Biology subjects

Moraga, C.

Publications and source records attributed to Moraga, C..

7 recordsLinked to original sources

bioRxiv2026

Environmental and spatiotemporal drivers of marine microbial communities from Antarctic and Subantarctic water masses

The Southern Ocean harbors diverse marine microbial communities shaped by both local oceanographic conditions and dispersal limitations. However, this knowledge is mainly based on coastal Antarctic sites, whereas circumpolar Antarctic open sea and subantarctic ecosystems remain poorly explored. Here, we characterize marine microbial communities (using 16S rDNA high-throughput sequencing) and marine oceanographic data across two regions: the Subantarctic, involving two localities (the Magellan Strait and the Beagle Channel), and Antarctic open sea, involving two localities (Eastern Indian and Central South Pacific). We found extensive differences across regions and localities, characterized by distinct taxonomic patterns, alpha diversity, microbial composition, and enriched taxa profiles. Despite these differences, Clade Ia, Amylibacter, NS5 marine group, and NS2b marine group exhibited high prevalence across regions. Oceanographic parameters had variable relationships with microbial alpha diversity across regions: Sea surface temperature and salinity had a negative and positive correlation, respectively, in the Magellan Strait during 2024. In the Antarctic region, dissolved oxygen displayed a negative correlation in the Indian Ocean during 2024, whereas salinity displayed a more variable relationship in the Indian Ocean: positively correlated during 2024, while negatively correlated during 2025. Collectively, our results highlight a strong microbiological biogeographic structure in the Southern Ocean, both across broad scales (between Subantarctic and Antarctic regions) and within regions. Furthermore, our results show dynamic relationships between oceanographic variables and marine microbial diversity across Antarctic and Subantarctic regions.

microbiology↗

bioRxiv2026

Accurate haplotype-resolved de novo assembly of human genomes with RFhap

Haplotype-resolved de novo assemblies enable genome-wide separation of maternal and paternal variation, improving the interpretation of complex variants relevant to human disease. Trio-aware assemblers such as Hifiasm-Trio leverage parental short reads by deriving parent-specific k-mers to guide phasing within the long-read assembly graph; however, fixed k-mer length and heuristics cannot be optimal in the presence of sequencing errors and graph complexity in repetitive regions, contributing to phasing errors and reduced haplotype-resolved contiguity. Here we present RFhap, a trio-based long-read phasing method that integrates multi-k-mer parent-specific markers with an alignment-free k-mer lookup engine and a random forest classifier to assign long reads to maternal, paternal, or unknown haplotypes prior to de novo assembly. We benchmarked RFhap on four human trio datasets from the Human Pangenome project spanning two ONT chemistries (R10.4 and R9.4.1). Using Merqury to evaluate downstream assemblies, RFhap nearly doubled corrected haplotype NG50 (mean 24.3 Mb vs 13.1 Mb) and halved switch error rates (mean 0.111% vs 0.236%) relative to Hifiasm-Trio, while remaining competitive in consensus QV and parental k-mer completeness. Consistent with improved phasing, RFhap reduced long-switch errors by [~]3-fold across datasets, particularly within interspersed repeats. Together, these results demonstrate that RFhap improves phasing accuracy from standard trio data, representing a step toward accurate and automated diploid human de novo assembly from long reads.

bioinformatics↗

bioRxiv2026

Ultra-deep sequencing reveals intra-host diversity and co-infection-driven evolution of SARS-CoV-2

As COVID-19 enters an endemic phase, SARS-CoV-2 continues to diversify under ongoing immune pressure, with Omicron sublineages and episodic emergent variants sustaining reinfections worldwide. Intra-host evolution represents the earliest stage of this diversification, yet remains undercharacterized, particularly in regions with limited genomic surveillance. Here, we conducted high-throughput sequencing on 96 nasopharyngeal swab samples from Chilean individuals (2020-2022), achieving an average per-base genome coverage of [~]60,000x across the viral genome. This ultra-deep sequencing coverage enabled the identification of intra-host single-nucleotide variants (iSNVs) and co-infection events with high sensitivity and accuracy. Co-infections, especially with Omicron, significantly increased iSNV frequency and recombination, driving viral diversity. Evolutionary analysis based on the non-synonymous to synonymous ratio (dN/dS) shows that Omicron is under extensive purifying selection (global dN/dS [~] 0.55). However, Omicron co-infection cases exhibited higher dN/dS ratios ([~]0.58), suggesting a lower level of purifying selection and increased genetic diversity. Notably, the Spike gene showed dN/dS ratios indicative of positive selection (dN/dS > 1), which are more pronounced in co-infection cases than in Omicron alone. This suggests that co-infections are providing the substrate for the emergence of new variants with enhanced transmissibility and immune evasion capabilities. Together, these findings demonstrate that ultra-deep sequencing is crucial for mapping the evolutionary forces driving SARS-CoV-2 intra-host adaptation and the emergence of new variants.

genetics↗

bioRxiv2025

Clade-wide proteome analysis shows widespread non-canonical Dcr proteins in fungi.

