Biology subjects

Labadie, K.

Publications and source records attributed to Labadie, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Mosaic selection and gene flow at the onset of grain beetle domestication

Domestication is an evolutionary process that can begin before deliberate breeding, when association with humans reshapes gene flow and selection. The yellow mealworm, Tenebrio molitor, is undergoing this transition from a synanthropic pest of stored grain to farmed species. We asked whether gene flow between farmed populations contributes to adaptation to captivity and whether selection extends to production traits. We combined population genomics of 320 beetles from eight farmed and wild populations with genetic mapping of 15 production traits from 3,575 individuals. Farm stocks retained high diversity and weak differentiation, with Netherlands-related ancestry connecting populations across Europe and Canada. Farm-restricted sweep-like signatures were 2.06-fold enriched within regions of excess allele sharing, suggesting local selection on introgressed variation. Across 305 production-trait QTLs, overlaps with selection and introgression signals showed no significant enrichment or depletion, suggesting that adaptive gene flow may primarily contribute to adaptation to captivity rather than broadly shaping growth, development and fertility. Nevertheless, egg-hatching-rate and development-time QTLs overlapped regions of reduced nucleotide diversity and low Tajima's D. These findings support a model in which gene flow supplies variation for unintended selection under intensive rearing. Crowding and physiological stress may favour adaptation to captive environments before sustained breeding establishes a broad genomic response at production loci.

evolutionary biology↗

bioRxiv2025

Chromosome-Scale Genome Assembly of Australian Finger Lime and Resequencing Reveal the Hidden Diversity of Oceanian Citrus

Oceanian citrus species, including wild taxa native to Australia and Papua New Guinea, form a genetically distinct clade within the Citrus L. (1753) genus. These species remain largely underexplored, despite their adaptation to diverse environments and relevance for citrus improvement. To support their use in breeding and evolutionary studies, we generated a high-quality, Chromosome-scale genome assembly of an Australian finger lime accession (SRA 1002), a natural interspecific hybrid. The genome was assembled using long-read sequencing, optical mapping, and a high-density genetic map, resulting in nine pseudomolecules covering over 97% of the genome. Using this reference, we analyzed whole-genome resequencing data from 132 accessions representing the diversity of Asian and Oceanian citrus. Variant calling across the dataset produced a high-resolution catalogue of single nucleotide polymorphisms (SNPs) and derived database of SNP fully discriminant of 20 Citrus species (DSNPs), enabling detailed exploration of inter- and intra-specific diversity. The data reveal a strong population structure within the group with clear heterozygosity variation between ancestral species and admixed accessions, reflecting their complex evolutionary history and hybridization patterns. This study provides the first integrated genomic framework for Oceanian citrus diversity, offering essential tools for downstream applications in citrus breeding, conservation, and evolutionary genomics. The resources generated lay the groundwork for future association studies and the targeted introgression of beneficial traits into cultivated citrus.

plant biology↗

bioRxiv2025

The tiny germline chromosomes of Paramecium aurelia have anexceptionally high recombination rate and are capped by a new class of Helitrons

BackgroundParamecia belong to the ciliate phylum of unicellular eukaryotes characterized by nuclear dimorphism. A diploid germline micronucleus (MIC) transmits genetic information across sexual generations. A polyploid transcriptionally active somatic macronucleus (MAC) develops at each sexual generation from a copy of the MIC through programmed DNA elimination (PDE) of > 30% of germline DNA. PDE requires the domesticated PiggyMac (Pgm) transposase. Assembly of Paramecium germline genomes has presented an enormous challenge owing to the difficulty of MIC isolation. ResultsWe report chromosome-scale short-read MIC assemblies for 7 species from the P. aurelia species complex. We discovered a novel clade of Helitrons, with 9-10 kb transposase ORFs under purifying selection, that have remained active in all P. aurelia lineages. A long-read assembly for P. tetraurelia together with a genetic linkage map provided a nearly telomere-to-telomere assembly. Conclusions.The genome consists of tiny (300 kb - 1.2 Mb) and numerous ([~]160) germline chromosomes with the highest recombination rate ever reported for a eukaryote (420 cM/Mb). The ends of the chromosomes consist of Helitrons inserted in telomeric C4A2 repeats, forming a distinct genomic compartment that is eliminated very early during MAC development in a Pgm-independent manner.

