Biology subjects

Dainat, J.

Publications and source records attributed to Dainat, J..

10 recordsLinked to original sources

bioRxiv2026

The genome of the avian malaria parasite Haemoproteus majoris (lineage WW2) and its relationship to other Plasmodium species

Avian malaria parasites form a highly prevalent and genetically diverse group within the haemosporidians, yet they have long been overlooked relative to their human- and rodent-infecting counterparts. Among these, parasites of the genus Haemoproteus (Haemosporida, Haemoproteidae) are widespread and prevalent blood parasites of birds, transmitted by louse flies (Hippoboscidae) and biting midges (Ceratopogonidae). Recent phylogenomic analyses place Haemoproteus parasites at the root of the haemosporidian tree, making genomic data from these taxa essential for understanding the evolutionary origins of malaria parasites. To date, only two avian Plasmodium and one avian Haemoproteus genomes have been sequenced. We present the first assembled genome of Haemoproteus majoris (lineage WW2), a common blood parasite of passerine birds. As avian erythrocytes are nucleated, parasite DNA was enriched by FACS-based sorting to discriminate and isolate the parasite from host cell nuclei prior to whole-genome amplification. The genome was assembled using Nanopore long-read sequencing and polished with Illumina short-reads, yielding 145 contigs with a total assembly size of 23.9Mb and a G+C content of 27.85%. Genome annotation identified 5501 protein-coding genes, 69 non-coding RNA genes, and 57 long terminal repeat retrotransposons (LRT-RTs), including one full-length element. This genomic resource represents a critical step towards elucidating the evolutionary history and genomic architecture of avian malaria parasites. SIGNIFICANCE STATEMENTWe present the first assembled genome of Haemoproteus majoris (lineage WW2), a prevalent and generalist avian malaria parasite. Taxonomic resolution of this genus is difficult as there are few distinct morphological differences among closely-related species. This genome provides a valuable resource for studying the evolution within the Haemoproteus genus and to elucidate the evolutionary history of malaria parasites.

genomics↗

bioRxiv2026

EDTA v2: enabling scalable TE annotation in animal genomes

The Extensive de-novo TE Annotator (EDTA) automates transposable element annotation in plant genomes but lacks direct LINE/SINE detection, limiting its applicability to animal genomes. We present EDTA v2, which integrates LINE and SINE detection, completely rewrites TIR-Learner for deployability and scalability, and accelerates structural detectors by up to two orders of magnitude. Tested in 30 animal genomes from the Vertebrate Genomes Project Phase I, EDTA v2 bridges the non-LTR detection gap that has prevented automated TE annotation in animals.

genomics↗

bioRxiv2026

ViroSeek: a viral detection pipeline for second-generation sequencing

Arbovirus emergences represent a rising public health issue and are exacerbated by climate change and globalization. Virome analysis has become a key approach for monitoring and managing infectious diseases, yet existing tools often remain technically complex and inaccessible to non-specialists. In this context, we present ViroSeek, a reproducible and accessible bioinformatics pipeline specifically designed for the taxonomic analysis of second-generation sequencing data from target-enriched libraries. ViroSeek performs a series of automated steps: quality control, trimming, host and bacterial sequence removal, assembly, taxonomic assignment, read remapping for quantification, and PCR duplicate removal. The whole process is designed to produce a clear, usable viral taxonomy table that is suitable for diversity studies. ViroSeek was empirically validated on enriched control samples containing a known panel of viruses. All the expected viruses were correctly detected. Bacterial and host contaminant sequences were effectively removed. The pipeline is freely available and fully documented, supporting its adoption and adaptation by the research community.

bioinformatics↗

bioRxiv2025

Dengue virus harnesses mosquito Syntenin to load and secrete viral RNA into salivary exosomes

