Biology subjects

Normandeau, E.

Publications and source records attributed to Normandeau, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Chromosome-scale genome assemblies of duckweeds provide insights into genomic plasticity, aquatic adaptation and morphological reduction

BackgroundDuckweeds (Lemnaceae) present a striking example of convergent genome evolution following the return from land to water. As the smallest and fastest-growing angiosperms, they exhibit extreme morphological reduction yet retain remarkable genomic plasticity through recurrent interspecific hybridisation, chromosomal rearrangements, and selective gene-family remodelling. The genomic mechanisms that distinguish this secondarily aquatic lifestyle from terrestrial ancestors, and whether these changes are convergent with other aquatic lineages such as seagrasses, have remained incompletely resolved. ResultsHere we report chromosome-scale genome assemblies for four duckweed species, Spirodela polyrhiza, Lemna minuta, Lemna japonica, and Lemna aequinoctialis, generated with PacBio HiFi long reads and Omni-C chromatin conformation capture. These assemblies include the first genomic characterisation of an unresolved hybrid lineage (L. aequinoctialis x) that harbours a previously uncharacterised 3.5 Mb reciprocal translocation between subgenomes, as well as confirmation of the allodiploid origin of L. japonica. Comparative phylogenomics with land plants and the seagrass Zostera marina reveals a coherent, non-random programme of gene loss: effector-triggered immunity (ETI) components (EDS1 and PAD4) and the high-affinity nitrate transporter NRT2 are convergently absent across duckweeds and Zostera marina, consistent with relaxed pathogen pressure and abundant dissolved nutrients in aquatic habitats. In contrast, secondary-metabolite biosynthesis pathways for flavonoids, anthocyanins, flavones and flavonols are retained or expanded despite overall genome compaction. ConclusionThese findings illustrate how the return to aquatic environments following terrestrialisation shaped duckweed genome evolution through convergent gene loss and selective pathway retention, and provide high-quality genomic resources to support future research in plant evolutionary biology and biotechnology.

genomics↗

bioRxiv2024

Leveraging whole genomes, mitochondrial DNA, and haploblocks to decipher complex demographic histories: an example from a broadly admixed arctic fish

The study of phylogeography has transitioned from mitochondrial haplotypes to genome-wide analyses, blurring the line between this field and population genomics. Whole-genome sequencing offers the opportunity to join use both and provides the density of markers necessary to investigate genetic linkage and recombination along the genome. This facilitates the unraveling of complex demographic histories of admixture between divergent lineages, as is often the case in species evolving in recently deglaciated habitats. In this study, we sequenced 1120 Arctic Char genomes from 33 populations across Canada and Western Greenland to characterize patterns of genetic variation and diversity, and how they are shaped by hybridization between the Arctic and Atlantic glacial lineages. Several lines of evidence supported mito-nuclear discordance in lineage distribution, with all Canadian populations under the 66th parallel being characterized by introgression from the Atlantic lineage, leading to higher nuclear genetic diversity. By scanning the genome using local PCAs, we identified putative low-recombining haploblocks as local ancestry tracts from either lineage and described the impacts of recombination on the introgression landscape in admixed populations. Finally, we inferred conflicting origins of recolonization using whole genomes vs. ancestry tracts for the Arctic lineage, suggesting that haplotypes sheltered from introgression by low recombination could enlighten complex post-glacial histories. Overall, we argue that Whole-Genome Sequencing, even at low depths of coverage, provides a versatile approach to the study of phylogeographic dynamics.

evolutionary biology↗

bioRxiv2024

Chromosome-level genome assembly of a doubled haploid brook trout (Salvelinus fontinalis)

