Biology subjects

Bousquet, J.

Publications and source records attributed to Bousquet, J..

13 recordsLinked to original sources

bioRxiv2026

Ecogenomics of transcontinental black spruce: identification of climate adaptation genes across the Canadian boreal landscape

Black spruce (Picea mariana [Mill.] B.S.P.) is an emblematic and ubiquitous species of the North Americas boreal forest. While conifer breeding programs have traditionally focused on growth and wood property traits, the study of climate adaptation traits is becoming increasingly prevalent, given the predicted impact of climate change on North Americas boreal zone. Through this study, we aimed to identify genes associated with climate adaptation in black spruce across Canada. A total of 254 black spruce trees from 30 populations, covering most of the species distribution range, were sampled and genotyped for SNPs located in [~]5000 gene loci. Uni- and multivariate Genotype-Environment Association (GEA) approaches, namely LFMM and RDA, as well as an outlier method based on population differentiation (FST) were used to identify genes significantly associated with climatic factors. As such, a total of 77 genes carrying significant candidate SNPs were identified, among which 14 candidates were corroborated by at least two methods. Many of these gene SNPs were also confirmed at a smaller geographic scale, across west - east partitions corresponding to the two main black spruce historical lineages. Notably, significant gene SNPs were more frequently associated to moisture/aridity factors in the western part of the range, and more to temperature factors in the eastern part. The genes carrying these SNPs were also frequently associated to abiotic and biotic stress response. In the context of rapid climate change in the Canadian boreal forest, the results obtained within the framework of this study should support implementing gene conservation efforts while assisting prediction in black spruce breeding programs, which are instrumental to producing adapted planting stock for the large-scale reforestation efforts conducted annually across the Canadian boreal forest.

plant biology↗

bioRxiv2025

Variation in bud phenology, frost tolerance and non-structural carbohydrates among white spruce seed sources on climate-contrasted test sites: implications for assisted migration

To assess the potential impacts of climate change on white spruce local adaptation, six seed sources were evaluated seven years after plantation on two test sites with contrasting growing conditions and latitude in Quebec. Bud set, frost tolerance and analysis of non-structural carbohydrates (NSC) content showed important effects of test sites, seed sources, and their interactions on bud set phenology and growth. The average bud set initiation occurred one week later in the southern site compared to the northern site, whereas the late stage of bud set was similar between sites. Significant differences were observed between seed sources for some phenological stages. Frost tolerance was significantly lower in the southern site and below -12 {degrees}C for all seed sources sampled at the beginning of October. The trend in fructose and glucose content was opposite between sites in September. It decreased from September to October in the southern site and increased in the northern site, while sucrose content showed an opposite pattern, with the southwestern seed source harboring the lowest sucrose content. NSC content was also correlated to frost tolerance. Our study highlighted the crucial role of NSC in cold hardiness to early fall frosts and local adaptation. Implications for assisted migration are discussed.

plant biology↗

bioRxiv2025

Optimizing marker density for maximizing the accuracy of genomic prediction and heritability estimates in three major North American and European spruce species

Genomic prediction, also called genomic selection (GS), is being increasingly used in tree breeding with aim to accelerate genetic gains by shortening the long breeding cycles. However, high genotyping costs remain a challenge. This study aimed to determine the optimal marker density in genome coverage, to maximize GS accuracy and precision of heritability estimates for growth and wood quality traits. Thousands of SNPs representative of the exome of three major spruce species were used: 18,275 SNPs for black spruce (representing 10,894 distinct gene loci), 11,328 SNPs for white spruce (8647 gene loci), and 116,765 SNPs for Norway spruce (20,695 gene loci). For each species, a similar experimental design was used with related full-sib families replicated on two sites, and GBLUP prediction models were developed. The effect of varying the number of SNPs was examined by re-sampling subsets from 500 to 100,000 SNPs. Results indicated that plateaus in heritability estimates were reached as the marker density increased, stabilizing between 4000 to 8000 SNPs for a spruce genome size of around 2000 centimogans, a trend consistent across all traits and species. Predictive ability and prediction accuracy both increased with the number of SNPs up to a similar level, beyond which further improvements were marginal. Such optimal marker density should be financially attainable for most spruce breeding programs, striking a balance between the need for maximizing accuracy and that for minimizing genotyping costs. These findings should support the further deployment of GS in conifer breeding programs, with high selection precision and by reducing the financial burden of very high-density SNP coverage, even for conifers characterized by large giga-genomes.

