Biology subjects

Uribe, J. E.

Publications and source records attributed to Uribe, J. E..

4 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

Evolution and comparative genomics of tick-associated endosymbionts: insights into metabolic pathways and historical biogeographic patterns

AbstractTicks (Ixodida) are the second most important vectors of infectious diseases in vertebrates, after mosquitoes. They also maintain mutualistic relationships with bacteria, such as endosymbionts that provide essential B vitamins absent in their blood diet. The most studied endosymbionts belong to the genera Coxiella, Midichloria, and Francisella. Francisella includes endosymbionts (FE), pathogens (FP), putative intermediates (FI), and free-living (FL) strains, making them valuable for evolutionary and comparative genomics. In this study, total DNA from six adult female ticks of the genera Hyalomma and Amblyomma was sequenced to obtain new FE genomes. Additionally, two deep metagenomes from public data were assembled, resulting in a dataset of 22 Francisella strains. This dataset was used to reconstruct a phylogenomic framework and compare vitamin biosynthesis and virulence pathways. An MLST-based dense phylogeny was also built to explore biogeographic patterns. The resulting phylogenomic tree shows FE form a monophyletic group derived from FP, possibly due to historical biogeography or recent horizontal transfers. Comparative analyses reveal that FE retain key metabolic pathways while losing nonessential ones, reflecting a selective genome reduction. These results advance our understanding of symbiont evolution in a changing world, revealing molecular adaptations that underpin tick- symbiont relationships and offering genomic insights with potential applications for disease control.

evolutionary biology↗

bioRxiv2023

New insights into the systematics of the Afrotropical Amblyomma marmoreum complex (Acari, Ixodidae) and a novel Rickettsia africae strain using morphological and metagenomic approaches

The Amblyomma marmoreum complex includes some Afrotropical species, such as Amblyomma sparsum, a three-host tick that parasitizes reptiles, birds, and mammals, and is a recognized vector of Ehrlichia ruminatum. However, the lack of morphological, genetic and ecological data on A. sparsum has caused considerable confusion in its identification among A. marmoreum complex members. In this study, we used microscopy and metagenomic approaches to analyze A. sparsum ticks collected from a puff adder snake (Bitis arietans) in southwest Senegal (an endemic rickettsioses area) in order to supplement previous morphological descriptions, provide novel genomic data for the A. marmoreum complex, and search for some associated spotted fever agent. Based on stereoscope and scanning electron microscopy (SEM) morphological evaluations, we provided high-quality images and new insights about punctation and enameling in the male of A. sparsum to facilitate identification for future studies. Additionally, the metagenomic approach allowed us assembly the complete mitochondrial genome of A. sparsum, as well as the nearly entire chromosome and complete plasmid sequences of a novel Rickettsia africae strain. Phylogenomic analyses showed a close relationship between A. sparsum and A. nuttalli for the first time and confirmed the position of A. sparsum within the A. marmoreum complex. Our results provide new insights into the systematic of A. sparsum and A. marmoreum complex, as well as the genetic diversity of R. africae in Afrotropical region. Future studies should consider the possibility that A. sparsum may be a competent vector for R. africae.

zoology↗

bioRxiv2021

Diversification dynamics of hypermetamorphic blister beetles (Meloidae): Are homoplastic host shifts and phoresy key factors of a rushing forward strategy to escape extinction?

Changes in life history traits, including reproductive strategies or host shifts, are often considered triggers of speciation, affecting diversification rates. Subsequently, these shifts can have dramatic effects on the evolutionary history of a lineage. In this study, we examine the consequences of changes in life history traits, in particular host-type and phoresy, within the hypermetamorphic clade of blister beetles (Meloidae). This clade exhibits a complex life cycle involving multiple metamorphoses and parasitoidism. Most tribes within the clade are bee-parasitoids, phoretic or non-phoretic, while two tribes feed on grasshopper eggs. Species richness differs greatly between bee and grasshopper specialist clades, and between phoretic and non-phoretic genera. We generated a mitogenomic phylogeny of the hypermetamorphic clade of Meloidae, including 21 newly generated complete mitogenomes. The phylogeny and estimated lineage divergence times were used to explore the association between diversification rates and changes in host specificity and phoresy, using State-Dependent Speciation and Extinction (SSE) models, while accounting for hidden factors and phylogenetic uncertainty within a Bayesian framework. The ancestor of the hypermetamorphic Meloidae was a non-phoretic bee-parasitoid, and independent transitions towards phoretic bee-parasitoidism or grasshopper specialization occurred multiple times. Bee-parasitoid lineages that are non-phoretic have significantly higher relative extinction rates and lower diversification rates than grasshopper specialists or phoretic bee-parasitoids, while no significant differences were found between the latter two strategies. This suggests that these two life strategies contributed independently to the evolutionary success of Nemognathinae and Meloinae, allowing them to escape from the evolutionary constraints imposed by their hypermetamorphic life-cycle, and that the "bee-by-crawling" strategy may be an evolutionary "dead end". We show how SSE models can be used not only for testing diversification dependence in relation to the focal character but to identify hidden traits contributing to the diversification dynamics. The ability of blister beetles to explore new evolutionary scenarios including the development of homoplastic life strategies, are extraordinary outcomes along the evolution of a single lineage: the hypermetamorphic Meloidae.

evolutionary biology↗