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Comparative profiling of genome-wide small RNAs in non-heading Chinese cabbage [Brassica rapa subsp. chinensis (L.) Hanelt]

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Abstract

Non-heading Chinese cabbage is characterized with diversity of leaf shape and of leaf architecture. Small RNAs are broadly involved in leaf development. To understand how small RNAs regulated leaf shape and leaf architecture, we choose two representative genotypes of non-heading Chinese cabbage (Brassica. rapa ssp. chinensis cv Wut) with distinct leaf shapes, and performed small RNA deep sequencing. Huaq, a genotype with long blades and wide petioles, generated 13.30 million small RNA reads while Wut, a genotype with round blades and long petioles, produced 14.69 million. After normalizing to RP10M, they share 0.5 million small RNAs with about 4 million reads which are mapping to the genome. Four types of small RNAs were selected from the libraries: miRNAs, ta-siRNAs, mRNA-derived siRNAs and rasiRNAs. 45 miRNA members among 75 display different expressional level such as miR166 and miR319, which play important role in leaf development. It indicated the different leaf phenotype between Huaq and Wut that possibly regulated by miRNA dosage. One of the small RNAs originated from TAS3 is Huaq dominant. About 2 thousand small RNAs derived from genes were expressionally different between genotypes, and some of them derived from antisense chains of genes. Chloroplast derived small RNAs were found that Wut were more than Huaq, which is consistent with its greener leaves. Comparative analysis of small RNAs on genome-wide level will broaden our view of molecular events underling diversity of leaf shape and architecture.

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References

  • Adenot X, Elmayan T, Lauressergues D, Boutet S, Bouche N et al (2006) DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7. Curr Biol 16:927–932

    Article  CAS  Google Scholar 

  • Aukerman MJ, Sakai H (2003) Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 15:2730–2741

    Article  CAS  Google Scholar 

  • Axtell MJ, Bowman JL (2008) Evolution of plant microRNAs and their targets. Trends Plant Sci 13:343–349

    Article  CAS  Google Scholar 

  • Chitwood DH, Nogueira FTS, Howell MD, Montgomery TA, Carrington JC, Timmermans MCP (2009) Pattern formation via small RNA mobility. Genes Dev 23:549–554

    Article  CAS  Google Scholar 

  • Chuck G, Cigan AM, Saeteurn K, Hake S (2007) The heterochronic maize mutant Corngrass1 results from overexpression of a tandem microRNA. Nat Genet 39:544–549

    Article  CAS  Google Scholar 

  • Deisenroth C, Zhang Y (2010) Ribosome biogenesis surveillance: probing the ribosomal otein-Mdm2-p53 pathway. Oncogene 29(30):4253–60

    Article  CAS  Google Scholar 

  • Fujii H, Chiou TJ, Lin SI, Aung K, Zhu JK (2005) A miRNA involved in phosphate-starvation response in Arabidopsis. Curr Biol 15:2038–2043

    Article  CAS  Google Scholar 

  • Galichet A, Hoyerová K, Kamínek M, Gruissem W (2008) Farnesylation directs AtIPT3 subcellular localization and modulates cytokinin biosynthesis in Arabidopsis. Plant Physiol 146(3):1155–64. https://doi.org/10.1104/pp.107.107425

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hollister JD, Smith LM, Guo YL, Ott F, Weigel D, Gaut BS (2011) Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc Natl Acad Sci U S A. 108(6):2322–2327. https://doi.org/10.1073/pnas.1018222108

  • Hunter C, Willmann MR, Wut G, Yoshikawa M, de la Luz G-N, Poethig SR (2006) Transacting siRNA-mediated repression of ETTIN and ARF4 regulates heteroblasty in Arabidopsis. Development 133:2973–2981

    Article  CAS  Google Scholar 

  • Jamalkandi SA, Masoudi-Nejad A (2009) Reconstruction of Arabidopsis thaliana fully integrated small RNA pathway. Funct Integr Genomics 9:419–432

    Article  CAS  Google Scholar 

  • Juarez MT, Kui JS, Thomas J, Heller BA, Timmermans MC (2004) microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. Nature 428:84–88

    Article  CAS  Google Scholar 

  • Kidner CA, Martienssen RA (2004) Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature 428:81–84

    Article  CAS  Google Scholar 

  • Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25:1966–1967

    Article  CAS  Google Scholar 

  • Liu HH, Tian X, Li YJ, Wu CA, Zheng CC (2008) Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14(5):836–843. https://doi.org/10.1261/rna.895308

  • Mallory AC, Bartel DP, Bartel B (2005) MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell 17:1360–1375

    Article  CAS  Google Scholar 

  • Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE et al (2008) Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133:128–141

    Article  CAS  Google Scholar 

  • Mun JH, Kwon SJ, Yang TJ et al (2009) Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol 10:R111

