Table · dataset · 2026
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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<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).
Description
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>
Links
Where it is published
- DOI doi.org/10.15482/usda.adc/28850993.v1 ↗
DOI / persistent id · from figshare com
Catalogue records · 1
- OAI-PMH record api.figshare.com/v2/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3Af… ↗
metadata API · from figshare com
Topics
- From keywords
- Astronomy & Astrophysics · Chemistry · Computer Science & AI · Earth & Environmental Science · Economics & Finance · Engineering · Genetics · Humanities · Life Sciences · Medicine & Health · Ocean & Atmospheric Science · Sequence analysis · Social Science
- Inferred from text
- Sequencing 75%
Provenance · 1 source records, 19 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| figshare | oai:figshare.com:article/28850993 | 7 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].anzsrc:field:310206 | mapping · figshare com | vocabulary-mapper@1.0.0 | keywords['Sequence analysis'] |
| concepts[field].anzsrc:group:3105 | mapping · figshare com | vocabulary-mapper@1.0.0 | keywords['Genetics'] |
| concepts[field].local:field:astronomy | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:chemistry | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:computer-science-ai | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:economics-finance | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:engineering | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:humanities | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:ocean-atmospheric | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:social-science | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[modality].local:modality:sequencing | enrichment · figshare com | keyword-concept-rules@1.0.0 | title+description (75%) |
| description | source · figshare com | connector:figshare_com@1.0.0 | /metadata/dc/description |
| license | source · figshare com | connector:figshare_com@1.0.0 | /metadata/dc/rights |
| publication_date | source · figshare com | connector:figshare_com@1.0.0 | |
| title | source · figshare com | connector:figshare_com@1.0.0 | /metadata/dc/title |