Biology subjects

Diaz-Villanueva, W.

Publications and source records attributed to Diaz-Villanueva, W..

4 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↗

bioRxiv2019

Metagenomic dynamics in Olea europaea after root damage and Verticillium dahliae infection

The olive tree is of particular economic interest in the Mediterranean basin. Researchers have conducted several studies on one of the most devastating disorders affecting this tree, the Verticillium wilt of olive, which causes significant economic damage in numerous areas of this crop. We have analyzed the temporal metagenomic samples of a transcriptomic study in Olea europaea roots and leaves after root-damage and after a root Verticillium dahliae infection (Jimenez-Ruiz et al. 2017). Our results indicate that this infection, although led by Verticillium, is driven not by a single species but by a polymicrobial community, including their natural endophytes, which acts as a consortium in the attack to the host plant. This community includes both biotrophic and necrotrophic organisms that alternate and live together during the infection. Our results not only describe how the microbial community progresses along these processes, but also explain the high complexity of these systems, that in turn, could justify at least in part the occasional changes and disparity found at the time of classifying the kind of parasitism of a determined organism.

systems biology↗