Brook trout (Salvelinus fontinalis) is a socioeconomically important fish species for fisheries, aquaculture and aquatic conservation. We produced a 2.5 Gb reference assembly by combining Hi-C chromosome conformation capture with high-coverage short- and long-read sequencing of a fully homozygous mitotic gynogenic doubled haploid fish, which facilitates assembly of highly complex salmonid genomes. The assembly has a N50 of 50.98 Mb and 88.9% of the total assembled sequence length is anchored into 42 main chromosomes, of which 63.44% represents repeated contents, including 1,461,010 DNA transposons. 56,058 genes were found with the NCBI annotation pipeline, with 99% of the 3,640 expected conserved orthologs BUSCO genes (actinopterygii_odb10 lineage database). Additionally, we found significant homology within the 42 chromosomes, as expected for this pseudo-tetraploid species, as well as with the sister species lake trout (Salvelinus namaycush) and Atlantic salmon (Salmo salar). This assembly will serve as a reliable genomic resource for brook trout, thus enabling a wider range of reference-based applications to support ongoing research and management decision-making for the species.

genomics↗

bioRxiv2024

Telomere-to-telomere genome assembly of the clubroot pathogen Plasmodiophora brassicae

Plasmodiophora brassicae (Woronin, 1877), a biotrophic, obligate parasite, is the causal agent of clubroot disease in brassicas. The clubroot pathogen has been reported in more than 80 countries worldwide, causing economic losses of hundreds of millions every year. Despite its widespread impact, very little is known about the molecular strategies it employs to induce the characteristic clubs in the roots of susceptible hosts during infection, nor about the mechanisms it uses to overcome genetic resistance. Here, we provide the first telomere-to-telomere complete genome of Plasmodiophora brassicae. We generated [~] 27 Gb of Illumina, Oxford Nanopore, and PacBio HiFi data from resting spores of strain Pb3A and produced a 25.3 Mb assembly comprising 20 chromosomes, with an N50 of 1.37 Mb. The BUSCO score, the highest reported for any member of the group Rhizaria (Eukaryota: 88.2%), highlights the limitations within the Eukaryota database for members of this lineage. Using available transcriptomic data and protein evidence, we annotated the Pb3A genome, identifying 10,521 protein-coding gene models. This high-quality, complete genome of Plasmodiophora brassicae will serve as a crucial resource for the plant pathology community to advance the much-needed understanding of the evolution of the clubroot pathogen. SIGNIFICANCEPlasmodiophora brassicae (Woronin, 1877) is a devastating plant pathogen, member of the Rhizaria group, and is putting at risk the oilseed rape and cruciferous vegetable industry worldwide. Here, we present the first telomere-to-telomere genome of P. brassicae, and the first complete genome for a member of the Rhizaria taxon. We also provide a high-quality genome annotation featuring an enhanced gene model relative to previous studies. This complete genome will be of great interest to researchers focused on the ecology and evolution of the clubroot pathogen, as well as those studying other members of the Rhizaria group.

microbiology↗

bioRxiv2023

MTOR as a selectable genomic harbor for CRISPR-engineered CAR-T cell therapy

Chimeric antigen receptors (CARs) reprogram T cells to recognize and target cancer cells. Despite remarkable responses observed with CAR-T cell therapy in patients with hematological malignancies, CAR-T cell engineering still relies mostly on randomly integrating vectors, limiting the possibilities of fine-tuning T cell function. Here, we designed a CRISPR-based marker-free selection strategy to simultaneously target a therapeutic transgene and a gain-of-function mutation to the MTOR locus to enrich cells resistant to rapamycin, a clinically used immunosuppressant. We readily engineered rapamycin-resistant (RapaR) CAR-T cells by targeting CAR expression cassettes to the MTOR locus. Using in vitro cytotoxicity assays, and a humanized mouse model of acute lymphoblastic leukemia, we show that RapaR-CAR-T cells can efficiently target CD19+ leukemia cells in presence of immunosuppressing doses of rapamycin. Furthermore, our strategy allows multiplexed targeting of rapamycin-regulated immunoreceptors complexes (DARICs) to the MTOR and TRAC loci to pharmacologically control CAR-T cells activity. We foresee that our approach could both facilitate the enrichment of CRISPR-engineered CAR-T cells ex vivo and in vivo while improving tumor eradication.

