Biology subjects

de la Fuente, R.

Publications and source records attributed to de la Fuente, R..

7 recordsLinked to original sources

bioRxiv2026

Scaling laws of genome composition and the transitionto complex multicellularity

Genome architecture reorganizes over evolutionary time to support complex multicellularity without a proportional expansion of coding DNA. We conducted a cross-kingdom comparative analysis using high-quality RefSeq assemblies annotated by the NCBI Genome Annotation Pipeline, restricting the dataset to chromosome-level or complete genomes. Scaling relationships among genome size, gene content, and coding DNA content reveal compositional transitions that distinguish prokaryotic, unicellular eukaryotic, and multicellular lineages. Beyond [~]40 Mb of genic content, coding expansion slows and saturates, indicating compositional constraints that shaped the rise of multicellularity. These results establish scaling laws that quantify how noncoding sequence expansion dominates genome growth in complex eukaryotes.

genomics↗

bioRxiv2025

Evidence-driven biases in alternative splicing inferred from NCBI Eukaryotic Genome Annotation Pipeline metadata

The NCBI Eukaryotic Genome Annotation Pipeline (EGAP) predicts coding sequences by integrating transcriptomic and proteomic data with computational approaches, providing structural information that can be used to infer alternative transcript isoforms. However, accurate estimation of alternative splicing events depends on high-quality genome annotations, particularly in genome-wide analyses. The extent to which annotation pipelines influence these inferred splicing patterns has remained largely unexplored. In this study, we quantify potential biases associated with the EGAP annotation pipeline, and find that specific annotation features strongly influence these estimates, particularly the percentage of coding sequences that are supported by experimental evidence. Further, we implemented a polynomial regression model to normalize splicing levels, generating an adjusted metric that minimizes evidence-driven biases. This framework may serve as a basis for future investigations into splicing complexity and comparative genomics.

bioinformatics↗

bioRxiv2023

Evolutionary trends of alternative splicing

There is a growing understanding of how alternative splicing contributes to functional specialization and adaptation, especially in well-studied model organisms. However, its large-scale evolutionary dynamics remain poorly understood. Through a comparative analysis of alternative splicing across 1,494 species spanning the entire tree of life, this study integrates numerous lines of prior evidence to provide a unified view of alternative splicing. We propose a novel genome-scale metric designed to support cross-species comparison. Our findings indicate that alternative splicing is highly variable across lineages. While unicellular eukaryotes and prokaryotes display minimal splicing, mammals and birds exhibit the highest levels of alternative splicing. Despite sharing a conserved intron-rich genomic architecture, mammals and birds show considerable interspecies divergence in splicing activity. In contrast, plants display moderate levels of alternative splicing but exhibit high variability of genomic composition. Furthermore, a strong negative correlation is observed between alternative splicing and the proportion of coding content in genes, with the highest levels of alternative splicing observed in genomes containing approximately 50% intergenic DNA.

evolutionary biology↗

bioRxiv2023

Divergent patterns of meiotic double strand breaks and synapsis initiation dynamics suggest an evolutionary shift in the meiosis program between American and Australian marsupials

In eutherian mammals, hundreds of programmed DNA double-strand breaks (DSBs) are generated at the onset of meiosis. The DNA damage response is then triggered. Although the dynamics of this response is well studied in eutherian mammals, recent findings have revealed different patterns of DNA damage signaling and repair in marsupial mammals. To better characterize these differences, here we analyzed synapsis and the chromosomal distribution of meiotic DSBs markers in three different marsupial species (Thylamys elegans, Dromiciops gliorides, and Macropus eugenii) that represent South American and Australian Orders. Our results revealed inter-specific differences in the chromosomal distribution of DNA damage and repair proteins, which were associated with differing synapsis patterns. In the American species T. elegans and D. gliroides, synapsis progressed exclusively from the chromosomal ends towards interstitial regions. This was accompanied by sparse H2AX phosphorylation, mainly accumulating at chromosomal ends, which appeared conspicuously polarized in a bouquet configuration at early stages of prophase I. Accordingly, RAD51 and RPA were mainly localized at chromosomal ends throughout prophaseI in both American marsupials, likely resulting in reduced recombination rates at interstitial positions. In sharp contrast, synapsis initiated at both interstitial and distal chromosomal regions in the Australian representative M. eugenii, {gamma}H2AX had a broad nuclear distribution, and RAD51 and RPA foci displayed an even chromosomal distribution. Given the basal evolutionary position of T. elegans, it is likely that the meiotic features reported in this species represent an ancestral pattern in marsupials and that a shift in the meiotic program occurred after the split of D. gliroides and the Australian marsupial clade. Our results open intriguing questions about the regulation and homeostasis of meiotic DSBs in marsupials. The low recombination rates observed at the interstitial chromosomal regions in American marsupials can result in the formation of large linkage groups, thus having an impact in the evolution of their genomes.