Viruses exploit extracellular vesicles (EVs) to transfer infection-enhancing viral RNAs. However, mechanisms underlying viral RNA loading remain elusive. We leveraged our previous discovery that dengue virus secretes transmission-enhancing subgenomic flaviviral RNA (sfRNA) into mosquito salivary EVs to investigate viral RNA loading mechanism. We demonstrate that sfRNA alone promotes the secretion of sfRNA-containing EVs marked by the mosquito EV biogenesis protein AeSyntenin, by applying microscopy and viral genetic editing in in vitro and in vivo models. SfRNA via its stem loop structures interacts intracellularly with mosquito AeSyntenin and this interaction is selectively maintained within EVs as shown by complementary RNA-affinity chromatography and RNA immunoprecipitation, and AI-based prediction. Finally, we used systemic and salivary gland-specific protein depletion to establish a functional role for mosquito AeSyntenin in exosome production and salivary secretion of sfRNA. We propose that sfRNA binds AeSyntenin to drive its selective packaging and release into exosomes, elucidating a mechanism for viral RNA incorporation into EVs. Significance statementViruses hijack extracellular vesicles (EVs) to enhance viral dissemination, but the mechanisms enabling selective viral RNA packaging into EVs remain unclear. Specifically, dengue virus transmission by mosquitoes relies on EV-based delivery of an immune-inhibitory subgenomic flaviviral RNA (sfRNA). Here, we uncover how dengue virus sfRNA is actively sorted into EVs from mosquito saliva. We show that sfRNA alone induces its secretion via EVs. We discover that sfRNA directly interacts with AeSyntenin intracellularly, and that this interaction persists in secreted EVs. Functional depletion studies reveal AeSyntenins role in salivary EV formation and sfRNA secretion. These findings establish a novel paradigm by which viral RNAs exploit vector EV pathways for dissemination.

microbiology↗

bioRxiv2025

The complete genome and comparative analysis of a new Tequintavirus: Salmonella phage Tennessee Salten

The rise in multidrug-resistant pathogenic bacteria presents a major current challenge, highlighting the urgent need for alternatives and sustainable biocontrol strategies. Here, we report the genome analysis of a bacteriophage called Salmonella phage Tennessee Salten and attributed to a new Tequintavirus species. Salten was isolated following infection of Salmonella enterica subsp. enterica serotype Tennessee (sequence type ST5018). Its genome is 109,999 bp in length and contains 220 predicted proteins on which 197 are CDS and 23 tRNAs. Compared to its closest known relative phage Escherichia phage HildyBeyeler - sharing 84.6% identity - Salten harbours 16 unique or highly divergent genes. Of these, 13 encode proteins with unknown function, one encodes for a putative adenine methyltransferase and two encode HNH homing endonucleases. Moreover, the Long Tail Fibre protein, whose structure was predicted based on that of phage T5, was highly divergent among the Tequintavirus genus.

microbiology↗

bioRxiv2024

"This training is bound for glory": selection by experimental evolution of a bacteriophage with expanded host-range and increased virulence

Viral host range expansion is predicted to evolve at the cost of reduced mean fitness. We investigated the adaptive walks of a virulent phage (Tequintavirus) in a spatially variable environment composed of four susceptible bacterial isolates and four resistant ones (Salmonella enterica serotype Tennessee, sequence types ST5018 and ST319 respectively). Starting from a single ancestral phage, we evolved multiple independent populations through serial passages on non-coevolving bacteria, following the Appelmans protocol. The phage populations evolved an expanded host range and increased virulence. Whole-genome sequencing revealed recurrent parallel mutations across populations (i.e. convergent evolution), particularly in genes encoding exo- and endo-nucleases, dUTPase, and caudal proteins. Notably, two parallel mutations in the gene coding for the Long Tail Fibre became fixed early in the evolutionary trajectories. Reverse-genetics experiments introducing these mutations into the ancestral genome expanded the host range but yielded only marginal increases in virulence, highlighting the effect of compensatory mutations. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/584857v3_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@cec6b5org.highwire.dtl.DTLVardef@1579ba4org.highwire.dtl.DTLVardef@ab5ad5org.highwire.dtl.DTLVardef@1d88160_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights* A phage (Tequintavirus) was evolved on susceptible and resistant Salmonella enterica strains * Experimentally evolved phage populations displayed expanded host range and increased virulence * Convergent evolution revealed adaptive mutations modifying receptor recognition in caudal proteins * Reverse-genetic showed implication of two Long Tail Fibre mutations in host range expansion In BriefGeneralism is traditionally predicted to evolve at the cost of lower mean fitness. Contrary to this textbook view, we demonstrate that generalist phages with expanded host range and increased virulence can readily evolve in vitro and be purposely optimized for phage therapy applications.