cancer biology↗

bioRxiv2023

Comparative Restriction Enzyme Analysis of Methylation (CREAM) Reveals Methylome Variability Within a Clonal In Vitro Cannabis Population

The primary focus of medicinal cannabis research is to ensure the stability of cannabis lines for consistent administration of chemically consistent products to patients. In recent years, tissue culture has emerged as a valuable technique for genetic preservation and rapid production of cannabis clones. However, there is concern that the physical and chemical conditions of the growing media can induce somaclonal variation, potentially impacting the viability and uniformity of clones. To address this concern, we developed Comparative Restriction Enzyme Analysis of Methylation (CREAM), a novel method to assess DNA methylation patterns and used it to assess a population of 78 cannabis clones maintained in tissue culture. Through bioinformatics analysis of the methylome, we successfully detected 2,272 polymorphic methylated regions among the clones. Remarkably, our results demonstrated that DNA methylation patterns were preserved across subcultures within the clonal population, allowing us to distinguish between two subsets of clonal lines used in this study. These findings significantly contribute to our understanding of the epigenetic variability within clonal lines in medicinal cannabis produced through tissue culture techniques. This knowledge is crucial for understanding the effects of tissue culture on DNA methylation and ensuring the consistency and reliability of medicinal cannabis products with therapeutic properties. Additionally, the CREAM method is a fast and affordable technology to get a first glimpse at methylation in a biological system. It offers a valuable tool for studying epigenetic variation in other plant species, thereby facilitating broader applications in plant biotechnology and crop improvement.

plant biology↗

bioRxiv2023

Widespread deviant patterns of heterozygosity in whole-genome sequencing due to autopolyploidy, repeated elements and duplication

Most population genomic tools rely on accurate SNP calling and filtering to meet their underlying assumptions. However, genomic complexity, due to structural variants, paralogous sequences and repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter mismapping issues, leading to SNPs that deviate from Mendelian expected patterns of heterozygosity and allelic ratio. In this study, we employed the ngsParalog software to identify such deviant SNPs in whole-genome sequencing data from four species: Arctic Char (Salvelinus alpinus), Lake Whitefish (Coregonus clupeaformis), Atlantic Salmon (Salmo salar), and the American Eel (Anguilla rostrata), with low (2X) to intermediate (6X) coverage. The analyses revealed that deviant SNPs accounted for up to 62% of all SNPs in salmonid datasets and approximately 10% in the American Eel dataset. These deviant SNPs were particularly concentrated within repetitive elements and genomic regions that had recently undergone rediploidization in salmonids. Additionally, narrow peaks of elevated coverage were ubiquitous along all four reference genomes, encompassed most deviant SNPs and could be partially attributed to transposons and tandem repeats. Including these deviant SNPs in genomic analyses led to highly distorted site frequency spectra, apparent homogenization of populations and underestimating pairwise FST values. Considering the widespread occurrence of deviant SNPs arising from a variety of source, their important impact in estimating population parameters, and the availability of effective tools to identify them, we propose that excluding deviant-SNPs from WGS datasets is required to improve genomic inferences for a wide range of taxa and sequencing depths. Significance: Genomes can be very repetitive and hard to assemble into a reference, which can lead to biases when genotyping genetic markers in complex genomic regions. Here, we draw attention to this issue in various whole-genome datasets and validate a method to identify problematic SNPs at low coverage. We also explore processes creating such SNPs and their consequences on common population genomics analyses.

genomics↗

bioRxiv2023

SNPLift: Fast and accurate conversion of genetic variant coordinates across genome assemblies