genetics↗

bioRxiv2022

The origin of a new chromosome in gerbils

Chromosome-scale genome assemblies based on ultra-long read sequencing technologies are able to illuminate previously intractable aspects of genome biology such as fine-scale centromere structure and large-scale variation in genome features such as heterochromatin, GC content, recombination rate, and gene content. We present here a new chromosome-scale genome of the Mongolian gerbil (Meriones unguiculatus) which includes the complete sequence of all centromeres. Gerbil centromeres are composed of four different repeats of length 6pb, 37bp, 127bp, or 1747bp which occur in simple alternating arrays and span 1-6Mb. Gerbil genomes have both an extensive set of GC-rich genes and chromosomes strikingly enriched for constitutive heterochromatin. We sought to determine if there was a link between these two phenomena and found that the two heterochromatic chromosomes of the Mongolian gerbil have distinct underpinnings: Chromosome 5 has a large block of intra-arm heterochromatin as the result of a massive expansion of centromeric repeats, while chromosome 13 is comprised of extremely large (>150kb) repeated sequences. In addition to characterizing centromeres, our results demonstrate the importance of including karyotypic features such as chromosome number and the locations of centromeres in the interpretation of genome sequence data, and highlight novel patterns involved in the evolution of chromosomes.

genomics↗

bioRxiv2020

Massive genome decay and expansion of insertion sequences drive the evolution of a novel host-restricted bacterial pathogen

BackgroundThe emergence of new pathogens is a major threat to public and veterinary health. Changes in bacterial habitat such as those associated with a switch in host or disease tropism are often accompanied by genetic adaptation. Staphylococcus aureus is a multi-host bacterial species comprising strains with distinct tropisms for human and livestock species. A microaerophilic subspecies, Staphylococcus aureus subsp. anaerobius, is responsible for outbreaks of Morels disease, a lymphadenitis in small ruminants. However, the evolutionary history of S. aureus subsp. anaerobius and its relatedness to S. aureus are unknown. ResultsEvolutionary genomic analyses of clinical S. aureus subsp. anaerobius isolates revealed a highly conserved clone that descended from a S. aureus progenitor about 1000 years ago before differentiating into distinct lineages representing African and European isolates. S. aureus subsp. anaerobius has undergone limited clonal expansion, with a restricted population size, and an evolutionary rate 10-fold slower than S. aureus. The transition to its current restricted ecological niche involved acquisition of a pathogenicity island encoding a ruminant host-specific effector of abscess formation, several large chromosomal re-arrangements, and the accumulation of at least 205 pseudogenes resulting in a highly fastidious metabolism. Importantly, expansion of [~]87 insertion sequences (IS) located largely in intergenic regions provided distinct mechanisms for the control of expression of flanking genes, representing a novel concept of the IS regulon. ConclusionsOur findings reveal the remarkable evolutionary trajectory of a host-restricted bacterial pathogen that resulted from extensive remodelling of the S. aureus genome through an array of parallel mechanisms.

microbiology↗

bioRxiv2020

Tracking evolutionary trends towards increasing complexity: a case study in Cyanobacteria

Progressive evolution, the tendency towards increasing complexity, is a controversial issue in Biology, whose resolution requires a proper measurement of complexity. Genomes are the best entities to address this challenge, as they record the history and information gaining of organisms in their ongoing biotic and environmental interactions. Using six metrics of genome complexity, none of which is primarily associated to biological function, we measure genome complexity in 91 genomes from the phylum Cyanobacteria. Several phylogenetic analyses reveal the existence of progressive evolution towards higher genome complexity: 1) all the metrics detect strong phylogenetic signals; 2) ridge regressions detect positive trends towards higher complexity; and 3) classical proofs for progressive evolution (the minimum, the ancestor-descendent and the sub-clade tests), show that some of these positive trends are driven, being mainly due to natural selection. These findings support the existence of progressive genome evolution in this ancient and diverse group of organisms.

evolutionary biology↗