genomics↗

bioRxiv2025

Dosage compensation and meiotic sex chromosome inactivation are maintained in the absence of selection

Dosage compensation and meiotic sex chromosome inactivation (MSCI) are key mechanisms regulating gene expression from the X chromosome in male-heterogametic species. While the convergent evolution of these mechanisms is well-documented, their evolutionary fate under relaxed selection remains poorly understood. Here, we test whether dosage compensation and MSCI persist following three independent transitions to parthenogenesis in stick insects, where selection on male phenotypes is relaxed. Using rare males occasionally produced by parthenogenetic females, chromosome-level genome assemblies, RNA-seq from multiple tissues, and immunocytochemistry, we find that dosage compensation is fully conserved across all nine studied somatic tissues. This is even the case in the oldest, approximately 1.5 million years old all-female lineage, and for tissue-specific genes for which dosage variation is not expected to be very deleterious. Meiotic X inactivation in the germline is also conserved. Surprisingly however, expression data and cytological markers indicate that MSCI signatures are even stronger in parthenogenetic males, a pattern likely driven by prolonged autosomal transcription during meiosis. These results indicate that X-targeting dosage compensation and MSCI are highly stable over evolutionary time and may be maintained in all-female lineages by a combination of evolutionary constraint, pleiotropy, or very weak selection, whereas autosomal expression during meiosis shifts rapidly under relaxed selection. Significance StatementSex chromosomes are regulated by specialized mechanisms that balance gene expression between males and females in somatic tissues (dosage compensation) and silence the X chromosome during male meiosis (meiotic sex chromosome inactivation, MSCI). These processes are thought to decay when they become redundant, yet suitable systems to test this prediction are scarce. We studied rare males from parthenogenetic stick insect lineages that have been evolving without sex for up to 1.5 million years. Surprisingly, both dosage compensation and MSCI remain fully functional, despite relaxed selection. Instead, we find altered autosomal expression during meiosis. Our results reveal that sex chromosome regulation is evolutionarily stable and constrained, persisting even after the loss of its purpose.

evolutionary biology↗

bioRxiv2025

ERGA-BGE genome of Noah's Ark shell (Arca noae Linnaeus, 1758), a Mediterranean bivalve species

Arca noae, also known as the Noahs Ark clam, is a bivalve mollusk found in the shallow coastal waters of the Mediterranean Sea and the eastern Atlantic Ocean. This species plays a crucial ecological role by filtering plankton and organic particles from the water, helping maintain water quality and supporting nutrient cycling in marine ecosystems. It is also an important food source for various marine predators, including fish and crustaceans, thereby contributing to the coastal food web. Arca noae is notably resilient to environmental stressors, such as temperature fluctuations, changes in salinity, and pollution, making it a valuable model species for studying how bivalves adapt and respond to stress. While it is not commonly harvested commercially, Arca noae is of great interest to marine researchers due to its ability to thrive in diverse coastal habitats. The reference genome of Arca noae will thus provide important evolutionary insights. The entirety of the genome sequence was assembled into 19 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 1.5 Gb, composed of 257 contigs and 119 scaffolds, with contig and scaffold N50 values of 20.5 Mb and 84.7 Mb, respectively.

genomics↗

bioRxiv2025

ERGA-BGE genome of Pinctada radiata (Leach, 1814): one of the first Lessepsian migrants

Pinctada radiata, commonly known as the Gulf pearl oyster, is a species of pearl oyster found primarily in the warm waters of the Red Sea, the Persian Gulf, and parts of the Indian Ocean. Pinctada radiata contributes to marine ecosystems by filtering water, which helps maintain water quality and supports other marine life. This species is the first bivalve Lessepsian migrant, having migrated from the Red Sea to the Mediterranean Sea via the Suez Canal. The reference genome of Pinctada radiata could help identify genes enabling adaptation to varying temperatures and salinities, facilitating survival in diverse and newly colonized habitats allowing comparisons with other bivalves to uncover shared and unique genetic adaptations. Additionally, the genome could support targeted management practices and conservation initiatives, such as habitat restoration and selective breeding, ensuring the long-term sustainability of P. radiata. The entirety of the genome sequence was assembled into 14 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 0.93 Gb, composed of 220 contigs and 44 scaffolds, with contig and scaffold N50 values of 8.1 Mb and 63.8 Mb, respectively.

