Ashley Jones

This study shows that wheat- and barley-adapted Puccinia striiformis can sexually hybridize on a shared alternate host, producing progeny with novel host phenotypes.

This study evaluates the accuracy of eucalypt taxonomy by comparing gene tree topologies to a concatenated species tree, revealing inconsistencies in taxonomic groupings.

The paper presents the first T2T genome assembly of Eucalyptus recurva, revealing genomic features and conservation insights.

The paper identifies a novel class of resistance genes in Myrtaceae, TNJ, characterized by Jacalin domains replacing LRRs, and suggests their role in pathogen recognition.

This paper presents the first chromosome-scale, haplotype-resolved nuclear genome assembly for Chiloglottis trapeziformis, revealing structural variation and repeat-rich features.

The paper uses genomic data to predict disease resistance in Melaleuca quinquenervia, enabling marker-assisted restoration efforts against myrtle rust.

The paper identifies a cold-adaptation locus, CHILL1, in Eucalyptus species through pangenome analysis and landscape genomics, showing its strong predictive power for cold adaptation.

This paper presents a near telomere-to-telomere, haplotype-resolved genome of Spinifex sericeus, revealing structural variation and repetitive content that may drive genome evolution.

This study presents a chromosome-level genome of Austropuccinia psidii, revealing its unique genomic features and infection dynamics across diverse hosts.

The paper uses genomics and resistance assays to identify resistant individuals in two tree species affected by myrtle rust, highlighting the potential for genetic breeding programs.

The paper uses long-read genomics to study dikaryotic fungus genome biology, revealing nuclear-specific evolution and allele-specific expression.

The paper assembles a high-quality mite genome from contaminated host plant sequencing data, revealing genome streamlining and a novel telomere sequence.

The paper presents a chromosome-level, haplotype-resolved genome of Eucalyptus regnans, revealing structural variations and haplotype-specific genes that may contribute to environmental adaptation.

The paper analyzes genome architecture divergence in Eucalyptus species using long-read sequencing to show that rearrangements drive sequence divergence after lineage separation.

The paper identifies and characterizes interspecies structural variants in Eucalyptus species, revealing their role in genetic differentiation and adaptive divergence.

The paper evaluates bioinformatics tools for detecting human endogenous retroviral insertions in short-read genome sequencing data, finding performance variability across datasets and recommending a consensus approach.

The paper presents a chromosome-level pseudo-phased genome for Melaleuca quinquenervia and identifies allelic diversity in NLR-type resistance genes using a novel pipeline.

RetroSnake detects HERVs in NGS data using an end-to-end pipeline validated by wet-lab experiments, producing annotated insertions in an interactive HTML file.

The paper identifies and corrects phase switches in Hi-C data for dikaryotic fungus assemblies using Nanopore and HiFi sequencing, showing HiFi's superiority in phasing low heterozygosity genomes.

This paper reports the assembly of a large, highly contiguous genome for Austropuccinia psidii, revealing its expansion through transposable elements and low GC content.

This study examines how spatial, environmental, and ploidy factors influence genomic diversity and resilience in the grass species Themeda triandra.