genomics↗

bioRxiv2025

Development and validation of an exome-wide SNP genotyping array for genomic prediction, GWAS and assessment of introgressive hybridization between black and red spruces, and transferability to white and Norway spruces

Introgressive hybridization plays a major role in shaping the evolutionary dynamics and adaptive potential of forest trees. In this study, we developed and validated an exome-wide bispecific SNP genotyping array (Pmr25k) for the closely related species black spruce (Picea mariana) and red spruce (Picea rubens), two ecologically and economically important North American conifers that form a widespread hybrid zone in eastern Canada. Exome capture and sequencing of pooled red spruce samples yielded over 25,000 high-quality SNPs, which were used in conjunction with a previously developed black spruce gene SNP resource of over 97,000 high-quality SNPs, to construct the bispecific genotyping array. The final array comprised 21,573 successfully manufactured SNPs, representing 14,200 distinct gene loci, of which 85% were segregating when both species were considered together. More than 4000 segregating SNPs could also be successfully used and genotyped in each of white spruce (Picea glauca) and Norway spruce (Picea abies), highlighting the conserved nature of DNA attachment sites and presence of homologous SNPs for many gene loci. The Pmr25k array thus provides an efficient and reliable high-throughput genotyping tool to investigate introgression, genetic adaptation at the gene level, and to assist genomic-based prediction for breeding and conservation efforts in boreal spruces.

genomics↗

bioRxiv2025

Elucidating continental-wide phylogeographic and adaptive processes shaping the genome-wide diversity of North America's most widely distributed tree

Past population dynamics during the Pleistocene ice age and the Holocene era have profoundly influenced the genetic structure and diversity of species. Environmental heterogeneity has further shaped local and regional adaptive variation. Here, we ask how historical processes have led to the current genetic diversity of a key North American species across its vast natural range and what genomic signatures indicate regional adaptive divergence and local adaptation. We used sequencing data from 1,903 Populus tremuloides Michx. (quaking aspen) trees to assess historical population dynamics and identify genotype-environment associations within and among the species major genetic lineages. The two northern and western North American aspen lineages exhibited historical population expansion patterns, while the southernmost lineage experienced a historical bottleneck consistent with past glacial oscillations. We found that the earliest split between genetic lineages of P. tremuloides occurred in the southern part of its distribution range. We further identified larger blocks of adaptive SNPs within separate genomic sequence regions on chromosomes 2 and 8 that may exhibit suppressed genetic recombination, contributing to the maintenance of regional and local adaptation in the species. Our study provides key insights into the evolutionary processes affecting adaptive genetic variation and phylogeography at a broad continental and regional scale, with implications for predicting species responses to future climate change.

evolutionary biology↗

bioRxiv2024

Spruce hybrids show superior cumulative growth and intermediate response to climate anomalies, as compared to their ecologically divergent parental species

Climate change brings new constraints to which trees will have to adapt, including more frequent weather extremes. Black spruce and red spruce are phylogenetically close but adapted to different ecological conditions, and they form a natural hybrid zone where their distributions come into contact. Thus, they represent an interesting model to study the effect of introgressive hybridization in the context of climate change, given that interspecific gene flow could affect their capacity to adapt where their natural distributions overlap. Using a common-garden field test gathering 20-year-old progeny trees resulting from rigorous controlled crosses including previously verified genetic identity of the parents, growth patterns and wood density differences could be observed between species and between them and their F1 hybrids. A dendroecological analytical approach relying on wood cores was used and revealed similar wood responses to climatic variations between species, both through lifetime climate sensitivity and through episodic stress response indexes. They were however differentially expressed in early- and latewood between black spruce and red spruce, differences likely driven by diverging cambial phenology adaptations to different growing season lengths. F1 hybrids exhibited hybrid vigor for cumulative growth under the test site conditions, but showed intermediate values for traits related to climate response. These results offer new perspectives for understanding the dynamics of adaptation in hybrid zones in the context of climate change, as well as for guiding conservation and genetic improvement efforts. HighlightsO_LIF1 cumulative growth is higher than their ecologically contrasted parents. C_LIO_LIHybrids had intermediate climate responses C_LIO_LIParental species responded similarly to climate anomalies, but in various intra-ring part. C_LIO_LICambial phenology likely drives divergences in wood reaction to climate anomalies C_LI

plant biology↗

bioRxiv2023

Contrasting levels of transcriptome-wide SNP diversity and decoupled patterns of molecular and functional adaptive variation in conifers

