Biology subjects

Dauphin, B.

Publications and source records attributed to Dauphin, B..

6 recordsLinked to original sources

bioRxiv2025

Prevalence of water and nutrient availability in structuring fungal communities of healthy and decaying beech trees in forests

Background and aimsIn forest ecosystems, trees interact with a broad range of soil microorganisms, such as ectomycorrhizal fungi, improving nutrition and water uptake and mitigating biotic and abiotic stress. In the context of the predicted more frequent and more severe droughts, it is critical to characterise how trees and their associated fungal partners respond to water shortage to improve future forest management. MethodsWe investigated the importance of diverse environmental predictors (e.g., edaphic, climatic, topographic) on the fungal communities associated with the root systems of decaying and healthy beech trees in natural beech forests. In parallel, we identified specific fungal taxa linked with their host vitality and water stress gradient. ResultsWe observed that soil water shortage had a greater effect on the structuring of fungal communities than beech vitality or other environmental factors. We identified a core group of fungi that remained unaffected by water availability among all study sites, while other fungal species were more abundant in sampling sites more prone to water shortage. Finally, we showed that the abundance of ectomycorrhizal fungi was significantly associated with healthy beech root systems, while saprotrophic fungi prevailed in the roots of trees exhibiting severe decay. ConclusionsOverall, our study highlights the major role of drought in structuring fungal communities associated with beech root systems and pinpoints the key fungal taxonomic groups found in healthy beech trees.

ecology↗

bioRxiv2023

Temperature and day length drive local adaptation in the Patagonian foundation tree species Nothofagus pumilio

Climate change alters relationships among environmental conditions and thus has the potential to change the selection pressures acting on adaptive gene variants. Using a landscape genomic approach, we show that the southern beech species Nothofagus pumilio has notable genetic adaptations to climate along its 2000-kilometer-long range in the Andes. We screened 47,336 SNP loci in 1,632 contigs and found that high-latitude sampling sites have lower genetic diversity, likely due to greater impact of glacial oscillations at high latitudes. Using four genome scan methods, we identified 457 outlier SNPs that are either strongly differentiated among subpopulations or associated with environmental covariates related to temperature, day length, and precipitation. Temperature and day length parameters were associated with notably more outliers than precipitation (n = 133, 113, and 61 outliers, respectively), and almost half of all annotated outliers were related to stress response (n=38, 21%) or catabolism-metabolism (n=43, 24%). Our findings suggest that Nothofagus pumilio is an ideal Andean model of genetic adaptation to climate change because it is locally adapted to extant climate conditions, and shifting patterns among environmental parameters may be detrimental to its future survival and adaptation potential.

genetics↗

bioRxiv2023

Synchronous effective population size changes and genetic stability of forest trees through glacial cycles

The effect of past environmental changes on the demography and genetic diversity of natural populations remains a contentious issue and has rarely been investigated across multiple, phylogenetically distant species. Here, we performed comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasted European forest tree species based on concerted sampling of 164 populations across their natural ranges. For all seven species, the effective population size, Ne, increased or remained stable over many glacial cycles and up to 15 million years in the most extreme cases. Hence, surprisingly, the drastic environmental changes associated with the Pleistocene glacial cycles have had little impact on the level of genetic diversity of dominant forest tree species, despite major shifts in their geographic ranges. Based on their trajectories of Ne over time, the seven tree species can be divided into three major groups, highlighting the importance of life history and range size in determining synchronous variation in genetic diversity, over time. Altogether, our results indicate that forest trees were able to retain their evolutionary potential over very long periods of time despite strong environmental changes. One-Sentence SummaryPopulation genomic analyses reveal that forest trees retained their evolutionary potential over the Quaternary.

evolutionary biology↗

bioRxiv2021

Cryptic genetic structure and copy-number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum

