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Data from: Avirulence genes of <i>Magnaporthe oryzae</i> are a pathogen defense arsenal shaped by cognate rice resistance genes in the field

Published by Agricultural Research Service | Department of Agriculture | Catalog Last Checked: September 30, 2026 at 09:30 PM | Dataset Last Updated: September 18, 2026
The Pyricularia oryzae ‘70-15’ v3.0 (Dean et al, 2005) genome assembly and annotation files were downloaded from MycoCosm (Grigoriev et al, 2014). All the pathogen (P. oryzae) shotgun sequencing samples with collection dates, locations, and with “rice” listed as host were downloaded from the NCBI Sequence Read Archive (329 samples). Reads were trimmed using fastp v0.23.4 (Chen, 2023) and then aligned to the reference genome sequence using bwa-mem2 v2.2.1 (Vasimuddin et al, 2019). Alignments were sorted using samtools v1.20 and then fed through the bcftools v1.21-106-g2d84e07e mpileup-call pipeline (Danecek et al, 2021) to generate joint reference and variant calls at every reference genome position for all resequencing libraries.

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Complete Metadata
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accessLevel public
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contactPoint 
{
  "fn": "Jia, Yulin",
  "hasEmail": "mailto:yulin.jia@usda.gov"
}
description <p dir="ltr">The <i>Pyricularia oryzae</i> ‘70-15’ v3.0 (Dean et al, 2005) genome assembly and annotation files were downloaded from MycoCosm (Grigoriev et al, 2014). All the pathogen (<i>P. oryzae</i>) shotgun sequencing samples with collection dates, locations, and with “rice” listed as host were downloaded from the NCBI Sequence Read Archive (329 samples). Reads were trimmed using fastp v0.23.4 (Chen, 2023) and then aligned to the reference genome sequence using bwa-mem2 v2.2.1 (Vasimuddin et al, 2019). Alignments were sorted using samtools v1.20 and then fed through the bcftools v1.21-106-g2d84e07e mpileup-call pipeline (Danecek et al, 2021) to generate joint reference and variant calls at every reference genome position for all resequencing libraries.</p>
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identifier 10.15482/USDA.ADC/28850993.v1
keyword 
[
  "Avirulence genes",
  "Generalized Linear Modeling",
  "evolutionary arms-race",
  "longitudinal pathogen survey",
  "oryza sativa",
  "resistance gene",
  "rice blast fungus Pyricularia oryzae",
  "rice blast pathosystem"
]
license https://creativecommons.org/publicdomain/zero/1.0/
modified 2026-09-18
programCode 
[
  "005:040"
]
publisher 
{
  "name": "Agricultural Research Service",
  "@type": "org:Organization"
}
temporal 2025-01-01/2025-04-30
title Data from: Avirulence genes of <i>Magnaporthe oryzae</i> are a pathogen defense arsenal shaped by cognate rice resistance genes in the field

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