Genome-wide identification and profiling of microRNA-like RNAs from Metarhizium anisopliae during development

Fungal Biology

Volumn 116, Issue 11, 2012, Pages 1156-1162

  Zhou, Quan ^a   Wang, Zhangxun ^a   Zhang, Jun ^a   Meng, Huimin ^a   Huang, Bo ^a  

^a ANHUI AGRICULTURAL UNIVERSITY   (China)

Author keywords

Expression profiles; Highthroughput sequencing; M. anisopliae; MicroRNA like RNAs

Indexed keywords

FUNGAL RNA; MICRORNA;

BIOCONTROL AGENT; CARBON MONOXIDE; COMPUTER SIMULATION; DATABASE; ENTOMOPATHOGENIC ORGANISM; FUNGUS; GENE EXPRESSION; GENOME; GROWTH; IDENTIFICATION METHOD; PEST CONTROL; POLYMERASE CHAIN REACTION; RNA;

ALGORITHM; ARTICLE; CHEMISTRY; FUNGAL GENOME; FUNGUS SPORE; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; HIGH THROUGHPUT SEQUENCING; METARHIZIUM; MYCELIUM; PHYSIOLOGY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ALGORITHMS; GENE EXPRESSION REGULATION, FUNGAL; GENOME, FUNGAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METARHIZIUM; MICRORNAS; MYCELIUM; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, FUNGAL; SPORES, FUNGAL;

ANIMALIA; FUNGI; HEXAPODA; HYPOCREALES; METARHIZIUM ANISOPLIAE;

EID: 84869099026     PISSN: 18786146     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.funbio.2012.09.001     Document Type: Article

References (42)

