Genomic signatures of heterokaryosis in the oomycete pathogen Bremia lactucae

Abstract

Lettuce downy mildew caused by Bremia lactucae is the most important disease of lettuce globally. This oomycete is highly variable and rapidly overcomes resistance genes and fungicides. The use of multiple read types results in a high-quality, near-chromosome-scale, consensus assembly. Flow cytometry plus resequencing of 30 field isolates, 37 sexual offspring, and 19 asexual derivatives from single multinucleate sporangia demonstrates a high incidence of heterokaryosis in B . lactucae . Heterokaryosis has phenotypic consequences on fitness that may include an increased sporulation rate and qualitative differences in virulence. Therefore, selection should be considered as acting on a population of nuclei within coenocytic mycelia. This provides evolutionary flexibility to the pathogen enabling rapid adaptation to different repertoires of host resistance genes and other challenges. The advantages of asexual persistence of heterokaryons may have been one of the drivers of selection that resulted in the loss of uninucleate zoospores in multiple downy mildews.

Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages

“…5D). It should be noted that the B. lactucae genome assembly still has a large percentage of unresolved gaps likely due to its highly heterozygous nature (36). In comparison, all three selected regions that had clustered CoLT clusters within P. citricola contigs (PcContigs) were syntenic with P. sojae centromeres ( CEN3 /PcContig2, CEN9 /PcContig1, CEN5 /PcContig26) (Figs.…”

“…To predict centromeres of the two oomycete species, namely Phytophthora citricola P0716, (Genbank: GCA_007655245.1, with permission of the author) and Bremia lactucae SF5, (GenBank: GCA_004359215.1) (36), BLASTn searches were conducted utilizing the P. sojae Copia-like transposon (CoLT) as a query. Significant hits (>90% identity and > 500 bp) were retrieved, and were plotted to all scaffolds of the B. lactucae assembly and to contigs > 10 kb of the P. citricola assembly.…”

“…P. sojae genome assembly v3.0 (www.jgi.doe.gov) spans ~82 Mb and contains 82 scaffolds; however, there are ~3 Mb of unresolved gaps (N’s) persisting in the assembly. Recently, significant progress has been made in genome assemblies of oomycetes based on long-read sequencing (35, 36); however, the identity or the nature of the DNA sequences that form essential chromosomal elements such as centromeres, remain unknown. In this study, using the evolutionarily conserved kinetochore protein CENP-A as a tool, we investigated cellular dynamics of the kinetochore complex in P. sojae , and uncovered the nature of the oomycete centromeres with the aid of long-read genome sequencing and ChIP-seq technologies.…”

Identification of the first oomycete mating-type locus sequence in the grapevine downy mildew pathogen,Plasmopara viticola

“…infestans (Haas et al 2009, ASM14294v1 assembly), Br. lactucae (Fletcher et al 2019) and Pl. halstedii (Pecrix et al 2019), with the reciprocal best hits (RBH) method using BLASTP+ (-evalue 1e -6 -qcov_hsp_perc 50 -use_sw_tback, min.…”

Genetic diversity of the spinach downy mildew pathogen based on hierarchical sampling

“…The arsenal of combined effectors from both parents as a result of sexual reproduction enable the pathogen to infect a broader range of host cultivars; 3) In both sexual and asexual reproduction, the repairing of mismatchbases during homologous recombination may result in gene conversion, a process where one DNA sequence replaces its homologous sequence so that the sequences become identical after the conversion [19,20,29]; 4) Heterokaryosis by the fusion of hyphae in fungi and oomycetes could lead to genetic variation such as aneuploidy [30][31][32][33][34]. However, the genetic diversity of P. effusa populations has not been investigated thoroughly.…”