genomics↗

bioRxiv2024

An unexplored diversity for adaptation of germination to high temperatures in Brassica species

Elevated temperatures inhibit the germination of a concerning number of crop species. One strategy to mitigate the impact of warming temperatures is to identify and introgress adaptive genes into elite germplasm. Diversity must be sought in wild populations, coupled with an understanding of the complex pattern of adaptation across a broad range of landscapes. By investigating the landraces, wild, and feral populations of Algeria, Italy, France, Slovenia, Spain, and Tunisia, we assessed the response of germination to temperature increase in an unexplored diversity of 117 accessions of B. rapa and 66 of B. oleracea. Our results show that both species exhibit heat tolerance to the temperature range tested, especially B. rapa with an increase in speed and uniformity of germination time, as well as an increase in germination rate as temperature increased. As for B. oleracea accessions, the ability to germinate under heat conditions depended on the geographical origin; in particular, southern populations showed a higher germination rate than northern populations, possibly in relation to their warmer climates of origin. These findings highlight the complex interplay between domestication, feralization, and current agronomic practices in shaping germination characteristics in Brassica species.

evolutionary biology↗

bioRxiv2024

A super-pangenome for cultivated citrus reveals evolutive features during the allopatric phase of their reticulate evolution

Most of the rich genetic diversity observed in cultivated citrus results from a reticulate evolution involving four ancestral taxa, C. medica, C. reticulata, C. maxima and C. micrantha, whose radiation occurred in allopatry. In such an evolutive context, genome diversity studies, GWAS analysis and transcriptomic studies will be significantly enhanced through pangenome approaches. We report the implementation of a super-pangenome for cultivated citrus, established with de novo assemblies in pseudochromosomes of C. medica (346 Mb), C. reticulata (332 Mb) and C. micrantha (333 Mb), released for the first time alongside a previously published chromosome-scale assembly of C. maxima. Gene annotation of these four genome assemblies revealed 28,090, 29,477, 29,258 and 30,101 genes, respectively, with a focus on pattern recognition receptors. Repetitive element annotation revealed that nearly half of each genome consisted of transposable elements or DNA-satellites. The 3 new genome assemblies display strong synteny and collinearity, while significant discrepancies are observed with the C. maxima assembly. Resequencing information (single nucleotide polymorphisms [SNPs], small indels and gene presence-absence variation [PAV]) from 55 accessions were used to explore the intra- and interspecific diversity of the four ancestral taxa and their relationships with the main horticultural groups resulting from reticulate evolution. Diagnostic SNPs of the ancestral taxa, all over the four genomes assemblies, revealed interspecific introgressions in several accessions representative of C. reticulata, C. maxima and C. medica as well as insights into the origin and phylogenomic structures of modern horticultural groups. PAV analysis revealed a gene whose absence or presence was specific to one of the ancestral taxa (dPAV). Interestingly, diagnostic PAV (dPAV) analysis uncovered a large chloroplastic introgression in chromosome 4 of C. medica, inherited in horticultural groups and recent hybrids having this species as the male parent. Implementing the super-pangenome combined the identification of orthologous genes across the four genome assemblies and the PAV information from the resequencing data. Significant inter- and intraspecific variations were highlighted, including 25,291 core, 2,431 soft-core and 5,171 dispensable genes. The analysis of the functional enrichment and species-specific adaptations in the citrus super-pangenome revealed distinct functional specializations. This highlights the evolutionary paths that have shaped each species, contributing to the diversity in the citrus super-pangenome while maintaining a shared foundation of essential biological processes. The development of this super-pangenome is a significant milestone in citrus genomics, providing a comprehensive resource that captures the extensive genetic diversity of modern cultivated citrus. Additionally, we established a dedicated Genome Hub, offering a platform for continuous genomic research and allowing for ongoing updates and future inclusion of additional ancestral species.

genomics↗

bioRxiv2024

Genome-resolved diversity and biosynthetic potential of the coral reef microbiome

