DOI: 10.5061/dryad.h748p
title: Data from: Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes

description: The kingdom Stramenopile includes diatoms, brown algae, and oomycetes.
 Plant pathogenic oomycetes, including Phytophthora, Pythium and downy
 mildew species, cause devastating diseases on a wide range of host species
 and have a significant impact on agriculture. Here, we report comparative
 analyses on the genomes of thirteen straminipilous species, including
 eleven plant pathogenic oomycetes, to explore common features linked to
 their pathogenic lifestyle. We report the sequencing, assembly, and
 annotation of six Pythium genomes and comparison with other stramenopiles
 including photosynthetic diatoms, and other plant pathogenic oomycetes
 such as Phytophthora species, Hyaloperonospora arabidopsidis, and Pythium
 ultimum var. ultimum. Novel features of the oomycete genomes include an
 expansion of genes encoding secreted effectors and plant cell wall
 degrading enzymes in Phytophthora species and an over-representation of
 genes involved in proteolytic degradation and signal transduction in
 Pythium species. A complete lack of classical RxLR effectors was observed
 in the seven surveyed Pythium genomes along with an overall reduction of
 pathogenesis-related gene families in H. arabidopsidis. Comparative
 analyses revealed fewer genes encoding enzymes involved in carbohydrate
 metabolism in Pythium species and H. arabidopsidis as compared to
 Phytophthora species, suggesting variation in virulence mechanisms within
 plant pathogenic oomycete species. Shared features between the oomycetes
 and diatoms revealed common mechanisms of intracellular signaling and
 transportation. Our analyses demonstrate the value of comparative genome
 analyses for exploring the evolution of pathogenesis and survival
 mechanisms in the oomycetes. The comparative analyses of seven Pythium
 species with the closely related oomycetes, Phytophthora species and H.
 arabidopsidis, and distantly related diatoms provide insight into genes
 that underlie virulence.
description: Pythium aphanidermatum
 DAOM BR444 Genome Assembly and AnnotationPythium aphanidermatum
 DAOM BR444 Genome Assembly and Annotation Contents:
 pag1_functional_annotation.txt; pag1.maker.proteins.fasta;
 pag1.maker.transcripts.fasta; pag1_scaffolds_asm.fasta;
 pag1_scaffolds_asm.maker.gff3pag1_asm_anno.zipPythium arrhenomanes ATCC 12531 Genome Assembly and AnnotationPythium arrhenomanes ATCC 12531 Genome Assembly and Annotation Contents: par_functional_annotation.txt; par.maker.proteins.fasta; par.maker.transcripts.fasta; par_contigs_asm.fasta; par_contigs_asm.maker.gff3par_asm_anno.zipPythium irregulare DAOM BR486 Genome Assembly and AnnotationPythium irregulare DAOM BR486 Genome Assembly and Annotation Contents: pir_functional_annotation.txt; pir.maker.proteins.fasta; pir.maker.transcripts.fasta; pir_contigs_asm.fasta; pir_contigs_asm.maker.gff3pir_asm_anno.zipPythium iwayamai DAOM BR242034 Genome Assembly and AnnotationPythium iwayamai DAOM BR242034 Genome Assembly and Annotation Contents: piw_functional_annotation.txt; piw.maker.proteins.fasta; piw.maker.transcripts.fasta; piw_contigs_asm.fasta; piw_contigs_asm.maker.gff3piw_asm_anno.zipPythium ultimum var. sporangiiferum BR650 Genome Assembly and AnnotationPythium ultimum var. sporangiiferum BR650 Genome Assembly and Annotation Contents: pug3_functional_annotation.txt; pug3.maker.proteins.fasta; pug3.maker.transcripts.fasta; pug3_contigs_asm.fasta; pug3_contigs_asm.maker.gff3pug3_asm_anno.zipPythium vexans DAOM BR484 Genome Assembly and AnnotationPythium vexans DAOM BR484 Genome Assembly and Annotation Contents: pve1_func_anno.list; pve.maker.proteins.fasta; pve.maker.transcripts.fasta; pve_contigs_asm.fasta; pve_contigs_asm.maker.gff3pve_asm_anno.zip