1. Kapranov P, Willingham AT, Gingeras TR. Genome-wide transcription and the implications for genomic organization. Nat Rev Genet. 2007;8:413-23.
2. Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, et al. The reality of pervasive transcription. PLoS Biol. 2011;9:e1000625.
3. Wade JT, Grainger DC. Pervasive transcription: illuminating the dark matter of bacterial transcriptomes. Nat Rev Microbiol. 2014;12:647-53.
4. Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet. 2009;10:155-9.
5. Ma L, Bajic VB, Zhang Z. On the classification of long non-coding RNAs. RNA Biol. 2013;10:924-33.
6. Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell. 2009;136:629-41.
7. Laurent GS, Wahlestedt C, Kapranov P. The Landscape of long noncoding RNA classification. Trends Genet. 2015;31:239-51.
8. Gil N, Ulitsky I. Regulation of gene expression by cis-acting long non-coding RNAs. Nat Rev Genet. 2020;21:102-17.
9. Zhang X, Wang W, Zhu W, Dong J, Cheng Y, Yin Z, et al. Mechanisms and functions of long non-coding RNAs at multiple regulatory levels. Int J Mol Sci. 2019;20:5573.
10. Brannan CI, Dees EC, Ingram RS, Tilghman SM. The product of the H19 gene may function as an RNA. Mol Cell Biol. 1990;10:28-36.
11. Brockdorff N, Ashworth A, Kay GF, McCabe VM, Norris DP, Cooper PJ, et al. The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell. 1992;71:515-26.
12. Li L, Wang M, Wu X, Geng L, Xue Y, Wei X, et al. A long non-coding RNA interacts with Gfra1 and maintains survival of mouse spermatogonial stem cells. Cell Death Dis. 2016;7:e2140-e.
13. Jalali S, Jayaraj GG, Scaria V. Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs. Biol Direct. 2012;7:1-13.
14. Wang W, Zhuang Q, Ji K, Wen B, Lin P, Zhao Y, et al. Identification of miRNA, lncRNA and mRNA-associated ceRNA networks and potential biomarker for MELAS with mitochondrial DNA A3243G mutation. Sci Rep. 2017;7:1-13.
15. Zhang YC, Chen YQ. Long noncoding RNAs: new regulators in plant development. Biochem Biophys Res Commun. 2013;436:111-4.
16. Zaynab M, Fatima M, Abbas S, Umair M, Sharif Y, Raza MA. Long non-coding RNAs as molecular players in plant defense against pathogens. Microb Pathog. 2018;121:277-82.
17. Till P, Mach RL, Mach-Aigner AR. A current view on long noncoding RNAs in yeast and filamentous fungi. Appl Microbiol Biotechnol. 2018;102:7319-31.
18. Li J, Liu X, Yin Z, Hu Z, Zhang KQ. An overview on identification and regulatory mechanisms of long non-coding RNAs in fungi. Front Microbiol. 2021;12:638617.
19. Kramer C, Loros JJ, Dunlap JC, Crosthwaite SK. Role for antisense RNA in regulating circadian clock function in Neurospora crassa. Nature. 2003;421:948-52.
20. Till P, Pucher ME, Mach RL, Mach-Aigner AR. A long noncoding RNA promotes cellulase expression in Trichoderma reesei. Biotechnol Biofuels. 2018;11:1-16.
21. Till P, Derntl C, Kiesenhofer DP, Mach RL, Yaver D, Mach-Aigner AR. Regulation of gene expression by the action of a fungal lncRNA on a transactivator. RNA Biol. 2020;17:47-61.
22. Chacko N, Zhao Y, Yang E, Wang L, Cai JJ, Lin X. The lncRNA RZE1 controls cryptococcal morphological transition. PLoS Genet. 2015;11:e1005692.
23. Morrison EN, Donaldson ME, Saville BJ. Identification and analysis of genes expressed in the Ustilago maydis dikaryon: uncovering a novel class of pathogenesis genes. Can J Plant Pathol. 2012;34:417-35.
24. Parra-Rivero O, Pardo-Medina J, Gutiérrez G, Limón MC, Avalos J. A novel lncRNA as a positive regulator of carotenoid biosynthesis in Fusarium. Sci Rep. 2020;10:1-14.
25. Wang J, Zeng W, Xie J, Fu Y, Jiang D, Lin Y, et al. A novel antisense long noncoding RNA participates in asexual and sexual reproduction by regulating the expression of GzmetE in Fusarium graminearum. Environ Microbiol. 2021; doi:10.1111/1462-2920.15399.
26. Donaldson ME, Saville BJ. Ustilago maydis natural antisense transcript expression alters mRNA stability and pathogenesis. Mol Microbiol. 2013;89:29-51.
27. Arthanari Y, Heintzen C, Griffiths-Jones S, Crosthwaite SK. Natural antisense transcripts and long non-coding RNA in Neurospora crassa. PLoS ONE. 2014;9:e91353.