Coral reefs are marine biodiversity hotspots that provide a wide range of ecosystem services. They are also reservoirs of bioactive compounds, many of which are produced by microbial symbionts associated with reef invertebrate hosts. However, for the keystone species of coral reefs--the reef-building corals themselves--we still lack a systematic assessment of their microbially encoded biosynthetic potential, and thus the molecular resources that may be at stake due to the alarming decline in reef biodiversity and cover. Here, we analysed microbial genomes reconstructed from 820 reef-building coral samples of three representative coral genera collected at 99 reefs across 32 islands during a two-year expedition throughout the Pacific Ocean (Tara Pacific). By contextualising our analyses with the microbiomes of other reef species, we found that genomic information was previously available for only 10% of the 4,224 microbial species overall and for less than 1% of the 645 species exclusively identified in Tara Pacific samples. We found reef-building coral microbiomes to be host-specific and their biosynthetic potential to rival or even surpass that found in traditional targets for natural product discovery, such as sponges and soft corals. Fire corals were not only particularly diverse in microbially encoded biosynthetic gene clusters (BGCs), but also in BGC-rich bacteria, including Acidobacteriota spp., which have been recently highlighted for their promising natural product repertoire. Together, this study unveils new candidate sources for bioactive compound discovery, prioritises targets for microbial isolation, and underscores the importance of conservation efforts by linking macro-organismal biodiversity loss to host-specific microbiomes and their biotechnological potential.

microbiology↗

bioRxiv2024

Dynamics of X chromosome hyper-expression and inactivation in male tissues during stick insect development

Differentiated sex chromosomes are frequently associated with major transcriptional changes: the evolution of dosage compensation (DC) to equalize gene expression between the sexes and the establishment of meiotic sex chromosome inactivation (MSCI). Our study investigates the mechanisms and developmental dynamics of dosage compensation and meiotic sex chromosome inactivation in the stick insect species T. poppense. Stick insects are characterized by XX/XO sex determination and an X chromosome which likely evolved prior to the diversification of insects over 450 Mya. We generated a chromosome-level genome assembly and analyzed gene expression from various tissues (brain, gut, antennae, leg, and reproductive tract) across developmental stages in both sexes. Our results show that complete dosage compensation is maintained in male somatic tissues throughout development, mediated by upregulation of the single X chromosome. Contrarily, in male reproductive tissues, dosage compensation is present only in the early nymphal stages. As males reach the 4th nymphal stage and adulthood, X-linked gene expression diminishes, coinciding with the onset of MSCI. This reduction is associated with histone modifications indicative of transcriptional silencing, aligning with meiotic progression. These findings reveal the dynamic regulation of X-linked gene expression in T. poppense, and suggest that reduced X-expression in insect testes is generally driven by MSCI rather than an absence of dosage compensation mechanisms. Our work provides critical insights into sex chromosome evolution and the complex interplay of dosage compensation and MSCI across tissues and developmental stages.

evolutionary biology↗

bioRxiv2024

Functional monocentricity with holocentric characteristics andchromosome-specific centromeres in a stick insect

Centromeres are specialized genomic regions that are critical for chromosome segregation in eukaryotes. However, how the diversity of centromeres evolved, ranging from localized centromeres in monocentric species to complex chromosome-wide distributed centromere regions in holocentric species, remains elusive. Our cellular and genomic analyses in Timema stick insects reveal that within cell variation of the major centromere protein CenH3 recapitulates the variation typically observed across species. While CenH3-containing nucleosomes are distributed in a monocentric fashion on autosomes and bind tandem repeat sequences specific to individual or small groups of chromosomes, they exhibit a holocentric-like distribution on the sex chromosome and bind to more complex intergenic regions. Despite this contrasting distribution, all chromosomes, including the sex chromosome, attach to spindle microtubules at a single location, marking the first instance of a functionally monocentric species with holocentric-like attributes. Together, our findings highlight the potential for gradual transitions towards holocentricity or CenH3-independent centromere determination, and help to understand the rapid centromere sequence divergence between species.

evolutionary biology↗

bioRxiv2024

The evolutionary history and functional specialization of microRNA genes in Arabidopsis halleri and A. lyrata

