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

Abstract

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.

Genome analysis of three isolates of Stemphylium lycopersici differ in their virulence and sporulation ability: Identification of effectors, pathogenesis and virulence factors

“…Unlike CIDEFI 212 and CIDEFI 213, CIDEFI 216 has 19 OGs that encode putative effectors including NUDIX family proteins and Had‐superfamily phosphatase that belong to large multigene families probably related to the adaptation of pathogens to invade their hosts (Cox et al., 2022). If these gene families are conformed by tandem repeats of near‐identical genes, high‐quality genome assemblies are required for the analysis of evolutionary processes.…”

A method for quantifyingPhytophthoraoospore viability using fluorescent dyes and automated image analysis

“…P. agathidicida isolates NZFS 3770 and NZFS 3772 were provided by Scion (New Zealand Forest Research Institute, Rotorua, New Zealand). Genome sequences for both isolates are available (Studholme et al 2016; Cox et al 2022). SYTO 9, FUN-1, CFDA, TOTO-3, and PI were sourced from Thermo Fisher Scientific (Waltham, Massachusetts).…”

Exploring Phytophthora agathidicida Oospore Viability and Germination

“…Aotearoa has at least 30 different species of Phytophthora that affect plants important in agriculture, horticulture, exotic forests and natural ecosystems , including P. agathidicida, which causes kauri dieback disease (Beever et al, 2009;Weir et al, 2015). The genome of P. agathidicida was recently published; the genome size is is 57 Mb, consisting of 10 chromosomes, and is made up of 34% repeatitive regions (Cox et al, 2022).…”

“…Homologous sequences were found using the P. sojae sequences of GPR11, GK4 and GK5 (Hua et al, 2013;Wang et al, 2010;Yang et al, 2013), and P. infestans sequence of Cdc14 (Latijnhouwers & Govers, 2003). These sequences were searched within the P. agathidicida genome (Cox et al, 2022) using BLAST (Altschul et al, 1990). GK5 appeared to contain an intron as it mapped to two sections of the P. agathidicida genome separated by a short stretch of bases.…”