Biology subjects

Coronado-Zamora, M.

Publications and source records attributed to Coronado-Zamora, M..

7 recordsLinked to original sources

bioRxiv2026

Transposable element variation inferred from long-read sequences in wild house mice from temperate and tropical environments

Transposable elements (TEs) constitute a large fraction of mammalian genomes yet their contribution to variation among individuals within natural populations remains largely unexplored. While most TE insertions are deleterious, some may be beneficial and contribute to adaptation. We characterized TE variation and assessed its potential adaptive role using long-read whole-genome sequencing of wild-caught house mice (Mus musculus domesticus) sampled from two populations inhabiting contrasting temperate and tropical environments and differing in morphology, physiology, and behavior. We sequenced 10 mice from each population and created highly contiguous de-novo genome assemblies for each individual, allowing us to identify TEs that are not present in the mouse reference genome and to characterize individual variation. By performing manual TE curation, we identified 506 non-redundant TE consensus sequences among all mice. On average, each wild mouse genome contained 1.47 million TE insertions, ~4% of which were polymorphic among individuals. A small fraction of these polymorphic TE insertions were present in high frequency in just one of the populations, consistent with positive natural selection. Using liver RNA-seq in natural populations and in laboratory crosses, we studied gene expression at genes adjacent to polymorphic TEs. This identified a small set of TEs that are associated with the expression of nearby genes in a population-specific manner, nearly all of which showed independent signatures of positive selection. Together, these results provide the first detailed assessment of TE variation in natural populations of house mice and identify a small set of TE insertions that likely contribute to environmental adaptation.

evolutionary biology↗

bioRxiv2024

Estimating hierarchical F-statistics from Pool-Seq data

Introduced over seventy years ago, F -statistics have been and remain central to population and evolutionary genetics. Among them, FST is one of the most commonly used descriptive statistics in empirical studies, notably to characterize the structure of genetic polymorphisms within and between populations, to shed light on the evolutionary history of populations, or to identify marker loci under differential selection for adaptive traits. However, the use of FST in simplified population models can overlook important hierarchical structures, such as geographic or temporal subdivisions, potentially leading to misleading interpretations and increasing false positives in genome scans for adaptive differentiation. Hierarchical F -statistics have been introduced to account for multiple predefined levels of population structure. Several estimators have also been proposed, including robust ones implemented in the popular R package hierfstat. Nevertheless, these were primarily designed for individual genotyping data and can be computationally intensive for large genomic datasets. In this study, we extend previous work by developing unbiased method-of-moments estimators for hierarchical F -statistics tailored for Pool-Seq data, a cost-effective alternative to individual genome sequencing. These Pool-Seq estimators have been developed in an anova framework, using definitions based on identity-in-state probabilities. The new estimators have been implemented in an updated version of the R package poolfstat, together with estimators for sample allele count data derived from individual genotyping data. We validate and compare the performance of these estimators through extensive simulations under a hierarchical island model. Finally, we apply these estimators to real Pool-Seq data from Drosophila melanogaster populations, demonstrating their usefulness in revealing population structure and identifying loci with high differentiation within or between groups of subpopulations and associated with spatial or temporal genetic variation.

genetics↗

bioRxiv2024

Footprints of worldwide adaptation in structured populations of D. melanogaster through the expanded DEST 2.0 genomic resource

Large scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster, we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009-2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species demographic history and identify novel signs of adaptation across spatial and temporal dimensions. We showed that patterns of secondary contact, originally characterized in North America, are replicated in South America and Australia. We also found that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatio-temporal patterns of genetic variation in this classic model system.

evolutionary biology↗

bioRxiv2024

Transposable elements in a cold-tolerant fly species, Drosophila montana: a link to adaptation to the harsh cold environments

