Transcriptome characteristics of filamentous fungi deduced using high-throughput analytical technologies

Briefings in Functional Genomics

Volumn 13, Issue 6, 2014, Pages 440-450

  Meijueiro, Martha Lucía ^a   Santoyo, Francisco ^a   Ramírez, Lucía ^a   Pisabarro, Antonio G ^a  

^a PUBLIC UNIVERSITY OF NAVARRE   (Spain)

Author keywords

Filamentous fungi; Microarray; RNA Seq; Transcriptome

Indexed keywords

MESSENGER RNA; MICRORNA; RIBOSOME RNA; SMALL INTERFERING RNA; SMALL NUCLEAR RNA; SMALL NUCLEOLAR RNA; TRANSCRIPTOME; TRANSFER RNA;

ANALYTIC METHOD; ARTICLE; FILAMENTOUS FUNGUS; FUNGAL DEVELOPMENT; FUNGAL GENOME; GENE CLUSTER; GENE EXPRESSION; HIGH THROUGHPUT SEQUENCING; MICROARRAY ANALYSIS; MOLECULAR DYNAMICS; NONHUMAN; PLANT FUNGUS INTERACTION; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; SACCHAROMYCES CEREVISIAE; BIOLOGY; FUNGAL GENE; FUNGUS; GENETICS; HUMAN; PROCEDURES; SEQUENCE ANALYSIS;

FUNGI;

COMPUTATIONAL BIOLOGY; FUNGI; GENES, FUNGAL; GENOME, FUNGAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84918502361     PISSN: 20412649     EISSN: 20412657     Source Type: Journal    
DOI: 10.1093/bfgp/elu033     Document Type: Article

References (92)

