Biology subjects

Alioto, T.

Publications and source records attributed to Alioto, T..

11 recordsLinked to original sources

bioRxiv2026

ERGA-BGE reference genomes of Hyalomma lusitanicum and its obligate Francisella endosymbiont as a genomic resource for One Health research

Hyalomma lusitanicum is a characteristic tick species of the western Mediterranean region, with a well-established distribution across the Iberian Peninsula. It is strongly associated with wild ungulates, particularly red deer, as well as livestock, to which it can transmit a wide range of pathogens, including viruses, bacteria, and protozoa. Here, we present three genomic resources for H. lusitanicum: a scaffold-scale nuclear genome, the complete mitochondrial genome, and the complete genome of its associated Francisella bacterial endosymbiont. The nuclear genome assembly spans 1.81 Gb and comprises 59 scaffolds, with a scaffold N50 of 153.6 Mb (L50 = 5) and no gaps, indicating high contiguity and completeness with a gene annotation completeness BUSCO score of 97.1 %. Genome annotation of the nuclear assembly identified 20,638 protein-coding genes, 1,422 non-coding genes, and 5,775 pseudogenes. A total of 18 scaffolds were assembled as putative chromosomes, exceeding the 11 chromosomes inferred as ancestral; however, synteny analyses suggest that several scaffolds likely represent fragmented portions of the same chromosome, probably due to incomplete Hi-C scaffolding. Despite this, the assembly represents one of the most complete tick nuclear genomes generated to date. In addition, we report the complete genome of a Francisella endosymbiont (1.51 Mb, 1,679 genes), characterized by a high proportion of pseudogenes and reduced genome size, consistent with patterns of genome reduction associated with obligate symbiosis. Together, these genomic resources provide a framework to investigate local adaptation and host-symbiont evolution, and to support improved surveillance, control, and management strategies for species of public health relevance.

genomics↗

bioRxiv2025

Chromoanagenesis is a driver of structural variationin the smallest photosynthetic eukaryote

Marine microalgae populations can rapidly evolve resistance to viruses upon infection. In Ostreococcus mediterraneus resistance to the prasinovirus OmV2 emerged within five days in all virus-exposed populations. Whole-genome sequencing of pairs of resistant and susceptible cell lines revealed extensive structural genomic changes, particularly on the Small Outlier Chromosome (SOC). SOC alterations included large deletions, duplications, rearrangements, and whole chromosome duplication, yet no consistent structural variant or single nucleotide polymorphism could be directly associated with resistance. Hybrid de novo assemblies confirmed the unique SOC assembly of each strain, with a highly polymorphic [~]2 kb tandem repeat region exhibiting an "accordion-like" pattern of expansion and contraction. No new viral insertions were found, though endogenous viral elements were conserved across lines. Two interchromosomal translocations between the SOC and chromosomes 2 and 17 provide evidence for chromoplexy, thereby offering novel insights into the mechanisms underlying the distinctive evolutionary path of this chromosome. Together, these findings demonstrate that resistance to OmV2 evolves rapidly and consistently but cannot yet be linked to any specific structural variations; instead, the high rate of localized genomic structural variations points to a distinct mechanism of chromosome evolution. SignificanceThe mechanisms and consequences of structural variation remain poorly understood in many lineages, particularly in ecologically important marine microbes. This study shows that resistance to prasinovirus OmV2 in a cosmopolitan phytoplankton species, Ostreococcus mediterraneus evolves rapidly and consistently, even though no resistance-associated SNPs or shared structural variants were identified on standard chromosomes. Instead, extensive genomic rearrangements--particularly of a single chromosome--occur independently of viral infection. These findings highlight the role of chromoplexy as the driving mechanism underlying the diversification of the enigmatic Small Outlier Chromosome in this lineage.

genomics↗

bioRxiv2025

ERGA-BGE Reference Genome of Loboptera subterranea: a cave adapted cockroach endemic to the Canary Islands

