Haplotype-phased assemblies of the two poplar rust fungi species: Melampsora larici-populina and Melampsora allii-populina
Abstract
Dikaryotic rust fungi maintain 2 distinct haploid nuclei for most of their life cycle, making their large, repeat-rich genomes difficult to assemble and phase. Here we present haplotype-phased, near chromosome-scale genome assemblies for the poplar rust pathogens Melampsora larici-populina 98AG31 and Melampsora allii-populina 12AY07, generated using PacBio HiFi sequencing and Hi-C-guided scaffolding. For each species, we resolved 18 chromosomes per haplotype, providing the first near chromosome-level representations of poplar rust fungal species. M. larici-populina diploid assembly spans ∼203 Mb, while M. allii-populina reaches ∼416 Mb, with high completeness and strong collinearity between haplotypes. Compared with previous fragmented or collapsed references, these assemblies greatly improve contiguity, recover centromeric and telomeric features, and support the transposable element-driven genome size expansion in M. allii-populina. The haplotype-aware annotations of genes and predicted effectors derived from these resources will enable detailed analyses of genome architecture, repeat dynamics, and key loci such as avirulence genes. Together, these assemblies provide a robust genomic resource for investigating host adaptation, virulence evolution, and population diversity in poplar rust fungi.
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BibTeX
@article{corre2026haplotypephased,
title = {{Haplotype-phased assemblies of the two poplar rust fungi species: Melampsora larici-populina and Melampsora allii-populina}},
author = {Emma Corre and Emmanuelle Morin and Jana Sperschneider and Ammar Abdalrahem and Michael Pernaci and Igor V Grigoriev and Pascal Frey and Sébastien Duplessis and Cécile Lorrain},
journal = {G3},
year = {2026},
month = aug,
doi = {10.1093/g3journal/jkag247},
url = {https://hal.inrae.fr/hal-05787629v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Haplotype-phased assemblies of the two poplar rust fungi species: Melampsora larici-populina and Melampsora allii-populina
AU - Emma Corre
AU - Emmanuelle Morin
AU - Jana Sperschneider
AU - Ammar Abdalrahem
AU - Michael Pernaci
AU - Igor V Grigoriev
AU - Pascal Frey
AU - Sébastien Duplessis
AU - Cécile Lorrain
PY - 2026
DA - 2026/08/29
JO - G3
DO - 10.1093/g3journal/jkag247
UR - https://hal.inrae.fr/hal-05787629v1
AB - Dikaryotic rust fungi maintain 2 distinct haploid nuclei for most of their life cycle, making their large, repeat-rich genomes difficult to assemble and phase. Here we present haplotype-phased, near chromosome-scale genome assemblies for the poplar rust pathogens Melampsora larici-populina 98AG31 and Melampsora allii-populina 12AY07, generated using PacBio HiFi sequencing and Hi-C-guided scaffolding. For each species, we resolved 18 chromosomes per haplotype, providing the first near chromosome-level representations of poplar rust fungal species. M. larici-populina diploid assembly spans ∼203 Mb, while M. allii-populina reaches ∼416 Mb, with high completeness and strong collinearity between haplotypes. Compared with previous fragmented or collapsed references, these assemblies greatly improve contiguity, recover centromeric and telomeric features, and support the transposable element-driven genome size expansion in M. allii-populina. The haplotype-aware annotations of genes and predicted effectors derived from these resources will enable detailed analyses of genome architecture, repeat dynamics, and key loci such as avirulence genes. Together, these assemblies provide a robust genomic resource for investigating host adaptation, virulence evolution, and population diversity in poplar rust fungi.
SN - 2160-1836
ER -