Biology subjects

Verta, J.-P.

Publications and source records attributed to Verta, J.-P..

12 recordsLinked to original sources

bioRxiv2026

Gene expression dynamics through time reveal low pleiotropy genes underlying local adaptation in silver birch (Betula pendula)

Understanding the molecular mechanisms underlying local adaptation in boreal trees is important for assessing their adaptive potential under climate change. The role of pleiotropy in polygenic local adaptation remains poorly understood. Here we studied growth and temporal transcriptomic responses to photoperiod in three photoperiod treatments in three populations of Betula pendula within a two-week time period to identify genes and co-expression networks underlying local adaptation and to estimate the level of pleiotropy in population specific gene expression. We used RNA sequencing to characterize the temporal transcriptomic responses which were analyzed with variance partitioning, differential gene expression and weighted co-expression network analyses. Photoperiod treatment and sampling time were the main drivers of gene expression variation both at the co-expression module and single gene level. The majority of circadian clock and flowering time genes exhibited striking similarity across populations. Nevertheless, we detected small but significant population effects in the temporal gene expression patterns which were concentrated on the periphery of the co-expression networks consistent with low pleiotropy effects. Our findings suggest that local adaptation to growing season length among populations exhibiting very low genetic differentiation along a latitudinal cline in B. pendula is likely polygenic and potentially governed through low pleiotropy genes.

evolutionary biology↗

bioRxiv2025

A Comprehensive Analysis of Atlantic Salmon Gonad and Pituitary Transcriptomes Identifies Novel Players in Sexual Maturation

BackgroundSexual maturation is a key developmental process important for reproductive success. Understanding the molecular mechanisms behind variation in sexual maturation can provide insights into reproductive biology and how life history variation is encoded in the genome. Atlantic salmon (Salmo salar) has become an excellent sexual maturation research model due to its diversity of life history strategies and its ecological and economic importance. A major challenge has been the lack of a comprehensive transcriptional investigation of reproductive tissues that captures the dynamic transcriptional changes across individuals, tissues, and developmental stages. Long non-coding RNAs (lncRNAs) also play crucial roles in maturation, yet their functions in salmon maturation remain underexplored. ResultsIn this study, we sequenced 98 transcriptomes and found substantial transcriptomic complexity in the gonad and pituitary tissues of Atlantic salmon. We identified transcripts corresponding to 2,364 putative newly characterized protein-coding genes and 4,421 putative long intergenic non-coding RNAs (lincRNAs), many with tissue-specific expression. Gene co-expression network analysis (WGCNA) revealed tissue-specific gene network modules, linked to GO terms including Wnt signaling in immature testis, lipid metabolism, and cilia assembly in mature testis, ribosome biogenesis and DNA repair in the ovary, and hormone activity in pituitary. We identified new copies of known genes, such as gh1, pou3f2, and ier5 associated with the regulation of gonadal and pituitary functions. Some lncRNAs and their nearest genes showed correlated expression within modules, suggesting potential regulatory roles. Candidate lincRNAs indicated cis-acting regulatory potential on genes like tnfrsf11b and fgl1, which are implicated in immune privilege during gonadal development and sperm quality control. ConclusionsOur study provides a comprehensive transcriptomic analysis of Atlantic salmon gonad and pituitary tissues, significantly improving the functional annotation of the Atlantic salmon genome. These findings reveal key regulatory pathways and novel molecular players involved in sexual maturation, particularly in the testis. Importantly, our study highlights the regulatory potential of lncRNAs in reproductive biology and maturation age variation, advancing our understanding of the molecular mechanisms governing sexual maturation. They further unlock future gene expression analyses and regulatory network reconstruction for dissecting the roles of lncRNAs in Atlantic salmon life history variation.

genetics↗

bioRxiv2025

Testicular gene expression patterns suggest a heterochronic shift underlying vgll3-mediated maturation age variation in Atlantic salmon