Species of the genus Loboptera from the Canary Islands are adapted to life in subterranean environments, except Loboptera canariensis and Loboptera decipiens which inhabit epigean, often influenced by human activities. The genome of Loboptera subterranea provides a valuable resource for understanding the genetic basis of how the Canarian Loboptera species evolved and thrived in subterranean environments. A total of 14 contiguous chromosomal pseudomolecules were assembled from the genome sequence. This chromosome-level assembly encompasses 2.7 Gb, composed of 486 contigs and 90 scaffolds, with contig and scaffold N50 values of 13.1 Mb and 202.7 Mb, respectively.

genomics↗

bioRxiv2025

Over-expression and increased copy numbers of a cytochrome P450 and two UDP-glucuronosyltransferase genes in macrocyclic lactone resistant Psoroptes ovis of cattle

Psoroptes ovis is a mite species that feeds on sheep, cattle, other ungulates, rabbits, and horses, which can develop into a severe exudative dermatitis known as psoroptic mange. The macrocyclic lactone (ML) family of acaricides are commonly used to control psoroptic mange. However, certain strains of cattle and sheep mites have developed resistance against MLs, which has led to reduced treatment efficacy and even treatment failure. Here we investigated the genetic basis of ML resistance in mites collected from cattle across Belgium. We compared gene expression between susceptible and resistant mites before and after exposure to ivermectin and genetic diversity between a single susceptible and resistant populations. We generated chromosomal genome assemblies of Psoroptes ovis derived from sheep and cattle respectively and correlated genomic diversity of susceptible and resistant mite populations sampled across Belgium. Gene expression data revealed constitutive over-expression of a cytochrome P450 monooxygenase (CYP) gene and two tandemly located UDP-glucuronosyltransferase (UGT) genes among others. On investigation of the genomic data, we observed copy number variation at both loci in population genomic data. The CYP gene is not amplified in the susceptible population but occurs in multiple copies in all resistant populations and is associated with a peak in Fst between resistant and susceptible populations indicative of selection. By contrast, the two UGT genes are massively and tandemly amplified in all populations including the susceptible dataset with a weaker associated signal of selection than the amplified CYP. Hence, distinct mechanisms of amplification and gene regulation are occurring at these putative resistance loci in P. ovis. Author SummaryFor the first time, we investigated the genetic basis of resistance in scab mites to a key family of drugs (Macrocyclic Lactones) used to control this parasite. Scab mite infestations can cause serious welfare issues in affected cattle and sheep with associated economic impact on production. To identify genes associated with resistance, we applied a combination of approaches including targeted sequencing of candidate genes, genome sequencing and gene expression comparisons of resistant mites with mites that are still susceptible to treatment. We were able to rule-out one family of candidate genes but identified very high expression of genes from two gene families that metabolise, and thereby detoxify, the treatment drug in resistant mites. On examination of the genomic context of these genes we found that the genes had undergone an increase in copy number in the resistant mites compared to the susceptible mites. With our now much increased understanding of resistance in scab mites we can track the spread of resistance using markers in these genes present in resistant mites. We can also now test the suitability of alternative treatments that restore the lethality of Macrocyclic Lactones in scab mites, mitigating the damaging effects of resistance in this species.

genomics↗

bioRxiv2024

Chromosome-level genome assembly and annotation of Corallium rubrum: a Mediterranean coral threatened by overharvesting and climate change.