Adaptive convergence can arise when response to natural selection involves shared molecular or functional mechanisms among multiple taxa. Conifers are of ancient origin with delayed sexual maturity related to their woody perennial nature. Thus, they represent a relevant plant group to assess if convergence from selection may have become disconnected between molecular and functional levels. In this purpose, transcriptome-wide SNP diversity was assessed in seven partially sympatric and reproductively isolated conifer species populating the temperate and boreal forests of northeastern North America. SNP diversity was found highly heterogeneous among species, which would relate to variation in species-specific demography and history. Rapidly evolving genes with signatures of positive selection were identified, and their relative abundance among species reflected differences in transcriptome-wide SNP diversity. Their analysis also revealed very limited convergence among taxa in spite of sampling same tissues at same age. However, convergence increased gradually at the levels of gene families and biological processes, which were largely related to stress response and regulatory mechanisms in all species. Given their multiple small to large gene families and long time since inception, conifers may have had sufficient gene network flexibility and gene functional redundancy for evolving alternative adaptive genes for similar metabolic responses to environmental selection pressures. Despite a long divergence time of [~]350 Mya between conifers and Angiosperms, we also uncovered a set of 20 key genes presumably under positive selection in both lineages.

plant biology↗

bioRxiv2023

Conifers concentrate large numbers of NLR immune receptor genes on one chromosome

Nucleotide-binding domain and Leucine-rich Repeat (NLR) immune receptor genes form a major line of defence in plants, acting in both pathogen recognition and resistance machinery activation. NLRs are reported to form large gene clusters in limber pine (Pinus flexilis) but it is unknown how widespread this genomic architecture may be among the extant species of conifers (Pinophyta). We used comparative genomic analyses to assess patterns in the abundance, diversity and genomic distribution of NLR genes. Chromosome-level whole genome assemblies and high-density linkage maps in the Pinaceae, Cupressaceae, Taxaceae and other gymnosperms were scanned for NLR genes using existing and customised pipelines. Discovered genes were mapped across chromosomes and linkage groups, and analysed phylogenetically for evolutionary history. Conifer genomes are characterised by dense clusters of NLR genes, highly localised on one chromosome. These clusters are rich in TNL-encoding genes, which seem to have formed through multiple tandem duplication events. In contrast to angiosperms and non-coniferous gymnosperms, genomic clustering of NLR genes is ubiquitous in conifers. NLR-dense genomic regions are likely to influence a large part of the plants resistance, informing our understanding of adaptation to biotic stress and the development of genetic resources through breeding. Plain language summaryNLR immune receptor genes are important in pest, disease and drought resistance of plants. In the giga-genomes of conifers, they concentrate on very small chromosomal regions. These regions act as important reservoirs for NLR diversity and can be used in breeding to improve the resilience of conifer trees.

genomics↗

bioRxiv2023

Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene Betaglu-1 with large variations in white spruce but not Norway spruce

Conifers are long-lived and slow-evolving, thus requiring effective defences against their fast-evolving insect natural enemies. The copy number variation (CNV) of two key acetophenone biosynthesis genes Ugt5/Ugt5b and {beta}glu-1 may provide a plausible mechanism underlying the constitutively variable defence in white spruce (Picea glauca) against its primary defoliator, spruce budworm. This study develops a long-insert sequence capture probe set (Picea_hung_p1.0) for quantifying copy number of {beta}glu-1-like, Ugt5-like genes and single-copy genes on 38 Norway spruce (Picea abies) and 40 P. glauca individuals from eight and nine provenances across Europe and North America respectively. We developed local assemblies (Piabi_c1.0 and Pigla_c.1.0), full-length transcriptomes (PIAB_v1 and PIGL_v1), and gene models to characterise the diversity of {beta}glu-1 and Ugt5 genes. We observed very large copy numbers of {beta}glu-1, with up to 381 copies in a single P. glauca individual. We observed among-provenance CNV of {beta}glu-1 in P. glauca but not P. abies. Ugt5b was predominantly single-copy in both species. This study generates critical hypotheses for testing the emergence and mechanism of extreme CNV, the dosage effect on phenotype, and the varying copy number of genes with the same pathway. We demonstrate new approaches to overcome experimental challenges in genomic research in conifer defences.

evolutionary biology↗

bioRxiv2021

Full bandwidth electrophysiology of seizures and epileptiform activity enabled by flexible graphene micro-transistor depth neural probes

