The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome

详细信息    查看全文

• 作者：Damien Formey ; Erika Sallet ; Christine Lelandais-Brière ; Cécile Ben…
• 刊名：Genome Biology
• 出版年：2014
• 出版时间：September 2014
• 年：2014
• 卷：15
• 期：9
• 全文大小：1,621 KB
• 参考文献：1. López-Bucio, J, Cruz-Ramírez, A, Herrera-Estrella, L (2003) The role of nutrient availability in regulating root architecture. Curr Opin Plant Biol 6: pp. 280-287 CrossRef
  2. Denison, RF, Kiers, ET (2011) Life histories of symbiotic rhizobia and mycorrhizal fungi. Curr Biol 21: pp. R775-R785 CrossRef
  3. Maillet, F, Poinsot, VV, André, O, Puech-Pagès, V, Haouy, A, Gueunier, M, Cromer, L, Giraudet, D, Formey, D, Niebel, A, Martinez, EA, Driguez, H, Bécard, G, Dénarié, J, Andre, O, Puech-Pages, V, Becard, G, Denarie, J (2011) Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza. Nature 469: pp. 58-U1501 CrossRef
  4. Thomashow, LS (1996) Biological control of plant root pathogens. Curr Opin Biotechnol 7: pp. 343-347 CrossRef
  5. Jung, SC, Martinez-Medina, A, Lopez-Raez, JA, Pozo, MJ (2012) Mycorrhiza-induced resistance and priming of plant defenses. J Chem Ecol 38: pp. 651-664 CrossRef
  6. Ben, C, Toueni, M, Montanari, S, Tardin, M-C, Fervel, M, Negahi, A, Saint-Pierre, L, Mathieu, G, Gras, M-C, No?l, D, Prospéri, J-M, Pilet-Nayel, M-L, Baranger, A, Huguet, T, Julier, B, Rickauer, M, Gentzbittel, L (2013) Natural diversity in the model legume Medicago truncatula allows identifying distinct genetic mechanisms conferring partial resistance to Verticillium wilt. J Exp Bot 64: pp. 317-332 CrossRef
  7. Rey, T, Nars, A, Bonhomme, M, Bottin, A, Huguet, S, Balzergue, S, Jardinaud, M-F, Bono, J-J, Cullimore, J, Dumas, B, Gough, C, Jacquet, C (2013) NFP, a LysM protein controlling Nod factor perception, also intervenes in Medicago truncatula resistance to pathogens. New Phytol 198: pp. 875-886 CrossRef
  8. Liang, Y, Cao, Y, Tanaka, K, Thibivilliers, S, Wan, J, Choi, J, Ho, KC, Qiu, J, Stacey, G (2013) Nonlegumes respond to rhizobial Nod factors by suppressing the innate immune response. Science 341: pp. 1384-1387 CrossRef
  9. Chen, X (2010) Small RNAs - secrets and surprises of the genome. Plant J 61: pp. 941-958 CrossRef
  10. Khan, GA, Declerck, M, Sorin, CC, Hartmann, C, Crespi, M, Lelandais-Briere, C, Lelandais-Brière, C (2011) MicroRNAs as regulators of root development and architecture. Plant Mol Biol 77: pp. 47-58 CrossRef
  11. Furuta, K, Lichtenberger, R, Helariutta, Y (2012) The role of mobile small RNA species during root growth and development. Curr Opin Cell Biol 24: pp. 211-216 CrossRef
  12. Branscheid, A, Sieh, D, Pant, BD, May, P, Devers, EA, Elkrog, A, Schauser, L, Scheible, W-R, Krajinski, F (2010) Expression pattern suggests a role of MiR399 in the regulation of the cellular response to local Pi increase during arbuscular mycorrhizal symbiosis.. Mol Plant-Microbe Interact 23: pp. 915-926 CrossRef
  13. D’haeseleer, K, Herder, G, Laffont, C, Plet, J, Mortier, V, Lelandais-Brière, C, Bodt, S, Keyser, A, Crespi, M, Holsters, M, Frugier, F, Goormachtig, S (2011) Transcriptional and post-transcriptional regulation of a NAC1 transcription factor in Medicago truncatula roots. New Phytol 191: pp. 647-661 CrossRef
  14. Boualem, A, Laporte, P, Jovanovic, M, Laffont, C, Plet, J, Combier, J-P, Niebel, A, Crespi, M, Frugier, F (2008) MicroRNA166 controls root and nodule development in Medicago truncatula. Plant J 54: pp. 876-887 CrossRef
  15. Bazin, J, Khan,
• 刊物主题：Animal Genetics and Genomics; Human Genetics; Plant Genetics & Genomics; Microbial Genetics and Genomics; Fungus Genetics; Bioinformatics;
• 出版者：BioMed Central
• ISSN：1465-6906

文摘

Background Legume roots show a remarkable plasticity to adapt their architecture to biotic and abiotic constraints, including symbiotic interactions. However, global analysis of miRNA regulation in roots is limited, and a global view of the evolution of miRNA-mediated diversification in different ecotypes is lacking. Results In the model legume Medicago truncatula, we analyze the small RNA transcriptome of roots submitted to symbiotic and pathogenic interactions. Genome mapping and a computational pipeline identify 416 miRNA candidates, including known and novel variants of 78 miRNA families present in miRBase. Stringent criteria of pre-miRNA prediction yield 52 new mtr-miRNAs, including 27 miRtrons. Analyzing miRNA precursor polymorphisms in 26?M. truncatula ecotypes identifies higher sequence polymorphism in conserved rather than Medicago-specific miRNA precursors. An average of 19 targets, mainly involved in environmental responses and signalling, is predicted per novel miRNA. We identify miRNAs responsive to bacterial and fungal pathogens or symbionts as well as their related Nod and Myc-LCO symbiotic signals. Network analyses reveal modules of new and conserved co-expressed miRNAs that regulate distinct sets of targets, highlighting potential miRNA-regulated biological pathways relevant to pathogenic and symbiotic interactions. Conclusions We identify 52 novel genuine miRNAs and large plasticity of the root miRNAome in response to the environment, and also in response to purified Myc/Nod signaling molecules. The new miRNAs identified and their sequence variation across M. truncatula ecotypes may be crucial to understand the adaptation of root growth to the soil environment, notably in the agriculturally important legume crops.