1. Velculescu VE, Zhang L, Zhou W, et al. Characterization of the yeast transcriptome. Cell 1997;88:243-51.
2. Croucher NJ, Thomson NR. Studying bacterial transcriptomes using RNA-seq. Curr Opin Microbiol 2010;13:619-24.
3. Browne PD, Cadillo-Quiroz H. Contribution of transcriptomics to systems-level understanding of methanogenic Archaea. Archaea 2013;2013:586369.
4. Bhadauria V, Popescu L, Zhao WS, et al. Fungal transcriptomics. Microbiol Res 2007;162:285-98.
5. Wang L, Li P, Brutnell TP. Exploring plant transcriptomes using ultra high-throughput sequencing. Brief Funct Genomics 2010;9:118-28.
6. Roy NC, Altermann E, Park ZA, et al. A comparison of analog and Next-Generation transcriptomic tools for mammalian studies. Brief Funct Genomics 2011;10:135-50.
7. Brenner S, Johnson M, Bridgham J, et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 2000;18:630-4.
8. Velculescu VE, Zhang L, Vogelstein B, et al. Serial analysis of gene expression. Science 1995;270:484-7.
9. Conway T, Schoolnik GK. Microarray expression profiling: capturing a genome-wide portrait of the transcriptome. Mol Microbiol 2003;47:879-89.
10. Mutz KO, Heilkenbrinker A, Lönne M, et al. Transcriptome analysis using next-generation sequencing. Curr Opin Biotechnol 2013;24:22-30.
11. Rio DC, Ares M, Hannon GJ, et al. Removal of ribosomal subunits (and rRNA) from cytoplasmic extracts before solubilization with SDS and deproteinization. Cold Spring Harb Protoc 2010;2010: pdb.prot5442.
12. Dogini DB, Pascoal VD, Avansini SH, et al. The new world of RNAs. GenetMol Biol 2014;37:285-93.
13. Mendes Soares LM, Valcárcel J. The expanding transcriptome: the genome as the 'Book of Sand'. EMBOJ 2006;25: 923-31.
14. Dieci G, Preti M, Montanini B. Eukaryotic snoRNAs: a paradigm for gene expression flexibility. Genomics 2009; 94:83-8.
15. Cheng J, Kapranov P, Drenkow J, et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 2005;308:1149-54.
16. Hartmann B, Valcárcel J. Decrypting the genome's alternative messages. Curr OpinCell Biol 2009;21:377-86.
17. Steen BR, Lian T, Zuyderduyn S, et al. Temperatureregulated transcription in the pathogenic fungus Cryptococcus neoformans. GenomeRes 2002;12:1386-400.
18. DeRisi J, Penland L, Brown PO, et al. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet 1996;14:457-60.
19. Bruno VM, Wang Z, Marjani SL, et al. Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq. Genome Res 2010;20: 1451-8.
20. Malone JH, Oliver B. Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biol 2011;9:34.
21. Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies for transcriptome analysis. Annu Rev GenomicsHum Genet 2009;10:135-51.
22. Nicolás FE, Ruiz-Vázquez RM. Functional diversity of RNAi-associated sRNAs in fungi. Int J Mol Sci 2013;14: 15348-60.
23. Arthanari Y, Heintzen C, Griffiths-Jones S, et al. Natural antisense transcripts and long non-coding RNA in Neurospora crassa. PLoS One 2014;9:e91353.
24. Raman V, Simon SA, Romag A, et al. Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus, Magnaporthe oryzae. BMC Genomics 2013;14:326.
25. Arrial RT, Togawa RC, Brigido MeM. Screening noncoding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis. BMC Bioinformatics 2009; 10:239.
26. Zhou Y, Chen L, Fan X, et al. DeNovo assembly of auricularia polytricha transcriptome using illumina sequencing for gene discovery and SSR marker identification. PLoS One 2014;9:e91740.
27. de Bekker C, Bruning O, Jonker MJ, et al. Single cell transcriptomics of neighboring hyphae of Aspergillus niger. Genome Biol 2011;12:R71.
28. Meyer V, Arentshorst M, Flitter SJ, et al. Reconstruction of signaling networks regulating fungal morphogenesis by transcriptomics. Eukaryot Cell 2009;8:1677-91.
29. Emrich SJ, Barbazuk WB, Li L, et al. Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res 2007;17:69-73.
30. Morozova O, Marra MA. Applications of next-generation sequencing technologies in functional genomics. Genomics 2008;92:255-64.
31. Thudi M, Li Y, Jackson SA, et al. Current state-of-art of sequencing technologies for plant genomics research. Brief Funct Genomics 2012;11:3-11.
32. Jain M. Next-generation sequencing technologies for gene expression profiling in plants. Brief Funct Genomics 2012;11: 63-70.
33. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009;25: 1105-11.
34. Trapnell C, Salzberg SL. How to map billions of short reads onto genomes. Nat Biotechnol 2009;27:455-7.
35. Trapnell C, Williams BA, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010;28:511-15.
36. Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012;7:562-78.
