Comparative Genomics And Transcriptomics Of The Rice Endophyte Harpophora Oryzae

Interactions between plant and fungi span a broad continuum from detrimental pathogens to beneficial symbionts. Whereas asymptomatic fungal endophytes exemplify the mutualistic or commensalistic side of this spectrum, other fungi behave as virulent pathogens that kill their host plant, or at least strongly reduce its performance and fitness. Nevertheless, fungal endophytes are generally closely related to phytopathogens. If there are any evolutional transformations between endophytes and pathogens, how it realized? Clear answers have still been lacked for this fascinating and important question yet. Infection by fungal endophytes might affect the phenotype of the host in various ways, including promoting host growth and inducing resistance of the host to pathogens or herbivores. Based on that, endophytes become an emerging tool for biological control in agri-and horticulture. Gaining insight into the evolutional relationships between fungal endophytes and pathogens will greatly improve out undersanding of funal lifestules and interactions between fungi and host plants.As a beneficial DSE, the fungus Harpophora oryzae was first described among endophytes residing in domestic Chinese wild rice （Oryza granulata）, where H. oryzae can strongly promote rice growth and biomass accumulation. In addition, H. oryzae can protect rice roots from invasion by Magnaporthe oryzae and can induce systemic resistance to rice blast, which makes it an attractive candidate for biocontrol. Phylogenetic analyses have shown that Harpophora has a close relationship to other members of the Magnaporthaceae, such as Gaeumannomyces and Magnaporthe, most of which are plant pathogens. In this study, we intend to clarify the the evolution of H. oryzae and its relative species in Magnaporthaceae and illuminate the evolutional transformations between fungal endophytes and pathogens by ancestral state reconstruction （ASR）, comparative genomics and transcriptomics and chromatography-mass spectrometry （GC-MS）. The main results are listed below:1) The most recent common ancestor of H. oryzae and its relative speciesPhylogenetic analyses showed that H. oryzae and pathogenic relatives in Magnaporthaceae, including M. oryzae, M. poae and G. graminis, were clustered into a monophyletic clade which shared the most recent common ancestor （MRCA）. Furthermore, ASR analyses revealed a trend of pathogenic being the ancestral state of MRCA shared by H. oryzae and pathogenic relatives.2) Differentiated gene contents and regulations restlted in endophtic adptions of H. oryzaeMany gene families were expanded in H. oryzae genome, including gene families involved in handling plant immune responses, metabolism of carbohydrates, signaling and transport. Furthermore, transcript profiling revealed that expressions of these genes were also remarkable different between H. and M. oryzae. Hence, the striking differences existed among the genome of H. oryzae and related species maight result in differentiation of their traits. For example, to be a root endophyte,H. oryzae not only lost the ability to infect rice leaves by losing genes indispensable for appressorium-mediated infection but also encoded more arsenals to handle plant immune responses including LysM-bearing proteins and diverse small secreted cysteine-rich proteins （SSCRPs）. Besides, compared to M. oryzae, many G-protein-coupled receptors were lost in H. oryzae genome, and the left ones showed obvious differences in their expressions, indicating differentiation in their responses to extracellular signals from the same host. To maintain biotrophy, cell wall-degrading enzyme （CWDE） expressions were suppressed in H. oryzae to avoid destruction of the plant cell wall which was different to M. oryzae.3) The main factors in the evolution of H. oryzae genome.One of the most striking features observed in the H. oryzae genome was its relatively high number of transposon-like elements which disrupted929genes and tended to be associated with specie-specific and duplicated genes. As internal dynamics of genome evolution, enhanced activity of transposons was essential for gain or loss of orphan genes, gene duplications and gene family expansions in H. oryzae genome. Besides, a retrotransposon surveillance pathway was developed by H. oryzae to counteract the strong transposon activity. Our research highlights the importance of host in the evolutional processes of fungi. By phylogenetic analysis, we showed that differentiation among M. oryzae, M. poae, G. graminis and H. oryzae occurred in response to the divergence of their hosts. Furthermore, different allocations of carbon during endophytic and pathogenetic interactions with H. and M. oryzae were used by rice which resulted in opposing trends of cell wall-degrading enzyme （CWDE） expressions in these two fungi and changing their trophic modes. HAOR₁3605, encoded a phosphate ABC transporter periplasmic phosphate-binding protein was got by horizontal gene transfer （HGT） suggested that HGT might have partly affected the H. oryzae genome.4) Evaluating the safety of H. oryzae for agricultural applicationsComparative genomics revealed no ortholog groups shared by all symbiosis but absent in non-symbiosis fungi, i.e. no "symbiosis-determining genes" which revealed symbiosis is a systematic phenotype. In addition, our findings showed that it is a long geologic time for a pathogenic ancestor to transform evolutionally to an endophyte, and predictably, the equivalent time was needed for the evolutional transformation in opposite directions, although lacking clarified processes of transformation of fungal pathogens from endophytes until now. Furthermore, the evolutional process of H. oryzae indicated that after losing many virulence related genes and establishing a stable association with host which is different from pathogens, it was not possible for H. oryzae to transform back to a pathogen, at least under natural conditions and limited time framework.