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The stem rust fungus Puccinia graminis f. sp. tritici induces waves of small RNAs with opposing profiles during wheat infection

By Jana Sperschneider, Silke Jacques, Bo Xu, Narayana M. Upadhyaya, Rohit Mago, Ashley W Jones, Benjamin Schwessinger, Melania Figueroa, Karam B Singh, Eric A Stone, Ming-Bo Wang, Jennifer M Taylor, Peter N. Dodds

Posted 14 Nov 2018
bioRxiv DOI: 10.1101/469338

The fungus Puccinia graminis f. sp. tritici ( Pgt ) causes devastating stem rust disease on wheat. Infection occurs when rust spores germinate on the leaf surface and subsequently, specialized infection structures called haustoria form inside host cells followed by sporulation. Small RNA and transcriptome sequencing during Pgt -wheat infection reveals that the Pgt RNA interference (RNAi) machinery has functionally diversified. A number of Pgt RNAi genes are strongly up-regulated during late infection compared to the start of infection. This coincides with the production of two distinct Pgt small RNA (sRNA) profiles. At the start of infection, Pgt induces predominantly 21 nt sRNAs with a 5’ uracil derived from genes. In contrast, during late infection Pgt induces 22 nt sRNAs with a 5’ adenine derived from repeats. Strikingly, over 85% of Pgt sRNAs are differentially expressed during infection, compared to only 4% of wheat sRNAs. Using chromatin conformation capture assay data (Hi-C), we define Pgt centromeres and show that sRNAs up-regulated during late infection are derived from those repeat-rich, gene-poor and transcriptionally silent centromeric regions. We conclude that the Pgt RNAi machinery is highly regulated, resulting in differential accumulation of sRNA types throughout the infection cycle. Such tight temporal control of the RNAi machinery has thus far not been observed in fungi and might ensure genome stability during sporulation in rust fungi. Importance The wheat stem rust disease caused by Puccinia graminis f. sp. tritici ( Pgt) is one of the most devastating crop diseases and of significant global interest. Despite the availability of genomic resources, we have limited insight into how Pgt is able to quickly and aggressively overcome plant resistance. In this work, we deliver the first-time characterization of how Pgt utilizes small RNAs (sRNAs) during infection. Our work uncovers fundamental characteristics of the stem rust RNAi machinery and the first characterization of rust centromeres. Future research can use this knowledge to optimize methods of host-induced gene silencing where small RNAs from the plant operate via the fungus’s own RNAi machinery to silence genes important for causing disease.

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