37. Mortazavi A, Williams BA, McCue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. NatMethods 2008;5:621-8.
38. Zheng W, Chung LM, Zhao H. Bias detection and correction in RNA-Sequencing data. BMCBioinformatics 2011;12: 290.
39. Müller S, Baldin C, Groth M, et al. Comparison of transcriptome technologies in the pathogenic fungus Aspergillus fumigatus reveals novel insights into the genome and MpkA dependent gene expression. BMC Genomics 2012; 13:519.
40. Wu J, Delneri D, O'Keefe RT. Non-coding RNAs in Saccharomyces cerevisiae: what is the function? Biochem Soc Trans 2012;40:907-11.
41. Nagalakshmi U, Wang Z, Waern K, et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008;320:1344-9.
42. Mathioni SM, Patel N, Riddick B, et al. Transcriptomics of the rice blast fungus Magnaporthe oryzae in response to the bacterial antagonist Lysobacter enzymogenes reveals candidate fungal defense response genes. PLoS One 2013; 8:e76487.
43. Sibthorp C, Wu H, Cowley G, et al. Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters. BMC Genomics 2013;14: 847.
44. Guo L, Han L, Yang L, et al. Genome and transcriptome analysis of the fungal pathogen fusarium oxysporum f. sp. cubense causing banana vascular wilt disease. PLoS One 2014;9:e95543.
45. MacDonald J, Doering M, Canam T, et al. Transcriptomic responses of the softwood-degrading white-rot fungus Phanerochaete carnosa during growth on coniferous and deciduous wood. Appl EnvironMicrobiol 2011;77:3211-18.
46. Ellison CE, Kowbel D, Glass NL, et al. Discovering functions of unannotated genes from a transcriptome survey of wild fungal isolates. MBio 2014;5:e01046-01013.
47. Ohm RA, de Jong JF, Lugones LG, et al. Genome sequence of the model mushroom Schizophyllum commune. Nat Biotechnol 2010;28:957-63.
48. Gowda M, Venu RC, Raghupathy MB, et al. Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RLSAGE, oligoarray methods. BMCGenomics 2006;7:310.
49. Kramer C, Loros JJ, Dunlap JC, et al. Role for antisense RNA in regulating circadian clock function in Neurospora crassa. Nature 2003;421:948-52.
50. Traeger S, Altegoer F, Freitag M, et al. The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution. PLoS Genet 2013;9:e1003820.
51. Kapranov P, Cheng J, Dike S, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007;316:1484-8.
52. Kempken F. Alternative splicing in ascomycetes. Appl Microbiol Biotechnol 2013;97:4235-41.
53. Grützmann K, Szafranski K, Pohl M, et al. Fungal alternative splicing is associated with multicellular complexity and virulence: a genome-wide multi-species study. DNA Res 2014; 21:27-39.
54. Bing N, Hoeschele I. Genetical genomics analysis of a yeast segregant population for transcription network inference. Genetics 2005;170:533-42.
55. Curtis RE, Kim S, Woolford JL, et al. Structured association analysis leads to insight into Saccharomyces cerevisiae gene regulation by finding multiple contributing eQTL hotspots associated with functional gene modules. BMC Genomics 2013;14:196.
56. Oh Y, Donofrio N, Pan H, et al. Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae. Genome Biol 2008;9:R85.
57. Donofrio NM, Oh Y, Lundy R, et al. Global gene expression during nitrogen starvation in the rice blast fungus, Magnaporthe grisea. Fungal Genet Biol 2006;43: 605-17.
58. Tan KC, Ipcho SV, Trengove RD, et al. Assessing the impact of transcriptomics, proteomics and metabolomics on fungal phytopathology. MolPlantPathol 2009;10:703-15.
59. Cairns T, Minuzzi F, Bignell E. The host-infecting fungal transcriptome. FEMSMicrobiol Lett 2010;307:1-11.
60. Zhu S, Dai YM, Zhang XY, et al. Untangling the transcriptome from fungus-infected plant tissues. Gene 2013;519: 238-44.
61. Kawahara Y, Oono Y, Kanamori H, et al. Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction. PLoS One 2012;7:e49423.
62. Mathioni SM, Beló A, Rizzo CJ, et al. Transcriptome profiling of the rice blast fungus during invasive plant infection and in vitro stresses. BMCGenomics 2011;12:49.
63. Martínez-Soto D, Robledo-Briones AM, Estrada-Luna AA, et al. Transcriptomic analysis of Ustilago maydis infecting Arabidopsis reveals important aspects of the fungus pathogenic mechanisms. Plant Signal Behav 2013;8.
64. Inglis DO, Voorhies M, Hocking Murray DR, et al. Comparative transcriptomics of infectious spores from the fungal pathogen Histoplasma capsulatum reveals a core set of transcripts that specify infectious and pathogenic states. Eukaryot Cell 2013;12:828-52.
65. Gan P, Ikeda K, Irieda H, et al. Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi. New Phytol 2013;197: 1236-49.