MicroRNAs (miRNAs) are a class of small non-coding RNAs that play important regulatory roles in plant genomes. While some miRNA genes are deeply conserved, the majority appear to be species-specific, raising the question of how they emerge and integrate into cellular regulatory networks. To better understand this, we first performed a detailed annotation of miRNA genes in the closely related plants Arabidopsis halleri and A. lyrata and evaluated their phylogenetic conservation across 87 plant species. We then characterized the process by which newly emerged miRNA genes progressively acquire the properties of "canonical" miRNA genes, in terms of size and stability of the hairpin precursor, loading of their cleavage products into Argonaute proteins, and potential to regulate downstream target genes. Nucleotide polymorphism was lower in the mature miRNA sequence than in the other parts of the hairpin (stem, terminal loop), and the regions of coding sequences targeted by miRNAs also had reduced diversity as compared to their neighboring regions along the genes. These patterns were less pronounced for recently emerged than for evolutionarily conserved miRNA genes, suggesting a weaker selective constraint on the most recent miRNA genes. Our results illustrate the rapid birth-and-death of miRNA genes in plant genomes, and provide a detailed picture of the evolutionary processes by which a small fraction of them eventually integrate into "core" biological processes.

evolutionary biology↗

bioRxiv2024

Whole genome sequencing of four Ixodes species expands understanding of tick evolution

Ticks, hematophagous acari, pose a significant threat by transmitting various pathogens to their vertebrate hosts during feeding. Despite advances in tick genomics, high-quality genomes were lacking until recently, particularly in the genus Ixodes, which includes the main vectors of Lyme disease. Here, we present the complete genome sequences of four tick species, derived from a single female individual, with a particular focus on the European species Ixodes ricinus, achieving a chromosome-level assembly. Additionally, draft assemblies were generated for the three other Ixodes species, I. persulcatus, I. pacificus and I. hexagonus. The quality of the four genomes and extensive annotation of several important gene families have allowed us to study the evolution of gene repertoires at the level of the genus Ixodes and of the tick group. We have determined gene families that have undergone major amplifications during the evolution of ticks, while an expression atlas obtained for I. ricinus reveals striking patterns of specialization both between and within gene families. Notably, several gene family amplifications are associated with a proliferation of single-exon genes. The integration of our data with existing genomes establishes a solid framework for the study of gene evolution, improving our understanding of tick biology. In addition, our work lays the foundations for applied research and innovative control targeting these organisms.

genomics↗

bioRxiv2024

Nitrogen metabolism in the picoalgae Pelagomonas calceolata: disentangling cyanate lyase function under different nutrient conditions.

Cyanate (OCN-) is potentially an important organic nitrogen source in aquatic environments given the prevalence and activity of cyanate lyase genes in microalgae. However, the conditions under which these genes are expressed and the actual capacity of microalgae to assimilate cyanate remain underexplored. Here, we studied the nitrogen metabolism of the cosmopolitan picoalga Pelagomonas calceolata (Pelagophyceae, Stramenopiles) in environmental metatranscriptomes and transcriptomes from culture experiments under different nitrogen sources and concentrations. We observed that cyanate lyase is over-expressed in nitrate-poor oceanic regions, suggesting that cyanate is an important molecule contributing to the persistence of P. calceolata in oligotrophic environments. In the laboratory, we confirmed that this gene is over-expressed in low-nitrate medium together with several genes involved in nitrate recycling from endogenous molecules. Non-axenic cultures of P. calceolata were capable of growing on various nitrogen sources, including nitrate, urea and cyanate, but not ammonium. RNA sequencing of these cultures revealed that cyanate lyase was under-expressed in the presence of cyanate, indicating that this gene in not involved in the catabolism of extracellular cyanate to ammonia. Conversely, axenic P. calceolata cultures were not able to grow on cyanate, suggesting that the bacterial community consumes cyanate and provides an available form of nitrogen for growth of the alga. Based on environmental datasets and laboratory experiments, we propose that cyanate lyase is important in nitrate-poor environments to reduce the toxicity of intracellular cyanate produced by endogenous nitrogenous compound recycling, rather than being used to metabolise imported extracellular cyanate as an alternative nitrogen source.

genomics↗

bioRxiv2023

Pangenomic exploration of Theobroma cacao: new insights into gene content diversity and selection during domestication

