SAMN02927145
External Id
INRA
INSDC center name
2014-07-18T00:00:00Z
INSDC first public
2022-10-14T21:06:44.389Z
INSDC last update
SRS663233
INSDC secondary accession
live
INSDC status
MIGS.eu
NCBI submission model
MIGS/MIMS/MIMARKS.plant-associated
NCBI submission model
MIGS.eu.plant-associated.6.0
NCBI submission package
SRS663233
SRA accession
1994
collection date
Melampsora larici-populina is a fungal pathogen responsible for foliar rust disease on poplar trees causing important damages worldwide and particularly in plantations of Northern Europe. The reference genome of the isolate 98AG31 was previously sequenced by Sanger using a whole genome shotgun strategy revealing a large genome of 101 megabases containing 16,399 predicted genes including small secreted proteins (SSP) genes representing candidate poplar rust effectors. In order to explore the genetic variation of the poplar rust fungus at the genome scale, we used an Illumina-based resequencing approach and sequenced at a higher sequencing depth the genome of 15 isolates collected over the past 20 years throughout the French territory and presenting distinct virulence profiles, including the reference isolate 98AG31. Comparison to the reference genome sequence revealed a high level of polymorphism, with more than 611,824 single-nucleotide polymorphism (SNP) positions overall. We report here on the SNPs and insertions/deletions found in coding and non-coding regions as well as missing regions revealed by coverage and sequencing depth analysis between isolates. Based on the accumulation of non-synonymous substitutions in coding sequences and the amounts of synonymous and non-synonymous polymorphisms (i.e. PN/PS), we identify candidate genes, including those encoding SSPs that may be involved in fungal pathogenesis
description
poplar nursery
env biome
poplar nursery
env feature
poplar leaf
env_material
101
estimated size
France: Saulchoy
geo loc name
Populus euramericana Luisa Avanzo
host
PMID:21536894
isol_growth_condt
94ZZ15
isolate
50.3500 N 1.8333 E
lat lon
1
num_replicons
Melampsora laricis-populina
http://purl.obolibrary.org/obo/NCBITaxon_203908
organism
diploid
http://purl.obolibrary.org/obo/CL_0000415
ploidy
eukaryote: asexual
propagation
Melampsora larici-populina
http://purl.obolibrary.org/obo/NCBITaxon_203908
strain
MIGS Eukaryotic sample from Melampsora laricis-populina
title