Heterochrony, or shifts in developmental timing, drives phenotypic diversity within and between species and shapes life history traits that can be selected for in changing environments which in turn promotes population resilience. Despite its importance, the molecular basis of heterochrony remains largely unknown. Mutations in "heterochronic genes" that regulate these processes can induce stable timing shifts, impacting important life history traits like pubertal timing. Heterochronic shifts in gene transcription are often tissue-specific and in mammals, for example, the testis shows the most pronounced heterochrony across species, especially during spermatogenesis. Age at maturity is a key adaptive trait across species, with vgll3, a Hippo pathway co-factor, as a main determinant in Atlantic salmon. The roles of vgll3 in maturation timing, adiposity, and energy storage are evolutionarily conserved across fish and mammals. Recent studies in salmon show vgll3 alleles; early (E) and late (L), affect reproductive gene expression, reinforcing its role in regulating developmental timing. This study examines whether vgll3 influences testicular heterochrony in Atlantic salmon by analyzing Hippo pathway-related gene expression in E and L genotypes. We observed heterochronic divergence in Hippo pathway gene transcription, indicating accelerated spermatogenesis-linked changes in the testes of vgll3*EE individuals. Since maturation in Atlantic salmon is closely tied to environmental changes, and the Hippo pathway acts as an environmental sensor, these findings suggest that Hippo-vgll3 shifts may also respond to environmental signals. This positions vgll3 as a heterochronic gene which is potentially affected by environmental changes (heterokairic), making it an ideal target for studying ecological adaptation linked to heterochrony.

developmental biology↗

bioRxiv2024

Hippo-vgll3 signaling may contribute to sex differences in Atlantic salmon maturation age via contrasting adipose dynamics

Sexual maturation in Atlantic salmon entails a transition in energy utilization, governed in part by genes and environmental stimuli in sex-specific manner. Salmon males require less energy, in the form of adiposity, to mature compared to females and typically mature younger. Maturation age is also influenced in a sex-dependent fashion by the vgll3 genotype (vestigial-like 3), a co-factor in the Hippo pathway. The underlying molecular processes of sex-dependent maturation age, and how they interplay with adiposity and vgll3 genotypes, have remained unknown. To elucidate the molecular mechanisms underlying sex- and genotype-specific maturation differences, we investigated the association of early (E) and late (L) maturation vgll3 alleles and the transcriptional expression of > 330 genes involved in the regulation of the Hippo pathway and sexual maturation, and related to molecular signals in brain, adipose tissue, and gonads. The strongest effect of vgll3 genotype was observed in adipose tissue for females and in brain for males, highlighting a sex-specific expression difference in the main association of vgll3 genotype. Genes related to ovarian development showed increased expression in vgll3*EE compared to vgll3*LL females. Additionally, vgll3*EE females compared to vgll3*EE males exhibited reduced markers of pre-adipocyte differentiation and lipolysis yet enhanced expression of genes related to adipocyte maturation and lipid storage. Brain gene expression further showed sex-specific expression signals for genes related to hormones and lipids, as well as tight junction assembly. Overall, these sex-specific patterns point towards a greater lipid storage and slower energy utilization in females compared to males. These results suggest that Hippo-dependent mechanisms may be important mediators of sex differences in maturation age in salmon.

genetics↗

bioRxiv2024

Sex-, development-, and nutrition-dependent expression of a major age-at-maturity gene in Atlantic salmon

Sexual maturation is a key process in the life history of an organism and is influenced by both genetic and environmental factors. In Atlantic salmon (Salmo salar), alternative alleles at the gene vgll3 have been found to associate with a large proportion of the variation in maturation age, yet the molecular and physiological mechanisms of this association are still largely unknown. Here, we investigated the mechanisms by which genetic variation in this major age-at-maturity gene translated into phenotypic variation. We established a time series of gonadal vgll3 mRNA expression in male and female Atlantic salmon in a common garden setting, starting at the prepubertal stage and spanning multiple spawning seasons. We found that vgll3 mRNA expression is reduced in early-maturing males and females. However, for the second spawning season, vgll3 expression increased with gonadal development in males, but eventually decreased in females. Expression of vgll3 had context-dependent correlations with expression of amh and lhr. We also found signs of reduced testicular vgll3 expression in a low-fat feed treatment. By significantly widening the scope of our knowledge on temporal vgll3 expression dynamics, our results exemplify that major-effect genes may use different pathways in sexes but achieve similar outcomes.

genetics↗

bioRxiv2024

A salmon fish model reveals genetic signals in brain associated with early maturation