    Article  Google Scholar 

  • Nagasaki H, Itoh J, Hayashi K, Hibara K, Satoh-Nagasawa N et al (2007) The small interfering RNA production pathway is required for shoot meristem initiation in rice. Proc Natl Acad Sci USA 104:14867–14871

    Article  CAS  Google Scholar 

  • Nikovics K, Blein T, Peaucelle A, Ishida T, Morin H, Aida M, Laufs P (2006) The balance between the MIR164A and CUC2 genes controls leaf margin serration in Arabidopsis. Plant Cell 18:2929–2945

    Article  CAS  Google Scholar 

  • Palatnik JF, Allen E, Wut X, Schommer C, Schwab R, Carrington JC, Weigel D (2003) Control of leaf morphogenesis by microRNAs. Nature 425:257–263

    Article  CAS  Google Scholar 

  • Reyes JL, Huaq NH (2007) ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J 49:592–606

    Article  CAS  Google Scholar 

  • Shukla LI, Chinnusamy V, Sunkar R (2008) The role of microRNAs and other endogenous small RNAs in plant stress responses. Biochimica Biophysica Acta 1779:743–748

    Article  CAS  Google Scholar 

  • Sieber P, Wellmer F, Gheyselinck J, Riechmann JL, Meyerowitz EM (2007) Redundancy and specialization among plant microRNAs: role of the MIR164 family in developmental robustness. Development 134:1051–1060

    Article  CAS  Google Scholar 

  • Steeves TA, Sussex IM (1989) Patterns in plant development. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Sunkar R, Kapoor A, Zhu JK (2006) 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 18:2051–2065

    Article  CAS  Google Scholar 

  • Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136:669–687

    Article  CAS  Google Scholar 

  • Wang JW, Schwab R, Czech B, Mica E, Weigel D (2008) Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana. Plant Cell 20:1231–1243

    Article  CAS  Google Scholar 

  • Wang L, Yu X, Wang H, Lu Y, Ruiter M, Prins M, He Y (2011) A novel class of heat-responsive small rnas derived from the chloroplast genome of Chinese cabbage (Brassica rapa). BMC Genomics 12:289

    Article  Google Scholar 

  • Wenkel S, Emery J, Hou BH, Evans MM, Barton MK (2007) A feedback regulatory module formed by LITTLE ZIPPER and HD-ZIPIII genes. Plant Cell 19:3379–3390

    Article  CAS  Google Scholar 

  • Wenkel S, Emery J, Hou BH, Evans MM, Barton MK (2007b) A feedback regulatory module formed by LITTLE ZIPPER and HD-ZIPIII genes. Plant Cell 19:3379–3390

    Article  CAS  Google Scholar 

  • Wut MF, Tian Q, Reed JW (2006) Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction. Development 133:4211–4218

    Article  Google Scholar 

  • Xuemei C (2009) Small RNAs and their roles in plant development cell. Dev Biol 25:21–44

    Google Scholar 

  • Yu X, Wang H, Lu Y, de Ruiter M, Cariaso M, Prins M, van Tunen A, He Y (2011) Identification of conserved and novel miRNAs that are responsive to heat stress in Brassica rapa. J Exp Bot 2012(63):1025–1038

    Google Scholar 

  • Zhong R, Ye ZH (2007) Regulation of HD-ZIP III genes by microRNA 165. Plant Signal Behav 2:351–353

    Article  Google Scholar 

  • Zhou Y, Liu X, Engstrom EM, Nimchuk ZL, Pruneda-Paz JL, Tarr PT, Yan A, Kay SA, Meyerowitz EM (2015) Control of plant stem cell function by conserved interacting transcriptional regulators. Nature. 517(7534):377–80. https://doi.org/10.1038/nature13853

    Article  CAS  PubMed  Google Scholar 

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  1. Xuxin Liu and Xiang Yu have contributed equally to this paper.

Authors and Affiliations

  1. National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China

    Xuxin Liu, Xiang Yu, Han Wang & Yuke He

  2. Xinjiang Agricultural Vocational Technical College, Wenghua East Road No.29, Changji, 831100, Xinjiang, China

    Xuxin Liu

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  1. Xuxin Liu
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  2. Xiang Yu
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  3. Han Wang
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  4. Yuke He
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Correspondence to Yuke He.

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We declare that we have no financial and personal relationships with other people or organizations that can inappropriately influence our work, there is no professional or other personal interest of any nature or kind in any product, service and/or company that could be construed as influencing the position presented in, or the review of, the manuscript entitled, “Comparative profiling of genome-wide small RNAs in non-heading Chinese cabbage (Brassica rapa ssp. chinensis)”.

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Liu, X., Yu, X., Wang, H. et al. Comparative profiling of genome-wide small RNAs in non-heading Chinese cabbage [Brassica rapa subsp. chinensis (L.) Hanelt]. Genet Resour Crop Evol 69, 373–384 (2022). https://doi.org/10.1007/s10722-021-01236-y

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