evolutionary biology↗

bioRxiv2023

Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates

SLC22A10 is classified as an orphan transporter with unknown substrates and function. Here we describe the discovery of the substrate specificity and functional characteristics of SLC22A10. The human SLC22A10 tagged with green fluorescent protein was found to be absent from the plasma membrane, in contrast to the SLC22A10 orthologs found in great apes. Estradiol-17{beta}-glucuronide accumulated in cells expressing great ape SLC22A10 orthologs (over 4-fold, p<0.001). In contrast, human SLC22A10 displayed no uptake function. Sequence alignments revealed two amino acid differences including a proline at position 220 of the human SLC22A10 and a leucine at the same position of great ape orthologs. Site-directed mutagenesis yielding the human SLC22A10-P220L produced a protein with excellent plasma membrane localization and associated uptake function. Neanderthal and Denisovan genomes show human-like sequences at proline 220 position, corroborating that SLC22A10 were rendered nonfunctional during hominin evolution after the divergence from the pan lineage (chimpanzees and bonobos). These findings demonstrate that human SLC22A10 is a unitary pseudogene and was inactivated by a missense mutation that is fixed in humans, whereas orthologs in great apes transport sex steroid conjugates.

pharmacology and toxicology↗

bioRxiv2022

Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level

Supergenes govern balanced polymorphisms in a wide range of systems. The reciprocal placement of stigmas and anthers in pin and thrum floral morphs of distylous species constitutes an iconic example of a balanced polymorphism governed by a supergene, the distyly S-locus. Recent studies have shown that the Primula and Turnera distyly supergenes are both hemizygous in thrums, but it remains unknown if hemizygosity is pervasive among distyly S-loci. Here we have characterized the genetic architecture and evolution of the distyly supergene in Linum by generating a chromosome-level genome assembly of Linum tenue, followed by the identification of the S-locus using population genomic data. We show that hemizygosity and thrum-specific expression of S-linked genes, including a pistil-expressed candidate gene for style length, are major features of the Linum S-locus. Structural variation is likely instrumental for recombination suppression, and although the non-recombining dominant haplotype has accumulated transposable elements, S-linked genes are not under relaxed purifying selection. Our findings reveal remarkable convergence in the genetic architecture and evolution of independently derived distyly supergenes. The chromosome-level genome assembly and detailed characterization of the distyly S-locus in L. tenue will facilitate elucidation of molecular mechanisms underlying the different forms of flowers described by Darwin.

evolutionary biology↗

bioRxiv2019

Single-molecule genome assembly of the Basket Willow, Salix viminalis, reveals earliest stages of sex chromosome expansion

Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes and this leads to a range of non-adaptive modifications causing the gradual degeneration and gene loss on the sex-limited chromosome. However, because studies on sex chromosomes have primarily focused on old and highly differentiated sex chromosomes, the causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear. Here, we use long- and short-read single molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W divergence, largely the result of the accumulation of single nucleotide polymorphisms in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although a few genes present on the Z have already been lost from the W. Furthermore, we use multiple lines of evidence to test for inversions, which have long been assumed to halt recombination between the sex chromosomes. Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation.

evolutionary biology↗

bioRxiv2018

Pervasive hybridizations in the history of wheat relatives

Bread wheat and durum wheat derive from an intricate evolutionary history of three genomes, namely A, B and D, present in both extent diploid and polyploid species. Despite its importance for wheat research, no consensus on the phylogeny of the wheat clade has emerged so far, possibly because of hybridizations and gene flows that make phylogeny reconstruction challenging. Recently, it has been proposed that the D genome originated from an ancient hybridization event between the A and B genomes1. However, the study only relied on four diploid wheat relatives when 13 species are accessible. Using transcriptome data from all diploid species and a new methodological approach, we provide the first comprehensive phylogenomic analysis of this group. Our analysis reveals that most species belong to the D-genome lineage and descend from the previously detected hybridization event, but with a more complex scenario and with a different parent than previously thought. If we confirmed that one parent was the A genome, we found that the second was not the B genome but the ancestor of Aegilops mutica (T genome), an overlooked wild species. We also unravel evidence of other massive gene flow events that could explain long-standing controversies in the classification of wheat relatives. We anticipate that these results will strongly affect future wheat research by providing a robust evolutionary framework and refocusing interest on understudied species. The new method we proposed should also be pivotal for further methodological developments to reconstruct species relationship with multiple hybridizations.

evolutionary biology↗