Emerging evidence suggests a link between adiposity and early maturation, potentially impacting hormonal signaling pathways governing puberty timing. Fish models have proven invaluable in studying these processes, given their genetic and physiological similarities to humans. In Atlantic salmon, in addition to being linked with environmental shifts and lipid reserves, the timing of sexual maturation also has a strong genetic basis. A gene encoding a co-factor of Hippo pathway, vgll3, is a major determinant of maturation timing in salmon, and the same gene was found to be associated with maturation timing in humans. Intriguingly, vgll3 also inhibits adipogenesis in mice. Recent studies in salmon revealed correlations between vgll3 genotypes and reproductive axis gene expression, possibly modulated through the Hippo signaling pathway. The Hippo pathway is known for its role in sexual maturation and adipogenesis and responds to environmental cues such as dietary fat and temperature. In this study, we employed a custom gene expression panel in male Atlantic salmon with different vgll3 early (E) and late (L) maturation genotypes testing components of this pathway in brain at immature and mature stages. We found increased brain expression of a major Hippo pathway kinase (lats1b) and melanocortin receptor encoding genes (mc4ra and mc4rc) in individuals with early (E) maturation genotypes of vgll3 before maturation development of testes. Moreover, we found components and interacting partners of Hippo pathway showing differential expression in brain of individuals with early (E) and late (L) vgll3 genotypes prior to maturation. This could indicate extensive and complex roles of Hippo pathway in brain processes required for preparing for [the onset of] maturation at upstream of reproductive axis. This study elucidates molecular mechanisms underpinning early maturation, and for the first time in fish, offering insights into detecting it at molecular level in brain before visible gonadal changes occur.

genetics↗

bioRxiv2024

A complex mechanism translating variation of a simple genetic architecture into alternative life-histories

Linking genes to traits is a central goal in biology. Despite progress in discovering genes associated with trait differences, a poor understanding of the functional mechanisms underlying genetic associations leaves us critically far from connecting genetic and phenotypic variation. This knowledge-gap is particularly large in multifaceted phenotypes of ecological relevance such as life-history traits. Using a multiomic dissection of the genotype-phenotype association in a large-effect maturation age gene - the transcription cofactor vestigial-like 3 (vgll3) - in Atlantic salmon (Salmo salar), we show that vgll3 mediates concerted changes of distinct molecular phenotypes associated with puberty in male gonads. Vgll3 genotype conferring early maturity upregulates key genes controlling androgen production, cellular energy and adiposity, and TGF-{beta} signaling, among others, thereby increasing the likelihood of earlier pubertal initiation. Genotype-dependent developmental trajectories are produced through VGLL3 interaction with distinct transcription factors, thus coordinating differential activation of regulatory pathways. These results reveal a genetically simple, yet functionally complex, architecture underlying alternative life-histories where variation in a single major effect gene produces pleiotropic variation in a spectrum of cellular traits. Our results further suggest that evolution in correlated phenotypes such as exemplified by alternative life history strategies may be mediated by a surprisingly simple genetic architecture.

evolutionary biology↗

bioRxiv2023

Gene co-expression patterns in Atlantic salmon adipose tissue provide a molecular link between seasonal changes, energy balance and age at maturity

Sexual maturation in many fishes requires a major physiological change that involves a rapid transition between energy storage and usage. In Atlantic salmon, this transition for the initiation of maturation is tightly controlled by seasonality and requires a high-energy status. Lipid metabolism is at the heart of this transition since lipids are the main energy storing molecules. The balance between lipogenesis (lipid accumulation) and lipolysis (lipid use) determines energy status transitions. A genomic region containing a transcription co-factor of the Hippo pathway, vgll3, is the main determinant of maturation timing in Atlantic salmon. Interestingly, vgll3 acts as an inhibitor of adipogenesis in mice and its genotypes are potentially associated with seasonal heterochrony in lipid storage and usage in juvenile Atlantic salmon. Here, we explored changes in expression of more than 300 genes directly involved in the processes of adipogenesis, lipogenesis and lipolysis, as well as the Hippo pathway in the adipose tissue of immature and mature Atlantic salmon with distinct vgll3 genotypes. We found molecular evidence consistent with a scenario in which immature males exhibiting vgll3 genotype specific seasonal direction of change in their lipid profiles. We also identified components of the Hippo signaling pathway as potential major drivers of vgll3 genotype specific differences in adipose tissue gene expression. This study demonstrates the importance of adipose gene expression patterns for directly linking environmental changes with energy balance and age at maturity through genetic factors bridging lipid metabolism, seasonality and sexual maturation.