MotivationThe advent of high-throughput sequencing technologies and the availability of reference genomes have provided an unprecedented opportunity to discover and genotype millions of genetic variants in hundreds or even thousands of samples. Variant calling, the identification of genetic variants from raw sequencing data, is both time-consuming and computationally demanding. Currently, reference genomes are evolving very rapidly and new assembly versions come out more and more frequently. To take advantage of new or improved reference genomes, raw reads alignments, genotype calling, and filtration must typically all be redone. This is a costly and time consuming operation that is not always viable when projects are under time constraints. ResultsHere, we introduce SNPLift, a bioinformatic pipeline that can quickly transfer the coordinate of nucleotide variants (SNPs and Indels) between different versions of reference genomes. We tested SNPLift on nine SNP datasets in VCF format from different species (Homo sapiens, Arabidopsis thaliana, Coregonus clupeaformis, Medicato truncatula, Oriza sativa, Salvelinus namaycush, Solanum lycopersicum, Zea mays, and Glycine max). Depending on the species, we achieved accurate lifting of variants ranging from 92.92% to 99.69%. Importantly, SNPLift significantly reduces the computational resources and time required for variant analysis compared to performing a complete re-analysis using a new reference genome. SNPLift offers a fast and efficient solution to leverage the benefits of updated or improved reference genomes. Availability and implementationSNPLift is available at https://github.com/enormandeau/snplift with its documentation. It contains a script that runs an automated test on a small dataset, composed of 190,443 SNPs in chromosome 1 of Medicago truncatula. SNPLift uses only common tools that are easy to install and works under Linux and MacOS.

genomics↗

bioRxiv2022

Evidence for epigenetically influenced mutagenesis and genetic assimilation in nascent species complexes (Coregonus sp.)

Phenotypic diversification is classically associated with genetic differentiation and gene expression variation. However, increasing evidence suggests that DNA methylation is involved in evolutionary processes due to its phenotypic and transcriptional effects. Methylation can increase mutagenesis and could lead to increased genetic divergence between populations experiencing different environmental conditions for many generations, though there has been minimal empirical research on epigenetically induced mutagenesis in diversification and speciation. Whitefish, freshwater members of the salmonid family, are excellent systems to study phenotypic diversification and speciation due to the repeated divergence of benthic-limnetic species pairs serving as natural replicates. Here we investigate whole genome genetic and epigenetic differentiation between sympatric benthic-limnetic species pairs in lake and European whitefish (Coregonus clupeaformis and C. lavaretus) from four lakes (N=64). We found considerable, albeit variable, genetic and epigenetic differences between species pairs. All SNP types were enriched at CpG sites supporting the mutagenic nature of DNA methylation, though C>T SNPs were most common. We also found an enrichment of overlaps between outlier SNPs with the 5% highest FST between species and differentially methylated loci. This could possibly represent differentially methylated sites that have caused divergent genetic mutations between species, or divergent selection leading to both genetic and epigenetic variation at these sites. Our results support the hypothesis that DNA methylation contributes to phenotypic divergence and mutagenesis during whitefish speciation. Significance statementDNA methylation is an epigenetic mark known to change in response to the environment and induce genetic modifications such as point mutations, though its implications for evolution and speciation have not been thoroughly studied. We find considerable but variable genetic and epigenetic variation between whitefish benthic-limnetic species pairs, highlighting the potential for DNA methylation to contribute to mutagenesis and genetic evolution. Our study provides evidence that DNA methylation could have contributed to whitefish speciation, both through initially plastic methylation changes and by driving genetic divergence between species pairs.

evolutionary biology↗

bioRxiv2022

Fish-microbe systems in the hostile but highly biodiverse Amazonian blackwaters

Amazonian blackwaters are extremely biodiverse systems containing some of the most naturally acidic, dissolved organic carbon-rich and ion-poor waters on Earth. Physiological adaptations of fish facing these ionoregulatory challenges are unresolved but could involve microbially-mediated processes. Here, we characterize the physiological response of 964 fish-microbe systems from four blackwater Teleost species along a natural hydrochemical gradient, using dual RNA-Seq and 16S rRNA of gill samples. We find that responses to blackwaters are host-species-specific, but occasionally include the overexpression of Toll-receptors and integrins associated to interkingdom communication. Blackwater gill microbiomes are characterized by a transcriptionally-active betaproteobacterial cluster potentially interfering with epithelial permeability. We explore further blackwater fish-microbe interactions by analyzing transcriptomes of 320 axenic zebrafish larvae exposed to sterile, non-sterile and inverted (non-native bacterioplankton) blackwater. We find that axenic zebrafish do not survive well when exposed to sterile/inverted blackwater, suggesting an essential role of endogenous symbionts in blackwater fish physiology.

