The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides

Abstract

Phytophthora cactorum is a homothallic oomycete pathogen, which has a wide host range and high capability to adapt to host defense compounds and fungicides. Here we report the 121.5 Mb genome assembly of the P. cactorum using the third-generation single-molecule real-time (SMRT) sequencing technology. It is the second largest genome sequenced so far in the Phytophthora genera, which contains 27,981 protein-coding genes. Comparison with other Phytophthora genomes showed that P. cactorum had a closer relationship with P. parasitica, P. infestans and P. capsici. P. cactorum has similar gene families in the secondary metabolism and pathogenicity-related effector proteins compared with other oomycete species, but specific gene families associated with detoxification enzymes and carbohydrate-active enzymes (CAZymes) underwent expansion in P. cactorum. P. cactorum had a higher utilization and detoxification ability against ginsenosides–a group of defense compounds from Panax notoginseng–compared with the narrow host pathogen P. sojae. The elevated expression levels of detoxification enzymes and hydrolase activity-associated genes after exposure to ginsenosides further supported that the high detoxification and utilization ability of P. cactorum play a crucial role in the rapid adaptability of the pathogen to host plant defense compounds and fungicides.

Genome Sequence Resource for the Ramie Oomycete Pathogen Phytopythium vexans HF1

“…The corresponding annotated protein information between these two genomes was analyzed and presented in Supplementary Table S6. The obtained genome size and gene content of HF1 are similar to those of other oomycete phytopathogens reported earlier (Adhikari et al 2013;Yang et al 2018). Overall, due to the combined high-coverage Illumina HiSeq and PacBio sequencing of strain HF1, we believe that the HF1 genome assembly presented here is a more complete and accurate description of the P. vexans genome than that published previously for strain CBS 119.80.…”

“…The genome size for strain CBS 119.80 was estimated at 33.85 Mb, containing 11,957 protein-coding genes. This estimated genome size and gene number for P. vexans CBS 119.80 were the smallest among all the oomycete phytopathogens sequenced so far (Adhikari et al 2013;Yang et al 2018). These and additional genome annotation statistics of CBS 119.80 are shown in Table 1.…”

“…Comparisons with the fungal and oomycete virulence factors database via Diamond V0.8.35 revealed 1,461 putative virulence genes. By comparing with the published literature, 28 of the 1,461 putative virulence genes have been confirmed as virulence factors in oomycetes (Yang et al 2018) (Supplementary Table S2). Based on features related to signal peptide, transmembrane domain, cysteine number, and protein length, 239 of these 1,461 were identified as candidate effectors ( Supplementary Table S3).…”

Genome sequencing of oomycete isolates from Chile supports the New Zealand origin of Phytophthora kernoviae and makes available the first Nothophytophthora sp. genome

“…This revealed that the content of repetitive elements for the New Zealand strains was approximately 8.6% each, whereas the Chilean and UK isolates ranged from 10.7% to 16.48% and 5.98% to 7.48%, respectively (Table , see Supporting Information). Overall, these results are lower than those for previously reported genomes of Phytophthora species, such as P. cactorum (46.7%) (Yang et al ., ), P. ramorum (28%), P. sojae (38%) and P. infestans (74%) (Haas et al , ), but may simply reflect differences in sequencing and assembly methods, with redundant sequences being collapsed to single contigs. Of all the genomes analysed in this study, Chile 5 showed the greatest overall repetitive sequence content.…”

Characterization of Two Satellite DNA Families in the Genome of the Oomycete Plant Pathogen Phytophthora parasitica

“…Despite the numerous commonalities evoked above, oomycetes, which are grouped with diatoms and brown algae within stramenopiles (Adl et al, 2019), differ from fungi by a number of features, such as metabolic and structural particularities, as well as a probable, although largely understudied, diploidy (Kamoun et al, 2015). The assembly of genome sequences allowed identifying a large catalog of TEs of oomycetes (Tyler et al, 2006;Haas et al, 2009;Baxter et al, 2010;Jiang et al, 2013;Liu et al, 2016;Ye et al, 2016;Ali et al, 2017;Yang et al, 2018;Malar et al, 2019), but it did not provide any information on their chromosomal organization. The ploidy level and the chromosome number have been determined in a handful of Phytophthora species (Sansome and Brasier, 1974;Sansome et al, 1975;Brasier et al, 1999), which are far from reflecting the diversity of the thousands of oomycete species, and variability and abnormalities appear to be common (Biasi et al, 2016).…”