How do plant pathogens adapt to novel host groups? Divergent genome evolution after a host jump in the plant parasitic oomycete Hyaloperonospora crispula and its sister species Hyaloperonospora arabidopsidis.
General Genetics and Functional Genome Biology
Parasitology and Biology of Tropical Infectious Disease Pathogens
Final Report Abstract
Downy mildews are the most species rich group of oomycetes. They have diversified by host-jumps into highly host-specific species on hundreds of natural host plants. However, how they adapted to their hosts is unknown and genome analyses of sister taxa with distinct hosts are lacking for these obligate parasites. The downy mildew Hyaloperonospora crispula (Hpc) is a close relative of the Arabidopsis thaliana-infecting model species Hyaloperonospora arabidopsidis (Hpa). In contrast to Hpa and all other Hyaloperonospora species Hpc is special as it is the only species in its genus that has adapted to non-crucifer host plants of the genus Reseda. The main objective of the fellowships was to dissect molecular mechanisms that enable oomycete plant pathogens to colonise novel host groups using the obligate biotrophic oomycete Hyaloperonospora crispula (Hpc) as a model. To this end it was proposed to (A) determine differences in gene content and gene expression between Hpc and its sister species H. arabidopsidis (Hpa), (B) to use this information to select host specialization candidate genes and (C) to survey their ability to manipulate host defences in the Pseudomonas-host pathosystem. The project required reframing of the initial workplan and research goals as initial genome and RNAseq resources could not be generated due to low quantities and qualities of beforehand created DNA and RNA samples. Therefore, the initial bioinformatic screen for Hpc host specialization candidate genes which was needed to further survey their ability to manipulate host defences could not be performed. Due to a dry season new material from Hpc-infected plants occurred unusually late in the season in mid of August 2015. This did not give enough time to perform functional analyses as proposed in the application. Consequently, I focussed for the rest of the time on the identification of homologous and unique Hpc and plant genes and to perform a comparative genomics study. To this end, I performed metatranscriptomics of Reseda luteola leaves infected with H. crispula from a natural sampling site in Norwich, UK. This revealed exceptionally high quality transcriptome coverage of both parasite and host, and captured natural genetic variation. De novo assembled transcripts contained 22,387 unique open reading frames that cover 47.4% and 83.1% of conserved single-copy orthologs from plants and fungi, respectively. De novo assembled transcripts were screened for WY-fold protein-encoding genes, a sequence divergent class of virulence genes conserved in oomycete species of the Peronosporales. This revealed 47 candidate Hpc WY-fold virulence proteins in samples of Hpc-infected plants only. A phylogenetic analysis of these candidates together with 11 homologs of the close relative Hpa revealed two unique and two very distantly related homologs in Hpc, as well as two variants being absent in Hpc. This suggested gain and loss of WY-fold proteins to associate with host specialisation after the jump of Hpc to its non-Brassicaceae host group of Reseda. The broad coverage of plant genes in the obtained RNAseq dataset enabled us to survey differences in Reseda gene expression in response to an infection with Hpc. Applying a stringent adjusted p-value of 0.001 revealed 428 differentially expressed Reseda genes including genes involved in plant defense and susceptibility, e.g. several genes of the WRKY transcription factor family which encode plant specific proteins that play a major role in plant immunity. In addition, proteins of the nucleotide binding domain (NBD), leucine-rich repeat (NLR) super-family were transcriptionally de-regulated in Hpc-infected plants. In summary, gene expression in Hpc-infected plants significantly differed from healthy plants. Plant genes that are differentially expressed upon an infection suggest Hpc to interfere with its host innate immunity and defense signalling regulatory networks. Until the occurrence of Hpc in the field, I developed and performed a side project on the evolution of the plant autophagy receptor gene Atg8 that was published in Trends in Plant Science. Therein, I performed an extensive phylogenetic analysis of 376 plant Atg8s across the green plant lineage. This revealed two major lineages of plant ATG8s with one lineage being specific to embryophytes of which non-flowering land plants and gymnosperms seem to have promiscuous variants of the two clades. Each species has a distinct set of ATG8 variants that group into monophyletic clades of higher taxonomic order. Analysis of ratios of nonsynonymous and synonymous substitutions revealed overall strong purifying selection of plant ATG8 homologs and no apparent evidence for positive selection acting on particular residues. In summary, this suggests ATG8s to have radiated early during plant evolution which might have been driven by functional adaptation to different target proteins. In addition, I contributed to ongoing projects and manuscripts from the group of Sophien Kamoun.
Publications
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(2015). Identification of a new order of root-colonising fungi in the Entorrhizomycota: Talbotiomycetales ord. nov. on eudicotyledons. IMA Fungus 6(1):129-133
Riess K., Bauer R., Kellner R., Kemler M., Piątek M., Vánky K., Begerow D.
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(2016). ATG8 Expansion: A Driver of Selective Autophagy Diversification? Trends in Plant Science
Kellner, R., De la Concepcion, J. C., Maqbool, A., Kamoun, S., & Dagdas, Y. F.
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(2016). Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae. BMC Biology, 14(84), 1–11
Islam, M. T., Croll, D., Gladieux, P., Soanes, D. M., Persoons, A., Bhattacharjee, P., Hossain, Md. S., Gupta, D. R., Rahman, Md. M., Mahboob, M. G., Cook, N., Salam, M. U., Surovy, M. Z., Sancho, V. B., Maciel, J. L. N., NhaniJúnior, A., Castroagudín, V. L., de Assis Reges, J. T., Ceresini, P. C., Ravel, S., Kellner, R., Fournier, E., Tharreau, D., Lebrun, M.-H., McDonald, B. A., Stitt, T., Swan, D., Talbot, N. J., Saunders, D. G. O., Win, J., Kamoun, S.
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(2016). Emerging oomycete threats to plants and animals. Philos Trans R Soc Lond B Biol Sci, 371
Derevnina, L., Petre, B., Kellner, R., Dagdas, Y. F., Sarowar, M. N., Giannakopoulou, A., De Concepcion, J. C., Chaparro-Garcia, A., Pennington, H. G., Van West, P., Kamoun, S.
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(2016). Nine things to know about elicitins. New Phytologist
Derevnina L., Dagdas Y.F., de la Concepcion J.C., Bialas A., Kellner R., Petre B., Domazakis E., Du J., Wu C., Lin X., Aguilera-Galvez C., Cruz-Mireles N., Vleeshouwers V.G.A.A. & Kamoun S.