ecology↗

bioRxiv2022

Captive rearing effects on the methylome of Atlantic salmon after oceanic migration: sex-specificity and intergenerational stability

Captive rearing in salmon hatcheries can have considerable impacts on both fish phenotype and fitness within a single generation, even in the absence of genetic change. Evidence for hatchery-induced changes in DNA methylation is becoming abundant, though questions remain on the sex-specificity of these effects, their persistence until spawning, and potential for transmission to future generations. Here we performed whole genome methylation sequencing of fin tissue for 16 hatchery and 16 wild Atlantic salmon (Salmo salar) returning to spawn in the Rimouski River, Quebec. We identified two cohorts of hatchery-reared salmon through methylation analysis, one of which was epigenetically similar to wild fish, suggesting that supplementation efforts may be able to minimize the epigenetic effects of hatchery rearing. We found considerable sex-specific effects of hatchery rearing, with few genomic regions being affected in both males and females. We also analysed the methylome of 32 F1 offspring from four groups (pure wild, pure hatchery origin, and reciprocal hybrids). We found that few epigenetic changes due to parental hatchery rearing persisted in the F1 offspring though the patterns of inheritance appear to be complex, involving nonadditive effects. Our results suggest that the epigenetic effects of hatchery rearing can be minimal in F0. There may also be minimal epigenetic inheritance and rapid loss of epigenetic changes associated with hatchery rearing. However, due to sex-specificity and nonadditive patterns of inheritance, methylation changes due to captive rearing are rather complex and the field would benefit from further research on minimizing the epigenetic effects of captive rearing in conservation efforts.

evolutionary biology↗

bioRxiv2022

Searching for intra-locus sexual conflicts in the three-spined stickleback (Gasterosteus aculeatus) genome

Differences between sexes in trait fitness optima can generate intra-locus sexual conflicts that have the potential to maintain genetic diversity through balancing selection. However, these differences are unlikely to be associated with string selective coefficients and as a result are challenging to detect. Additionally, recent studies have highlighted that duplication on sexual chromosomes can create artefactual signals of inter-sex differentiation and increased genetic diversity. Thus, testing the relationship between intra-locus sexual conflicts and balancing selection requires a high-quality reference genome, stringent filtering of potentially duplicated regions, and dedicated methods to detect loci with low levels of inter-sex differentiation. In this study, we investigate intra-locus sexual conflicts in the three-spined stickleback using whole genome sequencing (mean coverage = 12X) of 50 females and 49 males from an anadromous population in the St. Lawrence River, Quebec, Canada. After stringent filtering of duplications from the sex chromosomes, we compared three methods to detect intra-locus sexual conflicts. This allowed us to detect various levels of inter-sex differentiation, from stronger single locus effects to small cumulative or multivariate signals. Overall, we found only four genomic regions associated with confidence to intra-locus sexual conflict that displayed associations with long-term balancing selection maintaining genetic diversity. Altogether, this suggests that most intra-locus sexual conflicts do not drive long-term balancing selection and are most likely transient. However, they might still play a role in maintaining genetic diversity over shorter time scales by locally reducing the effects of purifying selection and the rates of genetic diversity erosion.

evolutionary biology↗

bioRxiv2022

Isolation-by-distance and population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome

Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that return from multiyear ocean migrations to spawn in rivers that flow to the Northern Pacific Ocean. Southern stocks of coho salmon have significantly declined over the past quarter century, and unfortunately, conservation efforts have not reversed this trend. To assist in stock management and conservation efforts, we generated two chromosome-level genome assemblies and sequenced 24 RNA-seq libraries to better annotate the coho salmon genome assemblies. We also resequenced the genomes of 83 coho salmon across their North American range to identify nucleotide variants, characterize the broad effects of isolation-by-distance using a genome-wide association analysis approach, and understand the demographic histories of these salmon by modeling population size from genome-wide data. We observed that more than 13% of all SNPs were associated with latitude (before multiple test correction), likely an affect of isolation-by-distance. From demographic history modeling, we estimated that the SNP latitudinal gradient likely developed as recently as 8,000 years ago. In addition, we identified four genes each harboring multiple SNPs associated with latitude; all of these SNPs were also predicted to modify the function of the gene. Three of these genes have roles in cell junction maintenance and may be involved in osmoregulation. This signifies that ocean salinity may have been a factor influencing coho salmon recolonization after the last glaciation period - generating the current pattern of variation in these three genes.

genomics↗

bioRxiv2022

Genomic and environmental factors shape gill microbiome activity in an Amazonian teleost holobiont

Fish microbiomes provide functions critical for their hosts survival in contrasting environments. These communities are sensitive to a range of environmental-specific factors (i.e. physicochemical parameters, free-living bacterioplankton) and host-specific factors (i.e. host genetic background). The relative contribution of these genomic and environmental factors shaping Amazonian fish microbiomes is still unknown. Here, we investigated this topic by analyzing the gill microbiomes of 240 wild flag cichlids (Mesonauta festivus) from four different populations (genetic clusters) distributed in 12 sites of two contrasting water types (ion-poor/acidic black water and ion-rich/circumneutral white water). The transcriptionally active gill microbiomes were characterized by a 16S rRNA metabarcoding approach carried on RNA extractions. They were analyzed in light of comprehensive datasets from the hosts genetic background (Genotyping-By-Sequencing), the bacterioplanktonic pool of bacteria (16S rRNA) and a set of 34 environmental parameters. Results show that the transcriptional activity of gill microbiome samples was significantly different between the genetic clusters and between water types. However, they suggest that the contribution of the hosts genetic background was relatively weak in comparison to the environment-related factors in structuring the relative abundance of different gill microbiome transcripts. This result was also confirmed by a mixed-effects modeling analysis, which suggested that the dissimilarity between the transcriptional activity of bacterioplanktonic communities possessed the best explicative power regarding the dissimilarity between gill microbiomes transcripts, while pairwise fixation indexes (FST) from the hosts genetic data only had a weak explicative power. We discuss these results in terms of microbiome assembly processes and flag cichlid fish ecology. ImportanceHost-associated microbial communities respond to a range of factors specific to the host physiology, genetic backgrounds and life history. However, these communities also show different degrees of sensitivity to environment-dependant factors such as abiotic physico-chemical parameters and ecological interactions. The relative importance of host-versus environment-associated factors in shaping teleost microbiomes is still understudied and is paramount for their conservation and aquaculture. Here, we studied the relative importance of host- and environment-associated factors structuring teleost microbiomes using gill samples from a wild Amazonian teleost model (Mesonauta festivus) sampled in contrasting habitats along a 1500 km section of the Amazonian basin, thus ensuring high genetic diversity. Results showed that the contribution of the hosts genetic background was weak compared to environment-related bacterioplanktonic communities in shaping gill microbiomes, thereby suggesting that our understanding of teleost microbiome assembly could benefit from further studies focused on the ecological interplay between host-associated and free-living communities.

ecology↗

bioRxiv2022

Thermal regime during parental sexual maturation, but not during offspring rearing, modulates DNA methylation in brook charr (Salvelinus fontinalis)

