Browsing by Author "Sen D"

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    Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families
    (Frontiers Media S.A., 2022-11-02) Cox MP; Guo Y; Winter DJ; Sen D; Cauldron NC; Shiller J; Bradley EL; Ganley AR; Gerth ML; Lacey RF; McDougal RL; Panda P; Williams NM; Grunwald NJ; Mesarich CH; Bradshaw RE; Hane J
    Phytophthora species are notorious plant pathogens, with some causing devastating tree diseases that threaten the survival of their host species. One such example is Phytophthora agathidicida, the causal agent of kauri dieback - a root and trunk rot disease that kills the ancient, iconic and culturally significant tree species, Agathis australis (New Zealand kauri). A deeper understanding of how Phytophthora pathogens infect their hosts and cause disease is critical for the development of effective treatments. Such an understanding can be gained by interrogating pathogen genomes for effector genes, which are involved in virulence or pathogenicity. Although genome sequencing has become more affordable, the complete assembly of Phytophthora genomes has been problematic, particularly for those with a high abundance of repetitive sequences. Therefore, effector genes located in repetitive regions could be truncated or missed in a fragmented genome assembly. Using a combination of long-read PacBio sequences, chromatin conformation capture (Hi-C) and Illumina short reads, we assembled the P. agathidicida genome into ten complete chromosomes, with a genome size of 57 Mb including 34% repeats. This is the first Phytophthora genome assembled to chromosome level and it reveals a high level of syntenic conservation with the complete genome of Peronospora effusa, the only other completely assembled genome sequence of an oomycete. All P. agathidicida chromosomes have clearly defined centromeres and contain candidate effector genes such as RXLRs and CRNs, but in different proportions, reflecting the presence of gene family clusters. Candidate effector genes are predominantly found in gene-poor, repeat-rich regions of the genome, and in some cases showed a high degree of duplication. Analysis of candidate RXLR effector genes that occur in multicopy gene families indicated half of them were not expressed in planta. Candidate CRN effector gene families showed evidence of transposon-mediated recombination leading to new combinations of protein domains, both within and between chromosomes. Further analysis of this complete genome assembly will help inform new methods of disease control against P. agathidicida and other Phytophthora species, ultimately helping decipher how Phytophthora pathogens have evolved to shape their effector repertoires and how they might adapt in the future.
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    Genomic and culture-based analysis of Cyclaneusma minus in New Zealand provides evidence for multiple morphotypes
    (BioMed Central Ltd, 2024-12) Tarallo M; Dobbie KB; Leite LN; Waters TL; Gillard KNT; Sen D; Mesarich CH; Bradshaw RE; McDougal RL
    Cyclaneusma needle cast, caused by Cyclaneusma minus, affects Pinus species world wide. Previous studies suggested the presence of two distinct morphotypes in New Zealand, ‘verum’ and ‘simile’. Traditional mycological analyses revealed a third morphotype with clear differences in colony morphology and cardinal growth rates at varying temperatures. Genome sequencing of eight C. minus isolates provided further evidence of the existence of a third morphotype, named as ‘novus’ in this study. To further analyse these morphotypes, we predicted candidate effector proteins for all eight isolates, and also characterized a cell-death eliciting effector family, Ecp32, which is present in other pine phytopathogens. In concordance with their distinct classification into three different morphotypes, the number of Ecp32 family members differed, with patterns of pseudogenization in the ‘simile’ morphotype, and some members being found exclusively either in the ‘simile’ or ‘verum’ morphotypes. We also showed that the Ecp32 family proteins trigger cell death in non-host Nicotiana species, and, as previously demonstrated in other plant pathogens, the Ecp32 family proteins in C. minus adopt a β-trefoil fold. These analyses provide further evidence that the three morphotypes might be distinct species that need formal descriptions. Understanding the geographical range of different Cyclaneusma species and variations in virulence and pathogenicity will provide a better understanding of pine needle diseases and enable the development of more durable methods to control this disease.
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    Genomic, effector protein and culture-based analysis of Cyclaneusma minus in New Zealand provides evidence for multiple morphotypes
    (2023-05-21) Tarallo M; Dobbie K; Leite LN; Waters T; Gillard K; Sen D; McDougal RL; Mesarich CH; Bradshaw RE