Biology subjects

Dussert, Y.

Publications and source records attributed to Dussert, Y..

8 recordsLinked to original sources

bioRxiv2026

Living representatives of the spiralian ancestral karyotype revealed by two Lima genomes

Conserved synteny enables the reconstruction of ancestral chromosome organization across deeply diverged lineages, as demonstrated across metazoans. In Spiralia, comparative genomic analyses have suggested an ancestral karyotype comprising 20 chromosomes. We report high-quality genome assemblies for two Lima species (Lima caribaea and Lima lima) with 20 chromosomes and show that their chromosome organization matches this ancestral state, including four previously described fusion-with-mixing events. Interestingly, other Limidae genus did not retain the ancestral karyotype: they have undergone subsequent lineage-specific fusions. The conserved organization of Lima chromosomes provides a rare genomic anchor for reconstructing ancestral chromosome organization and lineage-specific chromosome evolution across Spiralia and, more broadly, Metazoa.

genomics↗

bioRxiv2025

A rapid and accurate PCR-based method for mating-type determination in the heterothallic oomycete Plasmopara viticola, the causal agent of grapevine downy mildew

Plasmopara viticola is a heterothallic diploid oomycete responsible for grapevine downy mildew, one of the most damaging grapevine diseases worldwide. Since no rapid method for mating type characterization of strains is currently available, mating type identification must be performed through crossing assays, which are time-consuming. This study reports the development of two PCR-based molecular markers (MT_indel1 and MT_indel2) based on size variation to distinguish between the mating-type alleles of the oomycete Plasmopara viticola. For both markers, P1 strains (Mat-a/Mat-b) exhibited a double-band profile, whereas P2 strains (Mat-a/Mat-a) displayed a single PCR band. The markers were validated on a set of 37 reference strains collected across Europe and showed perfect concordance with mating-type phenotypes determined by crossing tests. They provide a robust, sensitive, and inexpensive DNA-based detection system for mating-type identification in P. viticola, offering valuable insights into the pathogens reproductive biology and genetic diversity.

molecular biology↗

bioRxiv2025

Identification of a sex-determining locus potentially involved in a conflict over sex-ratio

Sex-determining genes remain largely uncharacterized outside classical models in vertebrates and insects, leaving a gap in our understanding of their evolutionary emergence and sex chromosome formation. Terrestrial isopods, particularly the common pill bug Armadillidium vulgare, provide an excellent model for investigating these processes due to the rapid turnover in sex-determination mechanisms they undergo. In A. vulgare, multiple genetic determinants coexist. Notably, a feminizing factor is transmitted at a rate exceeding Mendelian expectations, resulting in female-biased populations. Some lineages possess a masculinizing allele at a locus referred to as the "M gene", which is functionally analogous to an XY system. Its masculinizing dominant allele is hypothesized to have been selected due to the deficit of males caused by the feminizing factor. The existence of the M gene was inferred from crosses carried out in the 1990s, but its molecular nature remains unresolved. Here, we conducted a genome-wide SNP analysis combining pooled sequencing of male and female progenies with sequencing of individual parents across two families. Bayesian estimation of haplotype frequencies in progenies enabled us to delimit a candidate genomic region of approximately two megabases containing 34 annotated genes. Most notably, one of these genes encodes the androgenic gland hormone, a protein involved in male sexual differentiation. Our findings lay the groundwork for detailed genetic and functional investigations of the M gene, offering novel insights into the dynamics of sex determination in terrestrial isopods and into the turnover of sex chromosomes in response to sex-ratio distortion.

genomics↗

bioRxiv2025

Recurrent evolution of cryptic triploids in cultivated enset increases yield

The high incidence of polyploidy in crops could be explained if domestication involved the selection of polyploids (cytotypes with more than two sets of chromosomes). Ancestral horticulture could have targeted desirable traits including yield, robustness to stress and to disease, rather than requiring knowledge of polyploidy itself. We find evidence for this process underway in enset (Ensete ventricosum, Musaceae) - a highly resilient crop constituting the main staple for over 20 million people in Ethiopia, which is clonally propagated and cultivated for its starch-rich corm and pseudostem. Prior to this study, enset was thought to be exclusively diploid (2n = 2x = 18). Using a newly-assembled chromosome-scale reference genome, and sequence data from 723 wild and domesticated enset individuals from southwestern Ethiopia, we demonstrate that around 20% of cultivated enset clones are triploid. We show that triploidy has arisen multiple times independently, that the triploid lineages have been given distinct landrace names, and planted disproportionately frequently. As well as providing evidence for enduring selection on triploids, our results reveal valuable genetic diversity captured by these triploid lines. They represent key resources for scientifically directed breeding of this major crop in the Ethiopian agrosystem, and could improve food security in sub-saharan Africa. Author SummaryDuplication of a species entire genome (polyploidization) plays an important part in evolution. Domestication may have favoured polyploid crops including wheat, coffee, potato, cotton, strawberry, and banana. It has been proposed that this trend is explained by the selection of advantageous traits exhibited by polyploids compared to their relatives with unduplicated genomes. These desirable traits include bigger fruits, seeds or other edible organs, and better tolerance to stress and disease. We unexpectedly find that a large proportion of cultivated enset lines have three copies of their genome (triploidy) instead of two (diploid). Enset is a highly resilient crop in the banana family; its stem and leaves are processed to provide one of the main food sources for over 20 million people in Ethiopia. Prior to our study, enset was thought to be exclusively diploid. Farmers use landrace names that distinguish diploids from triploids without having this new genetic information, showing the differences between them are recognised and given importance. Triploids were planted disproportionately and appear to grow faster, suggesting they are being selected for their higher productivity. These triploid ensets are an important genetic resource for scientifically directed breeding of new varieties, which could improve food security in sub-saharan Africa.