Epigenetic inheritance can result in plastic responses to changing environments being faithfully transmitted to offspring. However, it remains unclear how epigenetic mechanisms such as DNA methylation can contribute to multigenerational acclimation and adaptation to environmental stressors. Brook charr (Salvelinus fontinalis), an economically important salmonid, is highly sensitive to thermal stress, and is of conservation concern in the context of climate change. We studied the effects of temperature during parental sexual maturation and offspring rearing on whole-genome DNA methylation in brook charr juveniles (fry). Parents were split between warm and cold temperatures during sexual maturation, mated in controlled breeding designs, then offspring from each family were split between warm (8{degrees}C) and cold (5{degrees}C) rearing environments. We found 188 differentially methylated regions (DMRs) due to parental maturation temperature after controlling for family structure. In contrast, offspring rearing temperature had a negligible effect on offspring methylation. Stable intergenerational inheritance of DNA methylation and minimal plasticity in progeny could result in transmission of acclimatory epigenetic states to offspring, priming them for a warming environment. Our findings have implications pertaining to the role of intergenerational epigenetic inheritance in response to ongoing climate change.

evolutionary biology↗

bioRxiv2022

Genome assembly, structural variants, and genetic differentiation between Lake Whitefish young species pairs (Coregonus sp.) with long and short reads

Nascent pairs of ecologically differentiated species offer an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks to long-read sequencing technology. We can now identify structural variants (SVs) like insertions, deletions, and other rearrangements, allowing further insights into the genetic architecture of speciation and how different types of variants are involved in species differentiation. Here, we investigated genomic patterns of differentiation between sympatric species pairs (Dwarf and Normal) belonging to the Lake Whitefish (Coregonus clupeaformis) species complex. We assembled the first reference genomes for both C. clupeaformis sp. Normal and C. clupeaformis sp. Dwarf, annotated the transposable elements, and analysed the genomes in the light of related coregonid species. Next, we used a combination of long-read and short-read sequencing to characterize SVs and genotype them at population-scale using genome-graph approaches, showing that SVs cover five times more of the genome than SNPs. We then integrated both SNPs and SVs to investigate the genetic architecture of species differentiation in two different lakes and highlighted an excess of shared outliers of differentiation. In particular, a large fraction of SVs differentiating the two species correspond to insertions or deletions of transposable elements (TEs), suggesting that TE accumulation may represent a key component of genetic divergence between the Dwarf and Normal species. Altogether, our results suggest that SVs may play an important role in speciation and that, by combining second and third generation sequencing, we now have the ability to integrate SVs into speciation genomics.

evolutionary biology↗

bioRxiv2021

Long distance migration is a major factor driving local adaptation at continental scale in Coho Salmon

Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species homing behavior may promote the establishment of local adaptation. We genotyped 7,829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. Results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidates SNP associated with long distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.

evolutionary biology↗

bioRxiv2021

A compendium of novel genomics technologies provides a chromosome-scale assembly and insights into the sex determining system of the Greenland Halibut

Despite the commercial importance of Greenland Halibut (Reinhardtius hippoglossoides), important gaps still persist in our knowledge of this species, including its reproductive biology and sex determination mechanism. In this study, we combined single molecule sequencing of long reads (Pacific Sciences) with Chromatin Conformation Capture sequencing (Hi-C) data to provide the first chromosome-level genome reference for this species. The high-quality assembly encompassed more than 598 Megabases (Mb) assigned to 1 594 scaffolds (scaffold N50 = 25 Mb) with 96 % of its total length distributed among 24 chromosomes. The investigation of its syntenic relationships with other economically important flatfish species revealed a high conservation of synteny blocks among members of this phylogenetic clade. Sex determination analysis revealed that flatfishes do not escape the rule applied to other teleost fish and exhibit a high level of plasticity and turnover in sex-determination mechanisms. A whole-genome sequence analysis of 198 individuals allowed us to draw a full picture of the molecular sex determination (SD) system for Greenland Halibut, revealing that this species possesses a very nascent male heterogametic XY system, with a putative major effect of the sox2 gene, also described as the main SD driver in two other flatfishes. Interestingly, our study also suggested for the first time in flatfishes that a putative Y-autosomal fusion could be associated with a reduction of recombination typical of early steps of sex chromosome evolution.

genomics↗