Biology subjects

Choisne, N.

Publications and source records attributed to Choisne, N..

8 recordsLinked to original sources

bioRxiv2026

Genomic detection of domoic acid biosynthesis uncovers expanded toxigenic diversity across Pseudo-nitzschia diatoms

Domoic acid (DA) production by diatom genus Pseudo-nitzschia causes recurrent harmful algal blooms with major consequences for marine ecosystems, fisheries, and human health. Predicting DA risk remains challenging because toxin production varies across morphologically similar and cryptic lineages. Consequently, morphology or single marker genes often fail to resolve toxigenic potential. Here, we expand genomic resources for Pseudo-nitzschia by generating and compiling high-quality genomes spanning diverse species and biogeographic origins, establishing a genus-wide phylogenomic framework to investigate the distribution and evolution of the DA biosynthesis (dab) gene cluster. Among chemically characterized strains, the dab pathway was detected in species only with confirmed DA production. While the cluster exhibits a conserved core structure, several lineages display signatures of ongoing evolution, including intronization, locus rearrangement, and pseudogenization. One striking example of dab variation occurs in toxigenic P. australis strains, in which its biochemically validated isodomoic acid A synthase-encoding gene dabC is located outside the dab locus. Metatranscriptomic surveys reveal widespread environmental dab expression across size classes and species, implicating taxa not typically associated with environmental DA events, such as P. cf. obtusa and P. cf. plurisecta. To connect dab expression with chemical output, nutrient limitation experiments in the historically inconsistent DA producer P. pseudodelicatissima combined transcriptional profiling and nontargeted metabolomics demonstrating coordinated dab expression across distinct co-expression modules and DA accumulation in response to silicon limitation. Together, these results refine the phylogenetic scope of DA production and provide a genome-resolved basis for improved molecular monitoring of toxigenic diversity.

genetics↗

bioRxiv2026

LTR transposable elements contribution to the apple genome, methylome and transcriptome evolution in Malus domestica

The whole genome duplication (WGD) shared by apple (Malus domestica) and pear (Pyrus communis) dated 27 Mya was followed 21 Mya by a burst of transposable elements (TE), making these organisms a prime choice for studying the evolution of duplicated genes. In this study, we conducted a meta-analysis of 149 RNA-Seq datasets and focused on gene pairs for which one ohnolog was systematically under-expressed compared to its duplicate. To understand this systematic differential expression, we investigated the TE environment (TE type, TE divergence and insertion position) of these genes pairs and found that under-expressed genes in apple and pear were enriched in recent Class I LTR TE Copia and Gypsy insertions in their immediate genic environment. In apple, we identified a quantitative relationship between the number of LTR insertions in the genes' environments and the level of differential expression among pairs of ohnologs. Finally, we found that these under-expressed genes displayed either hypomethylated or hypermethylated profiles in their sequence in the CG and CHG contexts.

evolutionary biology↗

bioRxiv2026

Chromosome-scale assembly of the Cupressus sempervirens genome unravels new insights into the evolutionary history of conifers

Conifers, which comprise nearly two-thirds of extant gymnosperm species, are ecologically and economically important but remain genomically understudied because of their exceptionally large, repeat-rich genomes. Here, we report a chromosome-level assembly of the haploid genome of Cupressus sempervirens generated using PacBio HiFi reads and scaffolded with optical and genetic maps. The 10 Gb assembly shows exceptional contiguity for a conifer genome (contig N50 = 29.8 Mb) and was organized into 11 pseudomolecules. Iso-Seq-supported annotation identified 42,980 protein-coding genes. Repetitive elements account for over 80% of the genome, with LTR retrotransposons alone representing 52.5%. Transposable elements (TE) are pervasive in both intergenic and genic regions and have a major impact on gene architecture: TE insertions within introns generate ultra-long introns, often exceeding 100 kb, and drive gene size expansion. Analyses of LTR retrotransposon dynamics indicate that genome enlargement in C. sempervirens was driven not by recent transpositional bursts, but by the long-term accumulation and incomplete removal of ancient LTR retrotransposons. Consistent with this pattern, paleogenomic reconstruction across representative gymnosperms found no evidence of whole-genome duplication in the Cupressus lineage. This reference genome provides a valuable resource for studying conifer genome evolution, gene structure, and traits of agronomic and ecological interest, including cypress pollinosis.

genomics↗

bioRxiv2025

The diversity and host range of endogenous caulimovirids illuminate the ancient origin and early evolution of the Caulimoviridae