physiology↗

bioRxiv2020

Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon

Whole genome duplications (WGD) have been considered as springboards that potentiate lineage diversification through increasing functional redundancy. Divergence in gene regulatory elements is a central mechanism for evolutionary diversification, yet the patterns and processes governing regulatory divergence following events that lead to massive functional redundancy, such as WGD, remain largely unknown. We studied the patterns of divergence and strength of natural selection on regulatory elements in the Atlantic salmon (Salmo salar) genome, which has undergone WGD 100-80 Mya. Using ChIPmentation, we first show that H3K27ac, a histone modification typical to enhancers and promoters, is associated with genic regions, tissue specific transcription factor binding motifs, and with gene transcription levels in immature testes. Divergence in transcription between duplicated genes from WGD (ohnologs) correlated with difference in the number of proximal regulatory elements, but not with promoter elements, suggesting that functional divergence between ohnologs after WGD is mainly driven by enhancers. By comparing H3K27ac regions between duplicated genome blocks, we further show that a longer polyploid state post-WGD has constrained asymmetric regulatory evolution. Patterns of genetic diversity across natural populations inferred from re-sequencing indicate that recent evolutionary pressures on H3K27ac regions are dominated by largely neutral evolution. In sum, our results suggest that post-WGD functional redundancy in regulatory elements continues to have an impact on the evolution of the salmon genome, promoting largely neutral evolution of regulatory elements despite their association with transcription levels. These results highlight a case where genome-wide regulatory evolution following an ancient WGD is dominated by genetic drift. Significance statementRegulatory evolution following whole genome duplications (WGD) has been investigated at the gene expression level, but studies of the regulatory elements that control expression have been lacking. By investigating regulatory elements in the Atlantic salmon genome, which has undergone a whole genome duplication 100-80 million years ago, we discovered patterns suggesting that neutral divergence is the prevalent mode of regulatory element evolution post-WGD. Our results suggest mechanisms for explaining the prevalence of asymmetric gene expression evolution following whole genome duplication, as well as the mismatch between evolutionary rates in enhancers versus that of promoters.

evolutionary biology↗

bioRxiv2019

Regulatory divergence in vgll3 underlies variation in age at maturity in male Atlantic salmon

A major goal in biology is to understand how evolution shapes variation in individual life histories. Genome-wide association studies have been successful in uncovering genome regions linked with traits underlying life history variation in a range of species. However, lack of functional studies of the discovered genotype-phenotype associations severely restrains our understanding how alternative life history traits evolved and are mediated at the molecular level. Here, we report a cis-regulatory mechanism whereby expression of alternative isoforms of the transcription co-factor vestigial-like 3 (vgll3) associate with variation in a key life history trait, age at maturity, in Atlantic salmon (Salmo salar). Using a common-garden experiment, we first show that vgll3 genotype associates with puberty timing in one-year-old salmon males. By way of temporal sampling of vgll3 expression in ten tissues across the first year of salmon development, we identify a pubertal transition in vgll3 expression where maturation coincided with a 66% reduction in testicular vgll3 expression. The late maturation allele was not only associated with a tendency to delay puberty, but also with expression of a rare transcript isoform of vgll3 pre-puberty. By comparing absolute vgll3 mRNA copies in heterozygotes we show that the expression difference between the early and late maturity alleles is largely cis-regulatory. We propose a model whereby expression of a rare isoform from the late allele shifts the liability of its carriers towards delaying puberty. These results reveal how regulatory differences can be a central mechanism for the evolution of life history traits. Author summaryAlternative life history strategies are an important source of diversity within populations and promote the maintenance of adaptive capacity and population resilience. However, in many cases the molecular basis of different life history strategies remains elusive. Age at maturity is a key adaptive life history trait in Atlantic salmon and has a relatively simple genetic basis. Using salmon age at maturity as a model, we report a mechanism whereby different transcript isoforms of the key age at maturity gene, vestigial-like 3 (vgll3), associate with variation in the timing of male puberty. Our results show how gene regulatory differences in conjunction with variation in gene transcript structure can encode for complex alternative life histories.

evolutionary biology↗

bioRxiv2018

Utilization of tissue ploidy level variation in de novo transcriptome assembly of Pinus sylvestris

Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies, including the utility of haploid (megagametophyte) tissue during de novo assembly as single-allele guides, for six individuals and five different tissues in Pinus sylvestris. We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity.

evolutionary biology↗

bioRxiv2018

Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks.

Regulation of gene expression is thought to play a major role in adaptation but the relative importance of cis- and trans-regulatory mechanisms in the early stages of adaptive divergence is unclear. Using RNAseq of threespine stickleback fish gill tissue from four independent marine-freshwater ecotype pairs and their F1 hybrids, we show that cis-acting (allele-specific) regulation consistently predominates gene expression divergence. Genes showing parallel marine-freshwater expression divergence are found near to adaptive genomic regions, show signatures of natural selection around their transcription start sites and are enriched for cis-regulatory control. For genes with parallel increased expression among freshwater fish, the quantitative degree of cis- and trans-regulation is also highly correlated across populations, suggesting a shared genetic basis. Compared to other forms of regulation, cis-regulation tends to show greater additivity and stability across different genetic and environmental contexts, making it a fertile substrate for the early stages of adaptive evolution.

genomics↗