Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families

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dc.citation.volume13
dc.contributor.authorCox MP
dc.contributor.authorGuo Y
dc.contributor.authorWinter DJ
dc.contributor.authorSen D
dc.contributor.authorCauldron NC
dc.contributor.authorShiller J
dc.contributor.authorBradley EL
dc.contributor.authorGanley AR
dc.contributor.authorGerth ML
dc.contributor.authorLacey RF
dc.contributor.authorMcDougal RL
dc.contributor.authorPanda P
dc.contributor.authorWilliams NM
dc.contributor.authorGrunwald NJ
dc.contributor.authorMesarich CH
dc.contributor.authorBradshaw RE
dc.contributor.editorHane J
dc.coverage.spatialSwitzerland
dc.date.accessioned2023-12-15T01:34:16Z
dc.date.accessioned2024-07-25T06:42:21Z
dc.date.available2022-11-02
dc.date.available2023-12-15T01:34:16Z
dc.date.available2024-07-25T06:42:21Z
dc.date.issued2022-11-02
dc.description.abstractPhytophthora 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.
dc.description.confidentialfalse
dc.format.pagination1038444-
dc.identifier.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/36406440
dc.identifier.citationCox 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. (2022). Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families.. Front Microbiol. 13. (pp. 1038444-).
dc.identifier.doi10.3389/fmicb.2022.1038444
dc.identifier.eissn1664-302X
dc.identifier.elements-typejournal-article
dc.identifier.issn1664-302X
dc.identifier.number1038444
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/70720
dc.languageeng
dc.publisherFrontiers Media S.A.
dc.publisher.urihttps://www.frontiersin.org/articles/10.3389/fmicb.2022.1038444/full
dc.relation.isPartOfFront Microbiol
dc.rights(c) The author/sen
dc.rights.licenseCC BY 4.0en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectPhytophthora
dc.subjectchromatin conformation capture
dc.subjectchromosome-level genome assembly
dc.subjecteffectors
dc.subjectforest disease
dc.subjectkauri dieback
dc.subjectoomycete
dc.titleChromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families
dc.typeJournal article
pubs.elements-id458087
pubs.organisational-groupOther
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