evolutionary biology↗

bioRxiv2024

Within-host environmental heterogeneity is associated with phenotypic but not genomic diversity in Wolbachia endosymbionts

The mechanisms underlying within-host diversification in parasite populations are poorly understood. Yet, phenotypic and genotypic variation in parasites can shape their evolutionary trajectories and have important epidemiological consequences. Our aim was to determine whether the constraints associated with infecting different host tissues lead to the emergence and coexistence of multiple parasite sub-populations with distinct phenotypes. We tested this hypothesis using the most widespread bacterial endosymbiont, Wolbachia. We injected Wolbachia bacteria isolated from three tissues of the common pill-bug (Armadillidium vulgare) into uninfected individuals and monitored the growth rate and virulence of each bacterial sub-population in the new hosts. Our results highlight that within-host tissue heterogeneity leads to diverse Wolbachia phenotypes. High-depth genome re-resequencing of Wolbachia sub-populations revealed that this polymorphism was not due to genomic variation but was more likely a result of phenotypic plasticity. Indeed, we found no recurrent tissue-specific genomic variation among infected individuals. Our single nucleotide polymorphism (SNP) filtration pipeline, developed to ensure SNP validity, detected only one substitution. This Wolbachia variant, observed in one female, was present in all three bacterial sub-populations, with frequencies ranging from 24% to 58% depending on the tissue. Overall, our results support the stability of the Wolbachia genome with respect to the rarity of point mutations, in agreement with reports from other symbiotic systems. From a methodological perspective, our study highlights the need for considerable caution when detecting variants in endosymbiont populations, as our conservative approach led us to exclude more than 99.5% of the initially called variants.

evolutionary biology↗

bioRxiv2020

Europe as a bridgehead in the worldwide invasion history of grapevine downy mildew, Plasmopara viticola

Europe is the historical cradle of viticulture, but grapevines have been increasingly threatened by pathogens of American origin. The invasive oomycete Plasmopara viticola causes downy mildew, one of the most devastating grapevine diseases worldwide. Despite major economic consequences, its invasion history remains poorly understood. Comprehensive population genetic analyses of ~2000 samples from the most important wine-producing countries revealed very low genetic diversity in invasive downy mildew populations worldwide. All the populations originated from one of five native North American lineages, the one parasitizing wild summer grape. After an initial introduction into Europe, invasive European populations served as a secondary source of introduction into vineyards worldwide, including China, South Africa and, twice independently, Australia. Invasion of Argentina probably represents a tertiary introduction from Australia. Our findings provide a striking example of a global pathogen invasion resulting from secondary dispersal of a successful invasive population. It will help designing quarantine regulations and efficient breeding for resistance against grapevine downy mildew.

evolutionary biology↗

bioRxiv2020

Identification of the first oomycete mating-type locus sequence in the grapevine downy mildew pathogen, Plasmopara viticola

Mating types are self-incompatibility systems that promote outcrossing in plants, fungi and oomycetes. Mating-type genes have been widely studied in plants and fungi, but have yet to be identified in oomycetes, eukaryotic organisms closely related to brown algae that cause many destructive animal and plant diseases. We identified the mating-type locus of Plasmopara viticola, the oomycete responsible for grapevine downy mildew, one of the most damaging grapevine diseases worldwide. Using a genome-wide association approach, we identified a 570 kb repeat-rich non-recombining region controlling mating types, with two highly divergent alleles. We showed that one mating type was homozygous, whereas the other was heterozygous at this locus. The mating-type locus encompassed 40 genes, including one encoding a putative hormone receptor. Our findings have fundamental implications for our understanding of the evolution of mating types, as they reveal a unique determinism involving an asymmetry of heterozygosity, as in sex chromosomes and unlike other mating-type systems. This identification of the mating-type locus in such an economically important crop pathogen also has applied implications, as outcrossing facilitates rapid evolution and resistance to harsh environmental conditions.

evolutionary biology↗

bioRxiv2018

A high-quality grapevine downy mildew genome assembly reveals rapidly evolving and lineage-specific putative host adaptation genes

Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high continuity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant-pathogen interactions. Pl. viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species.\n\nDATA AVAILABILITYRaw reads and genome assemblies have been deposited in GenBank (BioProjects PRJNA329579 for Pl. viticola and PRJNA448661 for Pl. muralis). Genome assemblies, gene annotations and analysis files (e.g. orthology relationships, full tables for GO enrichment analyses, pairwise dN/dS values and branch-site tests) have been deposited in Dataverse (Pl. viticola assembly and annotation: doi.org/10.15454/4NYHD6, Pl. muralis assembly and annotation: doi.org/10.15454/Q1QJYK, analysis files: doi.org/10.15454/8NZ8X9). Links to the data and information about the grapevine downy mildew genome project can be found at http://grapevine-downy-mildew-genome.com/.

genomics↗