Ectomycorrhizal (ECM) fungi associated with plants constitute one of the most successful symbiotic interactions in forest ecosystems. ECM support trophic exchanges with host plants and are important factors for the survival and stress resilience of trees. However, ECM clades often harbour morpho-species and cryptic lineages, with weak morphological differentiation. How this relates to intraspecific genome variability and ecological functioning is poorly known. Here, we analysed 16 European isolates of the ascomycete Cenococcum geophilum, an extremely ubiquitous forest symbiotic fungus with no known sexual or asexual spore forming structures but with a massively enlarged genome. We carried out whole-genome sequencing to identify single-nucleotide polymorphisms. We found no geographic structure at the European scale but divergent lineages within sampling sites. Evidence for recombination was restricted to specific cryptic lineages. Lineage differentiation was supported by extensive copy-number variation. Finally, we confirmed heterothallism with a single MAT1 idiomorph per genome. Synteny analyses of the MAT1 locus revealed substantial rearrangements and a pseudogene of the opposite MAT1 idiomorph. Our study provides the first evidence for substantial genome-wide structural variation, lineage-specific recombination and low continent-wide genetic differentiation in C. geophilum. Our study provides a foundation for targeted analyses of intra-specific functional variation in this major symbiosis. Originality-Significance StatementWe provide the first report on the genetic structure and copy-number variation of the globally ubiquitous and key forest symbiotic fungus Cenococcum geophilum using whole-genome sequencing data. We found divergent lineages within sampling sites, while closely related lineages appear over large geographic distances on a continental scale. Even though no sexual spore forming structures have been reported to date, we provide evidence of recombination in a specific lineage suggesting mating activity. Our findings help explain the high genetic diversity occurring within populations and their resilience to changing and adverse environmental conditions. Furthermore, we identify a single MAT1 idiomorph per genome, confirming heterothallism, and discover that major genomic rearrangements are found in their flanking regions based on chromosomal synteny analysis. Intriguingly, a pseudogene of the opposite functional idiomorph has been characterised in each genome, suggesting a common homothallic ancestor to the species. As Cenococcum geophilum is a pivotal mycorrhizal associate of a broad range of trees and shrubs providing nutrition and water supply to their hosts, we highlight and discuss the potential role of the large genome-wide structural variations in environmental selection.

genomics↗

bioRxiv2020

A reference transcriptome for the early-branching fern Botrychium lunaria enables fine-grained resolution of population structure

Ferns are the second most dominant group of land plants after angiosperms. Extant species occupy an extensive range of habitats and contribute significantly to ecosystem functioning. Despite the importance of ferns, most taxa are poorly covered by genomic resources. The genus Botrychium belongs to the family Ophioglossaceae, one of the earliest divergent lineages of vascular plants, and has a cosmopolitan distribution with 35 species, half of which are polyploids. Here, we establish a transcriptome for Botrychium lunaria, a diploid species with an extremely large genome with a 1C value of 12.10 pg. We assembled 25,701 high-quality transcripts with an average length of 1,332 bp based on deep RNA-sequencing of a single individual. We sequenced an additional 11 transcriptomes of individuals from two populations in Switzerland, including the population of the reference individual. Based on read mapping to reference transcript sequences, we identified 374,510 single nucleotide polymorphisms (SNPs) segregating among individuals for an average density of 14 SNPs per kb. The transcriptome-wide markers provided unprecedented resolution of the population genetic structure revealing substantial variation in heterozygosity among individuals. We also constructed a phylogenomic tree of 90 taxa representing all fern orders to ascertain the placement of the genus Botrychium. The high-quality transcriptomic resources enable powerful population and phylogenomic studies in an important group of ferns. Significance statementFerns pose substantial puzzles in terms of lifestyles, genome organization and population structure. Progress has been significantly hampered by the lack of genomic resources. Here, we present a transcriptome for Botrychium lunaria, a phylogenetically early-branching fern with an extremely large genome. We show that the new transcriptome improves phylogenetic resolution among early-branching ferns. Based on an additional 11 transcriptomes of the same species, we identify unexpected variation in population-level heterozygosity.

genomics↗

bioRxiv2018

Using transcriptome sequencing and pooled exome capture to study local adaptation in the giga-genome of Pinus cembra

Despite decreasing sequencing costs, whole-genome sequencing for population-based genome scans for selection is still prohibitively expensive for organisms with large genomes. Moreover, the repetitive nature of large genomes often represents a challenge in bioinformatic and downstream analyses. Here we use in-depth transcriptome sequencing to design probes for exome capture in Swiss stone pine (Pinus cembra), a conifer with an estimated genome size of 29.3 Gbp and no reference genome available. We successfully applied around 55,000 self-designed probes, targeting 25,000 contigs, to DNA pools of seven populations from the Swiss Alps and identified > 140,000 SNPs in around 13,000 contigs. The probes performed equally well in pools of the closely related species Pinus sibirica; in both species, more than 70% of the targeted contigs were sequenced at a depth [≥] 40x, i.e. the number of haplotypes in the pool. However, a thorough analysis of individually sequenced P. cembra samples indicated that a majority of the contigs (63%) represented multi-copy genes. We therefore removed paralogous contigs based on heterozygote excess and deviation from allele balance. Without putatively paralogous contigs, allele frequencies of population pools represented accurate estimates of individually determined allele frequencies. Using population genetic and landscape genomic methods, we show that inferences of neutral and adaptive genetic variation may be biased when not accounting for such multi-copy genes. Future studies should therefore put more emphasis on identifying paralogous loci, which will be facilitated by the establishment of additional high-quality reference genomes.

genomics↗