@article{okagaki_nunes_sailsbery_clay_brown_john_oh_young_fitzgerald_haas_et al._2015, title={Genome sequences of three phytopathogenic species of the Magnaporthaceae family of fungi}, volume={5}, number={12}, journal={G3-Genes Genomes Genetics}, author={Okagaki, L. H. and Nunes, C. C. and Sailsbery, J. and Clay, B. and Brown, D. and John, T. and Oh, Y. and Young, N. and Fitzgerald, M. and Haas, B. J. and et al.}, year={2015}, pages={2539–2545} }
 @article{nunes_gowda_sailsbery_xue_chen_brown_oh_mitchell_dean_2011, title={Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae}, volume={12}, DOI={10.1186/1471-2164-12-288}, abstractNote={Abstract
          
            Background
            Emerging knowledge of the impact of small RNAs as important cellular regulators has prompted an explosion of small transcriptome sequencing projects. Although significant progress has been made towards small RNA discovery and biogenesis in higher eukaryotes and other model organisms, knowledge in simple eukaryotes such as filamentous fungi remains limited.
          
          
            Results
            Here, we used 454 pyrosequencing to present a detailed analysis of the small RNA transcriptome (~ 15 - 40 nucleotides in length) from mycelia and appressoria tissues of the rice blast fungal pathogen, Magnaporthe oryzae. Small RNAs mapped to numerous nuclear and mitochondrial genomic features including repetitive elements, tRNA loci, rRNAs, protein coding genes, snRNAs and intergenic regions. For most elements, small RNAs mapped primarily to the sense strand with the exception of repetitive elements to which small RNAs mapped in the sense and antisense orientation in near equal proportions. Inspection of the small RNAs revealed a preference for U and suppression of C at position 1, particularly for antisense mapping small RNAs. In the mycelia library, small RNAs of the size 18 - 23 nt were enriched for intergenic regions and repetitive elements. Small RNAs mapping to LTR retrotransposons were classified as LTR retrotransposon-siRNAs (LTR-siRNAs). Conversely, the appressoria library had a greater proportion of 28 - 35 nt small RNAs mapping to tRNA loci, and were classified as tRNA-derived RNA fragments (tRFs). LTR-siRNAs and tRFs were independently validated by 3' RACE PCR and northern blots, respectively.
          
          
            Conclusions
            Our findings suggest M. oryzae small RNAs differentially accumulate in vegetative and specialized-infection tissues and may play an active role in genome integrity and regulating growth and development.
          }, journal={BMC Genomics}, author={Nunes, C. C. and Gowda, M. and Sailsbery, J. and Xue, M. F. and Chen, F. and Brown, D. E. and Oh, Y. and Mitchell, T. K. and Dean, Ralph}, year={2011} }
 @misc{nunes_dean_2012, title={Host-induced gene silencing: a tool for understanding fungal host interaction and for developing novel disease control strategies}, volume={13}, ISSN={["1364-3703"]}, DOI={10.1111/j.1364-3703.2011.00766.x}, abstractNote={SUMMARYRecent discoveries regarding small RNAs and the mechanisms of gene silencing are providing new opportunities to explore fungal pathogen–host interactions and potential strategies for novel disease control. Plant pathogenic fungi are a constant and major threat to global food security; they represent the largest group of disease‐causing agents on crop plants on the planet. An initial understanding of RNA silencing mechanisms and small RNAs was derived from model fungi. Now, new knowledge with practical implications for RNA silencing is beginning to emerge from the study of plant–fungus interactions. Recent studies have shown that the expression of silencing constructs in plants designed on fungal genes can specifically silence their targets in invading pathogenic fungi, such as Fusarium verticillioides, Blumeria graminis and Puccinia striiformis f.sp. tritici. Here, we highlight the important general aspects of RNA silencing mechanisms and emphasize recent findings from plant pathogenic fungi. Strategies to employ RNA silencing to investigate the basis of fungal pathogenesis are discussed. Finally, we address important aspects for the development of fungal‐derived resistance through the expression of silencing constructs in host plants as a powerful strategy to control fungal disease.}, number={5}, journal={MOLECULAR PLANT PATHOLOGY}, author={Nunes, Cristiano C. and Dean, Ralph A.}, year={2012}, month={Jun}, pages={519–529} }