28. Donaldson ME, Ostrowski LA, Goulet KM, Saville BJ. Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression. BMC Genomics. 2017;18:1-14.
29. Kim W, Miguel-Rojas C, Wang J, Townsend JP, Trail F. Developmental dynamics of long noncoding RNA expression during sexual fruiting body formation in Fusarium graminearum. mBio. 2018;9:e01292-18.
30. Tang J, Chen X, Yan Y, Huang J, Luo C, Tom H, et al. Comprehensive transcriptome profiling reveals abundant long non‐coding RNAs associated with development of the rice false smut fungus, Ustilaginoidea virens. Environ Microbiol. 2021; doi:10.1111/1462-2920.15432.
31. Skamnioti P, Gurr SJ. Against the grain: safeguarding rice from rice blast disease. Trends Biotechnol. 2009;27:141-50.
32. Dean R, Van Kan JA, Pretorius ZA, Hammond‐Kosack KE, Di Pietro A, Spanu PD, et al. The Top 10 fungal pathogens in molecular plant pathology. Mol Plant Pathol. 2012;13:414-30.
33. Fernandez J, Orth K. Rise of a cereal killer: the biology of Magnaporthe oryzae biotrophic growth. Trends Microbiol. 2018;26:582-97.
34. Dean RA, Talbot NJ, Ebbole DJ, Farman ML, Mitchell TK, Orbach MJ, et al. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature. 2005;434:980-6.
35. Kawahara Y, Oono Y, Kanamori H, Matsumoto T, Itoh T, Minami E. Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction. PLoS ONE. 2012;7:e49423.
36. Dong Y, Li Y, Zhao M, Jing M, Liu X, Liu M, et al. Global genome and transcriptome analyses of Magnaporthe oryzae epidemic isolate 98-06 uncover novel effectors and pathogenicity-related genes, revealing gene gain and lose dynamics in genome evolution. PLoS Pathog. 2015;11:e1004801.
37. Jeon J, Lee GW, Kim KT, Park SY, Kim S, Kwon S, et al. Transcriptome profiling of the rice blast fungus Magnaporthe oryzae and its host Oryza sativa during infection. Mol Plant Microbe Interact. 2020;33:141-4.
38. Weirick T, Militello G, Müller R, John D, Dimmeler S, Uchida S. The identification and characterization of novel transcripts from RNA-seq data. Brief Bioinform. 2016;17:678-85.
39. Marchese FP, Raimondi I, Huarte M. The multidimensional mechanisms of long noncoding RNA function. Genome Biol. 2017;18:1-13.
40. Quinn JJ, Chang HY. Unique features of long non-coding RNA biogenesis and function. Nat Rev Genet. 2016;17:47.
41. Quoc NB, Bao Chau NN. The role of cell wall degrading enzymes in pathogenesis of Magnaporthe oryzae. Curr Protein Pept Sci. 2017;18:1019-34.
42. Dodds PN, Rathjen JP. Plant immunity: towards an integrated view of plant–pathogen interactions. Nat Rev Genet. 2010;11:539-48.
43. Patel RK, Jain M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 2012;7:e30619.
44. Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12:357-60.
45. Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33:290-5.
46. Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016;11:1650.
47. Nawrocki EP, Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013;29:2933-5.
48. Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E, Eddy SR, et al. Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res. 2018;46:D335-42.
49. Wang L, Park HJ, Dasari S, Wang S, Kocher JP, Li W. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res. 2013;41:e74.
50. Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014;30:1236-40.
51. Consortium R. RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Res. 2021;49:D212-20.
52. Choi J, Cheong K, Jung K, Jeon J, Lee GW, Kang S, et al. CFGP 2.0: a versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes. Nucleic Acids Res. 2013;41:D714-9.
53. Zhang N, Cai G, Price DC, Crouch JA, Gladieux P, Hillman B, et al. Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi. Sci Rep. 2018;8:1-13.
54. Yanai I, Benjamin H, Shmoish M, Chalifa-Caspi V, Shklar M, Ophir R, et al. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics. 2005;21:650-9.
55. Tafer H, Hofacker IL. RNAplex: a fast tool for RNA–RNA interaction search. Bioinformatics. 2008;24:2657-63.
56. Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, et al. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 2008;36:3420-35.
57. Tian T, Liu Y, Yan H, You Q, Yi X, Du Z, et al. agriGO v2. 0: a GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Res. 2017;45:W122-9.
58. Urban M, Cuzick A, Seager J, Wood V, Rutherford K, Venkatesh SY, et al. PHI-base: the pathogen–host interactions database. Nucleic Acids Res. 2020;48:D613-20.
59. Ho EC, Donaldson ME, Saville BJ. Detection of antisense RNA transcripts by strand-specific RT-PCR. RT-PCR Protocols: Springer; 2010. p. 125-38.