BackgroundSubstantial discoveries during the past century have revealed that transposable elements (TEs) can play a crucial role in genome evolution by affecting gene expression and inducing genetic rearrangements, among other molecular and structural effects. Yet, our knowledge on the role of TEs in adaptation to extreme climates is still at its infancy. The availability of long-read sequencing has opened up the possibility to identify and study potential functional effects of TEs with higher precision. In this work, we used Drosophila montana as a model for cold-adapted organisms to study the association between TEs and adaptation to harsh climates. ResultsUsing the PacBio long-read sequencing technique, we de novo identified and manually curated TE sequences in five Drosophila montana genomes from eco-geographical distinct populations. We identified 489 new TE consensus sequences which represented 92% of the total TE consensus in D. montana. Overall, 11-13% of the D. montana genome is occupied by TEs, which as expected are non-randomly distributed across the genome. We identified five potentially active TE families, most of them from the retrotransposon class of TEs. Additionally, we found TEs present in the five analyzed genomes that were located nearby previously identified cold tolerant genes. Some of these TEs contain promoter elements and transcription binding sites. Finally, we detected TEs nearby fixed and polymorphic inversion breakpoints. ConclusionsOur research revealed a significant number of newly identified TE consensus sequences in the genome of D. montana, suggesting that non-model species should be studied to get a comprehensive view of the TE repertoire in Drosophila species and beyond. Genome annotations with the new D. montana library allowed us to identify TEs located nearby cold tolerant genes, and present at high population frequencies, that contain regulatory regions and are thus good candidates to play a role in D. montana cold stress response. Finally, our annotations also allow us to identify for the first time TEs present in the breakpoints of three D. montana inversions.

genomics↗

bioRxiv2023

The epigenetics effects of transposable elements are context dependent and not restricted to gene silencing

Transposable elements (TEs) represent a threat to genome integrity due to their proliferation capacity. Eukaryotic cells silence TEs through different epigenetic mechanisms, including the deposition of repressive histone marks. Previous studies have shown that repressive marks can spread to neighboring sequences. However, evidence for this spreading affecting nearby gene expression remains limited. Similarly, whether TEs induce changes in the enrichment of active histone marks genome-wide, and its potential impact on gene expression have not been widely studied. In this work, we performed a comprehensive study of the epigenetic effects of 2,235 TEs and their potential effects on nearby gene expression on D. melanogaster head, gut and ovary. While most of the TEs (816) induce the enrichment of the H3K9me3 repressive mark, with stronger epigenetic effects in the ovary, a substantial number (345 TEs) induce the enrichment of the H3K27ac active mark, particularly in the gut. We found that 70% of the H3K9me3 enriched TEs induced gene down-regulation, and 50% of the H3K27ac enriched TEs induced gene up-regulation. These changes in expression affect specific regulatory networks in head and gut while in ovary, genes were not enriched for any biological functions. Furthermore, TE epigenetic effects on gene expression are genomic context dependent. Finally, we found that TEs also affect gene expression by disrupting regions enriched for histone marks. Overall, our results show that TEs do generate regulatory novelty through epigenetic changes, with these epigenetic effects not restricted to gene silencing and being context dependent. Significance statementTransposable elements (TEs) are repetitive DNA sequences found in nearly all studied organisms that have the capacity to move within the genome. To prevent their proliferation, eukaryotic cells target TEs with repressive histone marks, an epigenetic signal that blocks their expression. While these repressive marks can spread to neighboring genes, the evidence of how this impacts gene expression is limited. Similarly, whether TEs also influence the enrichment and depletion of active histone marks and their genome-wide impact is not understood. In this work, we studied the histone mark enrichment of 2,235 polymorphic TEs across three body parts of D. melanogaster. Our results provide evidence for the genome-wide role of TEs in the generation of regulatory novelty through epigenetic changes.

evolutionary biology↗

bioRxiv2022

DrosOmics: the comparative genomics browser to explore omics data in natural strains of D. melanogaster

The advent of long-read sequencing technologies has allowed the generation of multiple high-quality de novo genome assemblies for multiple species, including well-known model species such as Drosophila melanogaster. Genome assemblies for multiple individuals of the same species are key to discover the genetic diversity present in natural populations, especially the one generated by transposable elements, the most common type of structural variant. Despite the availability of multiple genomic datasets for D. melanogaster populations, we lack an efficient visual tool to display different genomes assemblies simultaneously. In this work, we present DrosOmics, a comparative genomics-oriented browser for 52 high-quality reference genomes of D. melanogaster, including annotations from a highly reliable set of transposable elements, and functional transcriptomics and epigenomics data for half the populations. DrosOmics is based on JBrowse 2, which allows the visualization of multiple assemblies at once, key to unraveling structural and functional features of D. melanogaster natural populations.

genomics↗

bioRxiv2021

Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource

Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last 20 years. A major challenge is the integration of these disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution and population structure of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 population samples from over 100 locations in >20 countries on four continents based on a combination of 121 unpublished and 150 previously published genomic datasets. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.

genomics↗