The Cacao tree (Theobroma cacao L.) is a major cash crop and an important source of income for millions of farmers across Africa, Asia and Latin America. However, cacao farmers and producing countries are facing multiple challenges including pest and disease management, sustainable production under threat of climate changes and diversification of cocoa flavor profiles. Addressing these challenging requires a deeper understanding of the existing genetic diversity of the species. Yet, very little is known about the intraspecific gene content variation. In this study, we used the genome of 216 accessions of T. cacao (including 185 newly re-sequenced) covering a broad genetic diversity of the species to construct the first pan-genome of the cacao tree. As a result, we predicted a total of 30,489 pan-genes, enriching the reference Criollo genome with 1,407 new genes. Our analysis revealed that only a small fraction of these genes (9.2%) is dispensable, being absent in some individuals. However, these genes could represent a valuable resource for breeding efforts aimed at improving disease resistance in the species. We used this new pangenome resource to gain insights into how diversification and domestication processes have influenced genomic variability within the species. Notably, we observed a significant loss of genes within the domesticated Criollo genetic group. Furthermore, we found evidences suggesting that domestication processes have had an impact on the vigor and disease tolerance of Criollo accessions. In summary, our research has contributed to a better understanding of the cacao trees genome diversity. These findings offer new avenues for biological discovery and breeding, ultimately addressing the challenges faced by cacao farmers and producing countries.

genomics↗

bioRxiv2023

The Silene latifolia genome and its giant Y chromosome

In some species, the Y is a tiny chromosome but the dioecious plant Silene latifolia has a giant [~]550 Mb Y chromosome, which has remained unsequenced so far. Here we used a hybrid approach to obtain a high-quality male S. latifolia genome. Using mutants for sexual phenotype, we identified candidate sex-determining genes on the Y. Comparative analysis of the sex chromosomes with outgroups showed the Y is surprisingly rearranged and degenerated for a [~]11 MY-old system. Recombination suppression between X and Y extended in a stepwise process, and triggered a massive accumulation of repeats on the Y, as well as in the non-recombining pericentromeric region of the X, leading to giant sex chromosomes. One-Sentence SummaryThis work uncovers the structure, function, and evolution of one of the largest giant Y chromosomes, that of the model plant Silene latifolia, which is almost 10 times larger than the human Y, despite similar genome sizes.

genomics↗

bioRxiv2023

Unzipped assemblies of polyploid root-knot nematode genomes reveal new kinds of unilateral complex telomeric repeats

Telomeres play central roles in senescence, aging and chromosome integrity. Using ONT long read sequencing we have assembled the genomes of Meloidogyne incognita, M. javanica and M. arenaria, the three most devastating plant-parasitic nematodes at unparalleled contiguity. The telomeric repeat (TTAGGC)n, evolutionarily conserved in nematodes, was not found in these genomes. Furthermore, no evidence for a telomerase enzyme or for orthologs of C. elegans telomere-associated proteins could be found. Instead, we identified species-specific composite repeats mostly present at one end of contigs. These repeats were G-rich, oriented and transcribed, similarly to known telomeric repeats. Using FISH we confirmed these repeats were present at one single end of M. incognita chromosomes. The discovery of a new kind of telomeric repeat in these species highlights the evolutionary diversity of chromosome protection systems despite their central roles and opens new perspectives towards the development of more specific control methods against these pests.

genomics↗

bioRxiv2022

Global observation of plankton communities from space

Satellite remote sensing from space is a powerful way to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here we present an approach to identify representative communities from a global plankton network that included both zooplankton and phytoplankton and using global satellite observations to predict their biogeography. Six representative plankton communities were identified from a global co-occurrence network inferred using a novel rDNA 18S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to train a model that predicted these representative communities from satellite data. The model showed an overall 67% accuracy in the prediction of the representative communities. The prediction based on 17 satellite-derived parameters showed better performance than based only on temperature and/or the concentration of chlorophyll a. The trained model allowed to predict the global spatiotemporal distribution of communities over 19-years. Our model exhibited strong seasonal changes in the community compositions in the subarctic-subtropical boundary regions, which were consistent with previous field observations. This network-oriented approach can easily be extended to more comprehensive models including prokaryotes as well as viruses.

ecology↗