Biology subjects

Santos, C. A.

Publications and source records attributed to Santos, C. A..

4 recordsLinked to original sources

bioRxiv2026

338 coleopteran genomes reveal exceptional rearrangement variation compared to other insect orders

Chromosomal rearrangements reshape genome architecture, but rate variation across the tree of life remains poorly understood. Analysing 338 beetle (Coleoptera) genomes, we inferred eight ancestral linkage groups. No species retained these linkage groups, whereas the most frequent karyotypes of 10 or 11 chromosomes evolved at least 65 times through independent rearrangements. Rearrangement rates vary widely across lineages, with exceptionally high rates associated with major species radiations. Comparisons to 340 fly and 210 butterfly and moth genomes reveal the highest rates of long-term persistent rearrangements in beetles and that the beetle X chromosome traces back to the ancestor of Holometabola. We identified frequent X chromosome changes, mostly representing recent autosomal-X fusions, but no fissions. For autosomes, key rearrangement predictors include chromosome size, repeats and centromere position.

evolutionary biology↗

bioRxiv2025

A chromosome-level genome of the King penguin (Aptenodytes patagonicus): an emerging model-in-the-wild for studying evolution

The King penguin (Aptenodytes patagonicus) is an iconic species of the Southern Ocean and is currently being developed as a model-in-the-wild for understanding evolution. We present a high-quality, haplotype-resolved 1.35 Gb chromosome-level genome of an adult female King penguin - Pen/Se-guin - from the Crozet Archipelago, assembled using PacBio HiFi long-read sequencing and Hi-C proximity data. 94.93% of the assembly is assigned to 34 chromosomes (32 autosomes, plus the Z and W chromosomes), with a BUSCO completeness of 97.2%, a k-mer completeness of 99.7%, and a quality value (QV) of 63.8. We also assembled a circularised mitogenome (20,520 bp), which includes the avian tandem duplication (TD). Annotation of repetitive sequences revealed that 16.3% of the genome comprises repetitive elements, with LINEs being the most abundant transposable element class (5.6%). Gene prediction using an extensive multi-tissue RNA-seq dataset resulted in 18,081 predicted protein-coding genes, of which 17,081 were functionally annotated, with a BUSCO completeness of 98.4% and an OMArk completeness of 97.3%. The presented assembly substantially improves the quality of a previous draft genome, showing a 28-fold increase in assembly contiguity and a significantly improved genome annotation, exceeding the standards of the Earth BioGenome Project (EBP) and Vertebrate Genomes Project (VGP). This high-quality genome will enable ongoing and future studies harnessing the King penguin as a model-in-the-wild to test hypotheses on the genotype-to-fitness link, ageing, life-history trait evolution, and adaptation.

genomics↗

bioRxiv2024

Genomics of Neotropical biodiversity indicators: two butterfly radiations with rampant chromosomal rearrangements and hybridisation

A major question in evolutionary biology is what drives the diversification of lineages. Rapid, recent radiations are ideal systems for addressing how new species arise because they still show key morphological and ecological adaptations associated with speciation. While most studied recent radiations have evolved in an insular environment, less research has been carried out on continental radiations with complex species interactions. Melinaea and Mechanitis butterflies (Nymphalidae: Ithomiini) have rapidly radiated in the Neotropics. They are classical models for Amazonian biogeography and colour pattern mimicry and have been proposed as biodiversity indicators. We generated reference genomes for five species of each genus, and whole-genome resequencing data of most species and subspecies covering a wide geographic range to assess phylogeographic relationships, patterns of hybridisation and chromosomal rearrangements. Our data help resolve the classification of these taxonomically challenging butterflies and reveal very high diversification rates. We find rampant evidence of historical hybridisation and putative hybrid species in both radiations, which may have facilitated their rapid diversification. Moreover, dozens of chromosomal fusions and fissions were identified between congeneric species, and even some within species. We conclude that interactions between geography, hybridisation and chromosomal rearrangements have contributed to these two rapid radiations in the highly diverse Neotropical region. We suggest that rapid radiations may be spurred by repeated periods of geographic isolation during Pleistocene climate oscillations, combined with lineage-specific rapid accumulation of incompatibilities during allopatric phases, followed by secondary contact with some gene exchange. Significance StatementUnderstanding factors contributing to rapid speciation is a key aim of evolutionary biology. Here we focus on two rapid radiations of Neotropical butterflies. Our genomic data with broad taxonomic and geographic coverage reveal rampant hybridisation and chromosomal rearrangements, each likely contributing to the high diversification rates. Our study highlights the use of genomic data to resolve taxonomically challenging species groups and elucidate drivers of diversification in rapid radiations. We show that for biodiversity hotspots with recent radiations, barcoding is insufficient to characterise species richness due to gene flow and recent speciation. The taxonomic implications of both introgression and karyotype diversity for species delimitation are important to consider during monitoring and management of biodiversity in these vulnerable habitats.

evolutionary biology↗

bioRxiv2019

Systems Analysis of Subjects Acutely Infected with Chikungunya Virus

The largest ever recorded epidemic of the chikungunya virus (CHIKV) began in 2004 and affected four continents. Acute symptomatic infections are typically associated with the onset of fever and often debilitating polyarthralgia/polyarthritis. In this study, a systems biology approach was used to analyze the blood transcriptomes of adults acutely infected with CHIKV. Gene signatures that were associated with viral RNA amounts and to the onset of symptoms were identified. Among those genes, the putative role of Eukaryotic Initiation Factor (eIF) family genes and apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC3A) in the CHIKV replication process were displayed. We further compared these signatures with those induced by dengue virus infection and rheumatoid arthritis. Finally, we demonstrated that CHIKV infection in mice induced IL-1 beta production in a mechanism highly dependent on the inflammasome NLRP3 activation. The findings provided valuable insights into the virus-host interactions during the acute phase and could be useful in the investigation of new and effective therapeutic interventions.

immunology↗