1. Allen E., Xie Z., Gustafson A.M., Sung G.H., Spatafora J.W., Carrington J.C. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nature Genetics 2004, 36:1282-1290.
2. Allen E., Xie Z.X., Gustafson A.M., Carrington J.C. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 2005, 121:207-221.
3. Ambros V., Bartel B., Bartel D.P., Burge C.B., Carrington J.C., Chen X.M., Dreyfuss G., Eddy S.R., Griffiths-Jones S., Marshall M., Matzke M., Ruvkun G., Tuschl T. A uniform system for microRNA annotation. RNA - a Publication of the RNA Society 2003, 9:277-279.
4. Axtell M.J., Westholm J.O., Lai E.C. Vive la difference: biogenesis and evolution of microRNAs in plants and animals. Genome Biology 2011, 12.
5. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2007, 131:11-29. (Reprinted from Cell, vol. 116, pp. 281-297, 2004).
6. Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233.
7. Cao Y.Q., Li M., Xia Y.X. Mapmi gene contributes to stress tolerance and virulence of the entomopathogenic fungus, Metarhizium acridum. Journal of Invertebrate Pathology 2011, 108:7-12.
8. Chen C.F., Ridzon D.A., Broomer A.J., Zhou Z.H., Lee D.H., Nguyen J.T., Barbisin M., Xu N.L., Mahuvakar V.R., Andersen M.R., Lao K.Q., Livak K.J., Guegler K.J. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Research 2005, 33:9.
9. Dang Y.K., Yang Q.Y., Xue Z.H., Liu Y. RNA interference in fungi: pathways, functions, and applications. Eukaryotic Cell 2011, 10:1148-1155.
10. Denli A.M., Tops B.B.J., Plasterk R.H.A., Ketting R.F., Hannon G.J. Processing of primary microRNAs by the Microprocessor complex. Nature 2004, 432:231-235.
11. Enright A.J., John B., Gaul U., Tuschl T., Sander C., Marks D.S. MicroRNA targets in Drosophila. Genome Biology 2004, 5.
12. Frazzon A.P.G., Vaz I.D., Masuda A., Schrank A., Vainstein M.H. In vitro assessment of Metarhizium anisopliae isolates to control the cattle tick Boophilus microplus. Veterinary Parasitology 2000, 94:117-125.
13. Freimoser F.M., Hu G., St Leger R.J. Variation in gene expression patterns as the insect pathogen Metarhizium anisopliae adapts to different host cuticles or nutrient deprivation in vitro. Microbiology-Sgm 2005, 151:361-371.
14. Gao Q.A., Jin K., Ying S.H., Zhang Y.J., Xiao G.H., Shang Y.F., Duan Z.B., Hu X.A., Xie X.Q., Zhou G., Peng G.X., Luo Z.B., Huang W., Wang B., Fang W.G., Wang S.B., Zhong Y., Ma L.J., St Leger R.J., Zhao G.P., Pei Y., Feng M.G., Xia Y.X., Wang C.S. Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum. Plos Genetics 2011, 7.
15. Gardner P.P., Daub J., Tate J.G., Nawrocki E.P., Kolbe D.L., Lindgreen S., Wilkinson A.C., Finn R.D., Griffiths-Jones S., Eddy S.R., Bateman A. Rfam: updates to the RNA families database. Nucleic Acids Research 2009, 37:D136-D140.
16. Glazov E.A., Cottee P.A., Barris W.C., Moore R.J., Dalrymple B.P., Tizard M.L. A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Research 2008, 18:957-964.
17. Gonzalez-Ibeas D., Blanca J., Donaire L., Saladie M., Mascarell-Creus A., Cano-Delgado A., Garcia-Mas J., Llave C., Aranda M.A. Analysis of the melon (Cucumis melo) small RNAome by high-throughput pyrosequencing. BMC Genomics 2011, 12.
18. Griffiths-Jones S., Saini H.K., van Dongen S., Enright A.J. miRBase: tools for microRNA genomics. Nucleic Acids Research 2008, 36:D154-D158.
19. Grishok A., Mello C.C. RNAi (Nematodes: Caenorhabditis elegans). Advances in Genetics 2002, 46:339-360.
20. Grishok A., Pasquinelli A.E., Conte D., Li N., Parrish S., Ha I., Baillie D.L., Fire A., Ruvkun G., Mello C.C. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C-elegans developmental timing. Cell 2001, 106:23-34.
21. Gruber A.R., Lorenz R., Bernhart S.H., Neuboock R., Hofacker I.L. The Vienna RNA websuite. Nucleic Acids Research 2008, 36:W70-W74.
22. John B., Enright A.J., Aravin A., Tuschl T., Sander C., Marks D.S. Human microRNA targets. Plos Biology 2004, 2:1862-1879.
23. Jones-Rhoades M.W., Bartel D.P., Bartel B. MicroRNAs and their regulatory roles in plants. Annual Review of Plant Biology 2006, 57:19-53.
24. Ketting R.F., Fischer S.E.J., Bernstein E., Sijen T., Hannon G.J., Plasterk R.H.A. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C-elegans. Genes & Development 2001, 15:2654-2659.
25. Kim V.N., Han J., Siomi M.C. Biogenesis of small RNAs in animals. Nature Reviews Molecular Cell Biology 2009, 10:126-139.
26. Kozomara A., Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Research 2010, 39:D152-D157.
27. 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., Liu Y. Diverse pathways generate microRNA-like RNAs and dicer-independent small interfering RNAs in fungi. Molecular Cell 2010, 38:803-814.
28. Lee Y., Ahn C., Han J.J., Choi H., Kim J., Yim J., Lee J., Provost P., Radmark O., Kim S., Kim V.N. The nuclear RNase III Drosha initiates microRNA processing. Nature 2003, 425:415-419.
29. Leng Y.J., Peng G.X., Cao Y.Q., Xia Y.X. Genetically altering the expression of neutral trehalase gene affects conidiospore thermotolerance of the entomopathogenic fungus Metarhizium acridum. BMC Microbiology 2011, 11.
30. Li L., Chang S.S., Liu Y. RNA interference pathways in filamentous fungi. Cellular and Molecular Life Sciences 2010, 67:3849-3863.
31. Li R.Q., Yu C., Li Y.R., Lam T.W., Yiu S.M., Kristiansen K., Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009, 25:1966-1967.
32. Liu J., Cao Y.Q., Xia Y.X. Mmc, a gene involved in microcycle conidiation of the entomopathogenic fungus Metarhizium anisopliae. Journal of Invertebrate Pathology 2010, 105:132-138.
33. Livak K.J., Schmittgen T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(T)(-Delta Delta C) method. Methods 2001, 25:402-408.
34. Lord J.C. From Metchnikoff to Monsanto and beyond: the path of microbial control. Journal of Invertebrate Pathology 2005, 89:19-29.
35. Lu C., Meyers B.C., Green P.J. Construction of small RNA cDNA libraries for deep sequencing. Methods 2007, 43:110-117.
36. Schrank A., Vainstein M.H. Metarhizium anisopliae enzymes and toxins. Toxicon 2010, 56:1267-1274.
37. Schwab R., Palatnik J.F., Riester M., Schommer C., Schmid M., Weigel D. Specific effects of microRNAs on the plant transcriptome. Developmental Cell 2005, 8:517-527.
38. Schwarz D.S., Hutvagner G., Du T., Xu Z.S., Aronin N., Zamore P.D. Asymmetry in the assembly of the RNAi enzyme complex. Cell 2003, 115:199-208.
39. St Leger R.J., Wang C.S. Genetic engineering of fungal biocontrol agents to achieve greater efficacy against insect pests. Applied Microbiology and Biotechnology 2010, 85:901-907.
40. Yu Z.B., Jian Z.F., Shen S.H., Purisima E., Wang E. Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos. Nucleic Acids Research 2007, 35:152-164.
41. Zhou J., Fu Y., Xie J., Li B., Jiang D., Li G., Cheng J. Identification of microRNA-like RNAs in a plant pathogenic fungus Sclerotinia sclerotiorum by high-throughput sequencing. Molecular Genetics and Genomics 2012, 287:275-282.
42. Zimmermann G. Review on safety of the entomopathogenic fungus Metarhizium anisopliae. Biocontrol Science and Technology 2007, 17:879-920.