Dicers (Dcrs) are central proteins involved in the biogenesis of small RNAs (sRNAs) in eukaryotes. Most of the knowledge on Dcr structure, function and evolution comes from studies conducted in animal and plant species. Comparatively, much less is known in fungi, which are a genetically and ecologically diverse group with important roles in ecosystems, agriculture, medicine, and biotechnology. While canonical Dcrs in plants and animals contain a well-defined domain architecture, most fungal Dcrs with experimentally validated functions lack one or more identifiable canonical domains, raising questions about how RNA-binding and precise sRNA processing is retained. Here, we conducted the most extensive survey of fungal Dcr proteins, analyzing 1,593 proteomes across eight phyla. We found a diversity of Dcr domain architectures, with some of them lacking an identifiable PAZ, Helicase, and/or double-stranded RNA binding domains. Phylogenetic analyses showed that different Dcr classes are distributed across distinct clades that often align with fungal taxonomic groups. Despite the lack of canonical domain architectures, we found that fungal Dcrs fold into a characteristic L-shaped structure and show PAZ-like folds, even in proteins without detectable PAZ sequences. Molecular docking and electrostatic analyses further indicate that these divergent Dcrs maintain key RNA-binding surfaces for proper sRNA processing. Our results indicate a remarkable evolutionary plasticity of Dcr in fungi, showing that essential sRNA processing functions can be retained through structural conservation, and highlighting fungi as models to study the modular evolution of the RNAi machinery in eukaryotes. Significance statementDicer (Dcr) proteins are central to RNA interference (RNAi), a gene regulatory mechanism conserved across eukaryotes. However, current models of Dcr structure, function, and evolution are largely based on studies in animals and plants. Here, we present the most comprehensive analysis to date of Dcr proteins in fungi, a diverse eukaryotic group including many societally important pathogens and symbiotes which are reliant on RNAi. Our findings reveal that despite widespread divergence from canonical Dcr architecture, fungal Dcrs conserve critical folds and RNA-binding features, further suggesting that core RNAi functions are maintained. This work establishes fungi as key models for studying the evolution and functional robustness of the RNAi machinery, offering broader insight into the diversity and plasticity of sRNA biogenesis pathways across eukaryotes.

genomics↗

bioRxiv2023

The Silene latifolia genome and its giant Y chromosome

In some species, the Y is a tiny chromosome but the dioecious plant Silene latifolia has a giant [~]550 Mb Y chromosome, which has remained unsequenced so far. Here we used a hybrid approach to obtain a high-quality male S. latifolia genome. Using mutants for sexual phenotype, we identified candidate sex-determining genes on the Y. Comparative analysis of the sex chromosomes with outgroups showed the Y is surprisingly rearranged and degenerated for a [~]11 MY-old system. Recombination suppression between X and Y extended in a stepwise process, and triggered a massive accumulation of repeats on the Y, as well as in the non-recombining pericentromeric region of the X, leading to giant sex chromosomes. One-Sentence SummaryThis work uncovers the structure, function, and evolution of one of the largest giant Y chromosomes, that of the model plant Silene latifolia, which is almost 10 times larger than the human Y, despite similar genome sizes.

genomics↗

bioRxiv2020

BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data.

MicroRNAs (miRNAs) are small non-coding RNAs that are key players in the regulation of gene expression. In the last decade, with the increasing accessibility of high-throughput sequencing technologies, different methods have been developed to identify miRNAs, most of which rely on pre-existing reference genomes. However, when a reference genome is absent or is not of high quality, such identification becomes more difficult. In this context, we developed BrumiR, an algorithm that is able to discover miRNAs directly and exclusively from sRNA-seq data. We benchmarked BrumiR with datasets encompassing animal and plant species using real and simulated sRNA-seq experiments. The results demonstrate that BrumiR reaches the highest recall for miRNA discovery, while at the same time being much faster and more efficient than the state-of-the-art tools evaluated. The latter allows BrumiR to analyze a large number of sRNA-seq experiments, from plants or animals species. Moreover, BrumiR detects additional information regarding other expressed sequences (sRNAs, isomiRs, etc.), thus maximizing the biological insight gained from sRNA-seq experiments. Finally, when a reference genome is available, BrumiR provides a new mapping tool (BrumiR2ref) that performs an a posteriori exhaustive search to identify the precursor sequences. The code of BrumiR is freely available at https://github.com/camoragaq/BrumiR.

bioinformatics↗

bioRxiv2018

Whole genome sequence of Mapuche-Huilliche Native Americans

BackgroundWhole human genome sequencing initiatives provide a compendium of genetic variants that help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations and information on the genomic structure of Native Americans, especially those from the Southern Cone is scant.\n\nResultsHere we present a high-quality complete genome sequence of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile (85% genomic and 98% exonic coverage at > 30X), with 96-97% high confidence calls. We found approximately 3.1x106 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs that are not included in current sequencing databases. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a marginally admixed population from the Southern Cone, whose genetic component is derived from early Native American ancestors. In addition, we found that HUI genomes display highly divergent and novel variants with potential functional impact that converge in ontological categories essential in cell metabolic processes.\n\nConclusionsMapuche-Huilliche genomes contain a unique set of small- and large-scale genomic variants in functionally linked genes, which may contribute to susceptibility for the development of common complex diseases or traits in admixed Latinos and Native American populations. Our data represents an ancestral reference panel for population-based studies in Native and admixed Latin American populations.

genomics↗