Mapping the entire frequency bandwidth of neuronal oscillations in the brain is of paramount importance for understanding physiological and pathological states. The ability to record simultaneously infraslow activity (<0.1 Hz) and higher frequencies (0.1-600 Hz) using the same recording electrode would particularly benefit epilepsy research. However, commonly used metal microelectrode technology is not well suited for recording infraslow activity. Here we use flexible graphene depth neural probes (gDNP), consisting of a linear array of graphene microtransistors, to concurrently record infraslow and high frequency neuronal activity in awake rodents. We show that gDNPs can reliably record and map with high spatial resolution seizures, post-ictal spreading depolarisation, and high frequency epileptic activity through cortical laminae to the CA1 layer of the hippocampus in a mouse model of chemically-induced seizures. We demonstrate functionality of chronically implanted devices over 10 weeks by recording with high fidelity spontaneous spike-wave discharges and associated infraslow activity in a rat model of absence epilepsy. Altogether, our work highlights the suitability of this technology for in vivo electrophysiology research, in particular, to examine the contributions of infraslow activity to seizure initiation and termination.

neuroscience↗

bioRxiv2019

Largest Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates Complex Physical Structure

Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the 5.5 Mbp mitochondrial genome of Sitka spruce (Picea sitchensis), the largest complete mitochondrial genome of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads. The assembly graph shows a multipartite genome structure, composed of one smaller 168 kbp circular segment of DNA, and a larger 5.4 Mbp component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination.

genomics↗

bioRxiv2019

ntEdit: scalable genome sequence polishing

In the modern genomics era, genome sequence assemblies are routine practice. However, depending on the methodology, resulting drafts may contain considerable base errors. Although utilities exist for genome base polishing, they work best with high read coverage and do not scale well. We developed ntEdit, a Bloom filter-based genome sequence editing utility that scales to large mammalian and conifer genomes.\n\nWe first tested ntEdit and the state-of-the-art assembly improvement tools GATK, Pilon and Racon on controlled E. coli and C. elegans sequence data. Generally, ntEdit performs well at low sequence depths (<20X), fixing the majority (>97%) of base substitutions and indels, and its performance is largely constant with increased coverage. In all experiments conducted using a single CPU, the ntEdit pipeline executed in <14s and <3m, on average, on E. coli and C. elegans, respectively. We performed similar benchmarks on a sub-20X coverage human genome sequence dataset, inspecting accuracy and resource usage in editing chromosomes 1 and 21, and whole genome. ntEdit scaled linearly, executing in 30-40m on those sequences. We show how ntEdit ran in <2h20m to improve upon long and linked read human genome assemblies of NA12878, using high coverage (54X) Illumina sequence data from the same individual, fixing frame shifts in coding sequences. We also generated 17-fold coverage spruce sequence data from haploid sequence sources (seed megagametophyte), and used it to edit our pseudo haploid assemblies of the 20 Gbp interior and white spruce genomes in <4 and <5h, respectively, making roughly 50M edits at a (substitution+indel) rate of 0.0024.\n\nAvailabilityhttps://github.com/bcgsc/ntedit\n\nSupplemental materialavailable online.

bioinformatics↗

bioRxiv2017

Spontaneous mutations and transmission distortions of genic copy number variants shape the standing genetic variation in Picea glauca

Copy number variations (CNVs) are large genetic variations detected among the individuals of every multicellular organism examined so far. These variations are believed to play an important role in the evolution and adaptation of species. In plants, little is known about the characteristics of CNVs, particularly regarding the rates at which they are generated and the mechanics of their transmission from a generation to the next. Here, we used SNP-array raw intensity data for 55 two-generations families (3663 individuals) to scan the gene space of the conifer tree Picea glauca (Moench) Voss for CNVs. We were particularly interested in the abundance, inheritance, spontaneous mutation rate spectrum and the evolutionary consequences they may have on the standing genetic variation of white spruce. Our findings show that CNVs affect a small proportion of the gene space and are predominantly copy number losses. CNVs were either inherited or generated through de novo events. De novo CNVs present high rates of spontaneous mutations that vary for different genes and alleles and are correlated with gene expression levels. Most of the inherited CNVs (70%) are transmitted from the parents in violation of Mendelian expectations. These transmission distortions can cause considerable frequency changes between generations and be dependent on whether the heterozygote parents contribute as male or female. Transmission distortions were also influenced by the partner genotype and the parents genetic background. This study provides new insights into the effects of different evolutionary forces on copy number variations based on the analysis of a perennial plant.

genomics↗