Reference genomes are key resources in biodiversity conservation. Yet, sequencing efforts are not evenly distributed in the tree of life questioning our true ability to enlighten conservation with genomic data. Good quality reference genomes remain scarce in octocorals while these species are highly relevant target for conservation. Here, we present the first annotated reference genome in the red coral, Corallium rubrum (Linnaeus, 1758), a habitat-forming octocoral from the Mediterranean and neighboring Atlantic, impacted by overharvesting and anthropogenic warming-induced mass mortality events. Combining long reads from Oxford Nanopore Technologies (ONT), Illumina paired-end reads for improving the base accuracy of the ONT-based genome assembly and Arima Hi-C contact data to place the sequences into chromosomes, we assembled a genome of 475 Mb (21 chromosomes, 326 scaffolds) with contig and scaffold N50 of 1.6 Mb and 16.2 Mb, respectively. Fifty percent of the sequence (L50) was contained in eight superscaffolds. The consensus quality (QV) of the final assembly was 42 and the gene completeness reported by BUSCO was 74% (metazoa_odb10 database). We annotated 39,114 protein-coding genes and 32,678 non-coding transcripts. This annotated chromosome-level genome assembly, one of the first in octocorals, is currently used in a project based on whole genome re-sequencing dedicated to the conservation and management of C. rubrum. Significance StatementThe Mediterranean red coral, Corallium rubrum, is critically impacted by overharvesting and by mass mortality events linked to marine heat waves. Accordingly, C. rubrum is increasingly receiving conservation efforts. Previous population genetics studies based on microsatellites contributed to improving our knowledge of the species ecology. Yet, crucial questions regarding, admixture among lineages, demographic history, effective population sizes and local adaptation, are still open owing to a lack of genomic resources. Here, we present the first chromosome-level genome assembly for the species with high contiguity, good completeness and protein-coding genes and repeat sequence annotations. This genome, one of the first in octocorals, will pave the way for the integration of population genomics data into ongoing interdisciplinary conservation efforts dedicated to C. rubrum.

genomics↗

bioRxiv2024

A chromosome-level genome assembly of the Hispid cotton rat (Sigmodon hispidus), a model for human pathogenic virus infections

BackgroundThe cotton rat (Sigmodon hispidus), a rodent species native to the Americas, has emerged as a valuable laboratory model of infections by numerous human pathogens including poliovirus and respiratory syncytial virus (RSV). ResultsHere we report the first reference assembly of the cotton rat genome organized at a chromosomal level, providing annotation of 24,878 protein-coding genes. Data from PCR-free whole genome sequencing, linked-read sequencing and RNA sequencing from pooled cotton rat tissues were analyzed to assemble and annotate this novel genome sequence. Spectral karyotyping data using fluorescent probes derived from mouse chromosomes facilitated the assignment of cotton rat orthologs to syntenic chromosomes, comprising 25 autosomes and a sex chromosome in the haploid genome. Comparative phylome analysis revealed both gains and losses of numerous genes including immune defense genes against pathogens. We identified thousands of recently retrotransposed L1 and SINE B2 elements, revealing widespread genetic innovations unique to this species. ConclusionsWe anticipate that annotation and characterization of the first chromosome-level cotton rat genome assembly as described here will enable and accelerate ongoing investigations into its host defenses against viral and other pathogens, genome biology and mammalian evolution.

genomics↗

bioRxiv2023

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

A global genome database of all of Earths species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all [~]1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.

genomics↗

bioRxiv2022

A chromosome-level genome assembly enables the identification of the follicle stimulating hormone receptor as the master sex determining gene in Solea senegalensis

Sex determination (SD) mechanisms are exceptionally diverse and show high evolutionary rates in fish. Pleuronectiformes is an emblematic fish group characterized by its adaptation to demersal life and its compact genomes. Here, we present a chromosome-level genome assembly of Senegalese sole, a promising European aquaculture species. We combined long- and short-read sequencing and a highly dense genetic map to obtain a contiguous assembly of 613 Mb (N50 = 29.0 Mb, 99% of the assembly in the n = 21 chromosomes of its karyotype). The correspondence between this new assembly and the Senegalese sole chromosomes was established by fluorescence in situ hybridization with BAC probes. Orthology within Pleuronectiformes was assessed by using the chromosome-level genomes of six important commercial flatfishes covering a broad phylogenetic spectrum of the order. A total of 7936 single-gene orthologues, shared by the six species, were used to identify syntenies in Pleuronectiformes and to explore chromosome evolutionary patterns in the order. Whole genome resequencing of six males and six females enabled the identification of 41 fixed allelic variants in the follicle stimulating hormone receptor (fshr) gene, homozygous in females and heterozygous in males, consistent with an XX / XY chromosome system. The observed association between fshr SNPs and sex was confirmed at the species level in a broad sample, which allowed tuning up a molecular sexing tool. Fshr demonstrated differential gene expression between male and female gonads since 86 days post-fertilization, when the gonad was still an undifferentiated primordium, concomitant with the activation of other testis and ovary marker genes, such as amh and cyp19a1a genes, respectively. Interestingly, the Y-linked fshr allele, which included 24 non-synonymous variants, expressed to a higher level than the X-linked allele at all stages. We hypothesize a molecular mechanism hampering the action of the follicle stimulating hormone that would drive the undifferentiated gonad toward testis.