Endogenous viral elements (EVEs) are viral sequences integrated into the genomes of host organisms, analogous to molecular fossils. The majority of characterised EVEs in plants are derived from the Caulimoviridae, the only family of dsDNA viruses infecting this kingdom. Endogenous caulimovirids (ECVs) occur across taxonomically diverse vascular plant species and represent a significant resource for studying host-virus coevolution, host range dynamics, and the evolution of viral genomes over deep timescales. Previous evolutionary studies based on ECVs proposed either cospeciation or host-switching as the main drivers of Caulimoviridae evolution, but were limited by sparse genomic data from basal plant lineages. Using 93 plant genomes spanning all embryophyte lineages, including ferns and lycophytes, we identified 47,135 ECVs in 75 genomes. These were grouped into 71 operational taxonomic units (OTUs), including 35 novel ones, revealing unexpected Caulimoviridae diversity in vascular plants and a new clade restricted to gymnosperms. Phylogenetic comparisons with host plant taxonomy support a macroevolutionary scenario in which cospeciation with tracheophytes drove the diversification of Caulimoviridae. Our findings position Caulimoviridae and ECVs as a reference system for paleovirology, offering unprecedented insights into how plant viruses and their hosts coevolved, diversified, and sometimes went extinct.

evolutionary biology↗

bioRxiv2025

Comprehensive annotation of olfactory and gustatory receptor genes and transposable elements revealed their evolutionary dynamics in aphids

Understanding the molecular evolution of genes involved in parasite adaptation and the role of transposable elements (TEs) in driving their diversification is key to unraveling how populations adapt to their environments. In phytophagous insects like aphids, olfactory (OR) and gustatory receptor (GR) genes are crucial for host recognition, yet their post-duplication evolution remains insufficiently explored. Here, we analyzed 521 OR and 399 GR genes, alongside TEs, across 12 aphid genomes with varying host ranges. Aphid lineages with broader host ranges exhibited higher evolutionary rates, driven by gene family expansions linked to host interaction, including lipid metabolism, immune function, and transposase activity. The evolution of OR and GR genes post-duplication was shaped by diversifying selection, with bursts of positive selection followed by long periods of purifying selection, consistent with adaptation to new hosts. OR and GR genes originated from proximal and tandem duplications, with younger TE activity enriched near these genes compared to other genomic regions, suggesting a role for TEs in catalyzing tandem duplications and fueling diversification. The star-like topology of the OR phylogenetic tree, low synteny, and recent TE activity around OR genes support a faster evolutionary rate for ORs than GRs - a trend observed in other insect taxa. This study provides insights into molecular mechanisms underlying host adaptation in aphids and presents the first high-quality genome assembly of Dysaphis plantaginea, a major apple pest, with a comprehensive annotation of chemosensory genes and TEs. These resources offer a foundation for research on aphid genome evolution, insect-plant interactions.

molecular 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↗

bioRxiv2021

Transposable elements in the genome of the lichen-forming fungus Umbilicaria pustulata, and their distribution in different climate zones along elevation

BackgroundTransposable elements (TEs) are an important source of genome plasticity across the tree of life. Accumulating evidence suggests that TEs may not be randomly distributed in the genome. Drift and natural selection are important forces shaping TE distribution and accumulation, acting directly on the TE element or indirectly on the host species. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the hosts ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold-temperate. We trace the occurrence of the newly identified TEs in populations along three replicated elevation gradients using a Pool-Seq approach, to identify TE insertions of potential adaptive significance. ResultsWe found that TEs cover 21.26 % of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. Out of a total of 182 TE copies we identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function. ConclusionsThis pioneering study into the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution. Particularly, it may serve as a foundation for assessing the impact of TE dynamics on fungal adaptation to the abiotic environment, and the impact of TE activity on the evolution and maintenance of a symbiotic lifestyle.

genomics↗

bioRxiv2018

A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits

Rose is the worlds most important ornamental plant with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Rose has a complex genome with high heterozygosity and various ploidy levels. Our objectives were (i) to develop the first high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short read sequencing, and anchoring to a high-density genetic map and (ii) to study the genome structure and the genetic basis of major ornamental traits.\n\nWe produced a haploid rose line from R. chinensis Old Blush and generated the first rose genome sequence at the pseudo-molecule scale (512 Mbp with N50 of 3.4 Mb and L75 of 97). The sequence was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features including the pericentromeric regions through annotation of TE families and positioned centromeric repeats using FISH. Genetic diversity was analysed by resequencing eight Rosa species. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and number of flower petals. A rose APETALA2 homologue is proposed to be the major regulator of petals number in rose. This reference sequence is an important resource for studying polyploidisation, meiosis and developmental processes as we demonstrated for flower and prickle development. This reference sequence will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

genomics↗