, C.S., Zhang, B.H., and Wang, X.J., Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.), BMC Plant Biol., 2010, vol. 10, p. 3.CrossRef PubMed PubMedCentral
  8.Zhang, R., Marshall, D., Bryan, G.J., and Hornyik, C., Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing, PLoS One, 2013, vol. 8, pp. e57233.CrossRef
  9.Zhu, Q.H. and Helliwell, C.A., Regulation of flowering time and floral patterning by miR172, J. Exp. Bot., 2010, vol. 62, p. 9.
  10.Sakaguchi, J. and Watanabe, Y., MiR165/166 and the development of land plants, Dev. Growth Differ., 2012, vol. 54, pp. 93–99.CrossRef PubMed
  11.Williams, L., Grigg, S.P., Xie, M., Christensen, S., and Fletcher, J.C., Regulation of Arabidopsis shoot apical meristem and lateral organ formation by microRNA miR166g and its AtHD-ZIP target genes, Development, 2005, vol. 132, pp. 3657–3668.CrossRef PubMed
  12.Guo, H.S., Xie, Q., Fei, J.F., and Chua, N.H., MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development, Plant Cell Online, 2005, vol. 17, pp. 1376–1386.CrossRef
  13.Fujii, H., Chiou, T.J., Lin, S.I., Aung, K., and Zhu, J.K., A miRNA involved in phosphate-starvation response in Arabidopsis, Curr. Biol., 2005, vol. 15, pp. 2038–2043.CrossRef PubMed
  14.Sunkar, R., Kapoor, A., and Zhu, J.K., Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance, Plant Cell Online, 2006, vol. 18, pp. 2051–2065.CrossRef
  15.Zhao, B., Ge, L., Liang, R., Li, W., Ruan, K., Lin, H., and Jin, Y., Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor, BMC Mol. Biol., 2009, vol. 10, p. 29.CrossRef PubMed PubMedCentral
  16.Lin, J.S., Lin, C.C., Lin, H.H., Chen, Y.C., and Jeng, S.T., MicroR828 regulates lignin and H2O2 accumulation in sweet potato on wounding, New Phytol., 2012, vol. 196, pp. 427–440.CrossRef PubMed
  17.Xie, F., Burklew, C.E., Yang, Y., Liu, M., Xiao, P., Zhang, B., and Qiu, D., De novo sequencing and a comprehensive analysis of purple sweet potato (Ipomoea batatas L.) transcriptome, Planta, 2012, vol. 236, pp. 101–113.CrossRef PubMed
  18.Firon, N., LaBonte, D., Villordon, A., Kfir, Y., Solis, J., Lapis, E., Perlman, T.S., Doron-Faigenboim, A., Hetzroni, A., and Althan, L., Transcriptional profiling of sweet potato (Ipomoea batatas) roots indicates downregulation of lignin biosynthesis and up-regulation of starch biosynthesis at an early stage of storage root formation, BMC Genomics, 2013, vol. 14, p. 460.CrossRef PubMed PubMedCentral
  19.Zhang, B., Pan, X., Cox, S., Cobb, G., and Anderson, T., Evidence that miRNAs are different from other RNAs, Cell. Mol. Life Sci., 2006, vol. 63, pp. 246–254.CrossRef PubMed
  20.Allen, E., Xie, Z., Gustafson, A.M., and Carrington, J.C., MicroRNA-directed phasing during trans-acting siRNA biogenesis in plants, Cell, 2005, vol. 121, pp. 207–221.CrossRef PubMed
  21.Berezikov, E., Cuppen, E., and Plasterk, R.H.A., Approaches to microRNA discovery, Nat. Genetics, 2006, vol. 38, pp. S2–S7.CrossRef PubMed
  22.Dehury, B., Panda, D., Sahu, J., Sahu, M., Sarma, K., Barooah, M., Sen, P., and Modi, M., In silico identification and characterization of conserved miRNAs and their target genes in sweet potato (Ipomoea batatas L.) expressed sequence tags (ESTs), Plant Signal. Behav., 2013, vol. 8: e26543.CrossRef PubMed PubMedCentral
  23.Farh, K.K.-H., Grimson, A., Jan, C., Lewis, B.P., Johnston, W.K., Lim, L.P., Burge, C.B., and Bartel, D.P., The widespread impact of mammalian microRNAs on mRNA repression and evolution, Science, 2005, vol. 310, pp. 1817–1821.CrossRef PubMed
  24.Patanun, O., Lertpanyasampatha, M., Sojikul, P., Viboonjun, U., and Narangajavana, J., Computational identification of microRNAs and their targets in cassava (Manihot esculenta Crantz.), Mol. Biotechnol., 2013, vol. 53, pp. 257–269.CrossRef PubMed
  25.Xie, F., Frazier, T.P., and Zhang, B., Identification, characterization and expression analysis of microRNAs and their targets in the potato (Solanum tuberosum), Gene, 2011, vol. 473, pp. 8–22.CrossRef PubMed
  26.Wang, Y., Li, K., Chen, L., Zou, Y., Liu, H., Tian, Y., Li, D., Wang, R., Zhao, F., and Brett, J.F., MicroRNA167-directed regulation of the auxin response factors, GmARF8a and GmARF8b, is required for soybean (Glycine max L.) nodulation and lateral root development, Plant Physiol., 2015, doi 10.1104/pp.15.00265
  27.Gursinsky, T., Pirovano, W., Gambino, G., Friedrich, S., Behrens, S.-E., and Pantaleo, V., Homeologs of the Nicotiana benthamiana antiviral ARGONAUTE1 show different susceptibilities to microRNA168-mediated control, Plant Physiol., 2015, vol. 168, pp. 938–952. doi 10.1104/pp.15.00070CrossRef PubMed PubMedCentral
  
• 作者单位：X. Bian (1)
  Z. E (2)
  P. Ma (1)
  Z. Jia (1)
  X. Guo (1)
  Y. Xie (1)
  
  1. Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
  2. China National Rice Research Institute, Hangzhou, China
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Plant Physiology
  Plant Sciences
  Russian Library of Science
  
• 出版者：MAIK Nauka/Interperiodica distributed exclusively by Springer Science+Business Media LLC.
• ISSN：1608-3407

文摘

MicroRNAs (miRNAs) are small endogenous RNAs, involved in plant growth and development as well as in stress responses. Among them, some are highly evolutionally conserved in the plant kingdom, which provides a powerful strategy for identifying miRNAs in a new species. Sweet potato (Ipomoea batatas L.) is one of the important food crops in the world, but few of its miRNAs have been determined. In this study, a total of 24 conserved miRNAs belonged to 14 miRNA families, and 16 novel miRNAs were identified by deep sequencing. Using previously established protocols, a total of 48 potential target genes were predicted for the conserved and novel miRNAs. These target genes are involved in transcription, metabolism, defense response, oxidationreduction processes, etc. Overall, this study provides information concerning the miRNAs precursors in I. batatas, mature miRNAs, and miRNA targets, and it is valuable as the basis for the future research of miRNA functions in I. batatas.