genomics↗

bioRxiv2019

Transposons played a major role in the diversification between the closely related almond (Prunus dulcis) and peach (P. persica) genomes: Results from the almond genome sequence

Combining both short and long-read sequencing, we have estimated the almond Prunus dulcis cv. Texas genome size in 235 Mbp and assembled 227.6 Mb of its sequence. The highly heterozygous compact genome of Texas comprises eight chromosomes, to which we have anchored over 91% of the assembly. We annotated 27,042 protein-coding genes and 6,800 non-coding transcripts. High levels of genetic variability were characterized after resequencing a collection of ten almond accessions. Phylogenomic comparison with the genomes of 16 other close and distant species allowed estimating that almond and peach diverged around 5.88 Mya. Comparison between peach and almond genomes confirmed the high synteny between these close relatives, but also revealed high numbers of presence-absence variants, many attributable to the movement of transposable elements (TEs). The number and distribution of TEs between peach and almond was similar, but the history of TE movement was distinct, with peach having a larger proportion of recent transpositions and almond preserving a higher level of polymorphism in the older TEs. When focusing on specific genes involved in key characters such as the bitter vs. sweet kernel taste and the formation of a fleshy mesocarp, we found that for one gene associated with the biosynthesis of amygdalin that confers the bitter kernel taste, several TEs were inserted in its vicinity only in sweet almond cultivars but not in bitter cultivars and Prunus bitter kernel relatives, including P. webbii, P. mume, and other species like peach and cherry. TE insertions likely to produce affects in the expression of six more genes involved in the formation of the fleshy mesocarp were also identified. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond with respect to peach.

genomics↗

bioRxiv2018

De novo assembly and annotation of the larval transcriptome of two spadefoot toads widely divergent in developmental rate

Introduction Introduction Methods Results and Discussion Conclusion Data and materials References Most amphibian species exhibit a complex life-cycle including two or more life stages separated by an ontogenetic switch point such as hatching or metamorphosis. Adaptations to divergent environments can require the modification of the timing of such switch points and the relative investment in growth and differentiation between subsequent stages [1]. Such alterations of developmental trajectories, however, often have substantial repercussions at several organismal levels, from physiology to morphology and even genomic structure. Adaptive divergence in developmental rate tracking aquatic habitats of different duration in spadefoot toads is a well-known example of this. Spadefoot toads from Europe and ...

genomics↗

bioRxiv2018

Selective single molecule sequencing and assembly of a human Y chromosome of African origin

Mammalian Y chromosomes are often neglected from genomic analysis. Due to their inherent assembly difficulties, high repeat content, and large ampliconic regions1, only a handful of species have their Y chromosome properly characterized. To date, just a single human reference quality Y chromosome, of European ancestry, is available due to a lack of accessible methodology2-5. To facilitate the assembly of such complicated genomic territory, we developed a novel strategy to sequence native, unamplified flow sorted DNA on a MinION nanopore sequencing device. Our approach yields a highly continuous and complete assembly of the first human Y chromosome of African origin. It constitutes a significant improvement over comparable previous methods, increasing continuity by more than 800%6, thus allowing a chromosome scale analysis of human Y chromosomes. Sequencing native DNA also allows to take advantage of the nanopore signal data to detect epigenetic modifications in situ7. This approach is in theory generalizable to any species simplifying the assembly of extremely large and repetitive genomes.

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