Biology subjects

Echeverry-Perez, J. S.

Publications and source records attributed to Echeverry-Perez, J. S..

3 recordsLinked to original sources

bioRxiv2026

Genomic architecture of the major histocompatibility complex genes in the Neotropical Midas cichlid

The Major Histocompatibility Complex (MHC) plays a central role in vertebrate adaptive immunity, yet its genomic architecture remains poorly characterized in many evolutionary model systems, including the Neotropical Midas cichlid Amphilophus citrinellus. Here, we integrate chromosome-level functional genome annotation, transposable element (TE) profiling, transcriptomics, phylogenetics, molecular selection analyses, and protein structural modeling to characterize its MHC repertoire. We identified 298 MHC-related loci across 18 chromosomes, including 30 MHC-I genes, 15 MHC-IIA genes, and 20 MHC-IIB genes, together with antigen-processing and regulatory components. MHC-I and MHC-II genes were located on different chromosomes, consistent with the MHC non-linkage pattern characteristic of many teleosts. Gene duplication and phylogenetic patterns support birth-and-death evolution, resulting in a structurally diverse repertoire with broadly conserved protein domains. TE distribution varied across MHC genomic regions, suggesting a potential contribution to genomic diversification. Molecular selection analyses detected positive selection in MHC-I and IIB genes, whereas MHC-IIA showed more limited evidence of positive selection. Expression patterns varied across tissues, with relatively high expression of several MHC genes in the spleen and thymus, while structural models retained characteristic MHC folds. Phylogenetic analyses placed previously characterized MHC sequences with broader multilocus repertoire, suggesting that population level diversity may reflect both allelic polymorphism and variation among paralogous loci. Together, these findings provide a comprehensive chromosome-resolved characterization of the MHC repertoire in a Neotropical cichlid and establish a genomic framework for investigating immune gene diversification during the Midas cichlid radiation.

evolutionary biology↗

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↗