66. O'Connell RJ, Thon MR, Hacquard S, et al. Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nat Genet 2012;44: 1060-5.
67. McDowell JM. Genomic and transcriptomic insights into lifestyle transitions of a hemi-biotrophic fungal pathogen. New Phytol 2013;197:1032-4.
68. Alfaro M, Oguiza JA, Ramírez L, et al. Comparative analysis of secretomes in basidiomycete fungi. J Proteomics 2014; 102C:28-43.
69. Ambrose KV, Belanger FC. SOLiD-SAGE of endophyteinfected red fescue reveals numerous effects on host transcriptome and an abundance of highly expressed fungal secreted proteins. PLoS One 2012;7:e53214.
70. Tisserant E, Kohler A, Dozolme-Seddas P, et al. The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont. New Phytol 2012;193:755-69.
71. Larsen PE, Trivedi G, Sreedasyam A, et al. Using deep RNA sequencing for the structural annotation of the Laccaria bicolor mycorrhizal transcriptome. PLoS One 2010;5:e9780.
72. Ceccaroli P, Buffalini M, Saltarelli R, et al. Genomic profiling of carbohydrate metabolism in the ectomycorrhizal fungus Tuber melanosporum. NewPhytol 2011;189:751-64.
73. Wolfe BE, Kuo M, Pringle A. Amanita thiersii is a saprotrophic fungus expanding its range in the United States. Mycologia 2012;104:22-33.
74. Larsen PE, Sreedasyam A, Trivedi G, et al. Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome. BMCSyst Biol 2011;5:70.
75. Rineau F, Roth D, Shah F, et al. The ectomycorrhizal fungus Paxillus involutus converts organic matter in plant litter using a trimmed brown-rot mechanism involving Fenton chemistry. EnvironMicrobiol 2012;14:1477-87.
76. Trushina N, Levin M, Mukherjee PK, et al. PacC and pH-dependent transcriptome of the mycotrophic fungus Trichoderma virens. BMCGenomics 2013;14:138.
77. Jacob C, Courbot M, Martin F, et al. Transcriptomic responses to cadmium in the ectomycorrhizal fungus Paxillus involutus. FEBS Lett 2004;576:423-7.
78. Cools HJ, Fraaije BA, Bean TP, et al. Transcriptome profiling of the response of Mycosphaerella graminicola isolates to an azole fungicide using cDNA microarrays. Mol Plant Pathol 2007;8:639-51.
79. Ferreira ME, Marques EoR, Malavazi I, et al. Transcriptome analysis and molecular studies on sulfur metabolism in the human pathogenic fungus Paracoccidioides brasiliensis. Mol Genet Genomics 2006;276:450-63.
80. Nunes LR, Costa de Oliveira R, Leite DB, et al. Transcriptome analysis of Paracoccidioides brasiliensis cells undergoing mycelium-to-yeast transition. Eukaryot Cell 2005;4:2115-28.
81. Fekete C, Tholander M, Rajashekar B, et al. Paralysis of nematodes: shifts in the transcriptome of the nematode-trapping fungus Monacrosporium haptotylum during infection of Caenorhabditis elegans. Environ Microbiol 2008;10:364-75.
82. Cornman RS, Bennett AK, Murray KD, et al. Transcriptome analysis of the honey bee fungal pathogen, Ascosphaera apis: implications for host pathogenesis. BMC Genomics 2012;13:285.
83. Gao Q, Jin K, Ying SH, et al. Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum. PLoS Genet 2011;7:e1001264.
84. DiGuistini S, Wang Y, Liao NY, et al. Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. ProcNatl Acad Sci USA 2011;108:2504-9.
85. Wang TY, Chen HL, Lu MY, et al. Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses. Biotechnol Biofuels 2011;4:24.
86. Georg RC, Gomes SL. Transcriptome analysis in response to heat shock and cadmium in the aquatic fungus Blastocladiella emersonii. Eukaryot Cell 2007;6:1053-62.
87. Zajc J, Liu Y, Dai W, et al. Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent. BMCGenomics 2013;14: 617.
88. Jiang M, Li X, Zhang L, et al. Gene expression analysis of Phanerochaete chrysosporium during the transition time from primary growth to secondary metabolism. JMicrobiol 2009; 47:308-18.
89. Minami M, Kureha O, Mori M, et al. Long serial analysis of gene expression for transcriptome profiling during the initiation of ligninolytic enzymes production in Phanerochaete chrysosporium. ApplMicrobiol Biotechnol 2007;75:609-18.
90. Vanden Wymelenberg A, Gaskell J, Mozuch M, et al. Comparative transcriptome and secretome analysis of wood decay fungi Postia placenta and Phanerochaete chrysosporium. Appl EnvironMicrobiol 2010;76:3599-610.
91. Sato S, Feltus FA, Iyer P, et al. The first genomelevel transcriptome of the wood-degrading fungus Phanerochaete chrysosporium grown on red oak. Curr Genet 2009;55:273-86.
92. Martinez D, Challacombe J, Morgenstern I, et al. Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc Natl Acad Sci USA 2009;106: 1954-9.