Biology subjects

Langlands-Perry, C.

Publications and source records attributed to Langlands-Perry, C..

3 recordsLinked to original sources

bioRxiv2026

Additive and epistatic QTL contribute to the adaptation of the fungus Leptosphaeria maculans to Brassica carinata

Leptosphaeria maculans is a plant-pathogenic fungus that infects Brassica species, including Brassica napus (oilseed rape). Breeding oilseed rape varieties with genetic resistance is an efficient way to control the disease; however, L. maculans can adapt and overcome these resistances. Understanding the mechanisms that enable L. maculans to adapt is crucial for managing the emergence of better-adapted isolates. Brassica carinata, the Ethiopian Mustard, although closely related to B. napus, is considered a nonhost species of L. maculans because this fungus cannot infect it. Despite the extreme resistance of B. carinata, one natural L. maculans isolate has been identified as unable to infect B. napus, causing moderate and atypical symptoms on this species. We performed a cross between this isolate and an isolate adapted to B. napus, followed by a QTL analysis, which identified seven QTL, each encompassing candidate genes involved in L. maculans adaptation to B. carinata or B. napus. Additionally, we observed transgression in the progeny, wherein a few strains caused significantly more or less aggressive symptoms on both species of Brassica. We found that epistasis within the L. maculans genome contributes to the observed transgression. These initial findings provide further opportunities to study the adaptive capacities of L. maculans, as well as data to initiate analysis of the extreme resistance of B. carinata to L. maculans. HighlightsO_LISeven pathogenicity QTL identified, carrying several interesting candidate genes C_LIO_LITransgression of some progeny isolates on B. napus and B. carinata was reported C_LIO_LIEpistasis plays a significant role in the adaptation of L. maculans toward host and nonhost Brassica species C_LI

genetics↗

bioRxiv2026

EffectorGeneP: accurate gene annotation in pathogen genomes from infection transcriptomes

Accurate gene annotation is crucial for inference of biological knowledge from genomes. However, non-canonical genes such as orphan or single-exon genes as well as those residing in rapidly evolving regions are routinely dismissed in annotation pipelines. In filamentous pathogen genomes, this disproportionately affects the annotation of genes encoding disease-promoting effector proteins. We introduce EffectorGeneP, a machine learning tool that self-trains on transcript data, predicts the most likely coding sequence from transcripts and effectively separates bona fide genes from transcriptional noise. EffectorGeneP annotates over 95% of known effectors correctly, while other state-of-the-art methods annotate 15%-78%. We show that EffectorGeneP expands the predicted secretome of pathogens by over 50% and that high-throughput screening of an effector library in plant protoplasts uncovers the previously poorly annotated AvrSr26 gene family in the wheat stem rust fungus. EffectorGeneP decodes genomes at unprecedented resolution and will enable the study of biological processes in important pathogen species.

microbiology↗

bioRxiv2025

Novel clonal lineages of wheat stem rust in the Southern Cone of South America

Puccinia graminis f. sp. tritici (Pgt) causes wheat stem rust, a devastating disease of cereals. Recent approaches to examine populations at a genomic level have provided valuable information on the genotypic diversity of Pgt populations in Africa, Europe and North America and evolutionary mechanisms underlying the emergence of new races. However, an in-depth characterisation of Pgt populations in South America has been lacking. To bridge this knowledge gap, 91 Pgt isolates were collected from Argentina and Uruguay in 2020 and 2021 and used to generate transcriptome and whole genome sequence data and pathotype information. Phylogenetic analyses revealed that this South American Pgt population includes three clonal lineages, two of which have not been detected elsewhere. The third lineage is globally dispersed, including isolates from Africa and the Middle East. The predominant lineage, unique to South America, encompassed 90% of the samples and showed related pathotypes differing by virulence on single resistance genes consistent with evolution by stepwise mutation within the clonal lineage. There was no evidence of sexual recombination giving rise to new genetic diversity in this population. These observations urge to routinely incorporate and compare genotypic data from South American Pgt isolates to surveillance data from other geographic regions.

evolutionary biology↗