Biology subjects

Vargas-Chavez, C.

Publications and source records attributed to Vargas-Chavez, C..

13 recordsLinked to original sources

bioRxiv2026

LINGUINE: a phylogeny-aware, orthogroup-based framework for robust ancestral linkage group inference

Reconstructing the chromosomal architecture of ancestral genomes is a central challenge in comparative genomics, yet existing methods for ancestral linkage group (ALG) inference struggle in clades with rapid genome evolution. Current approaches rely predominantly on single-copy orthologous genes to anchor linkage groups between species, limiting marker density and lacking mechanisms to resolve paralogy, which leads to systematic inflation of inferred ALG counts and propagates structural artifacts in downstream analyses. Here we present LINGUINE (LINkage GroUps INfErence), a phylogeny-aware pipeline for robust ALG reconstruction addressing these limitations. LINGUINE uses orthogroups to maximise marker density, employs a Hidden Markov Model to delineate syntenic blocks while accommodating gene loss, rearrangements, and assembly fragmentation, and incorporates an explicit paralogy resolution step prior to ancestral reconstruction. Ancestral states are inferred through iterative post-order traversal of the species tree, progressively integrating information from all descendants. Using GARLIC (Genome reARrangement simuLator for Inferring Chromosomal landscapes), we characterise the limits of synteny signal detectability and define the conditions under which ALG reconstruction remains reliable. Benchmarking on nematodes demonstrates concordant performance with existing tools while incorporating a substantially larger fraction of the gene repertoire. Applied to clitellate annelids, a clade with highly rearranged genomes, LINGUINE recovers biologically coherent ancestral architectures that existing methods fail to resolve. These results establish LINGUINE as a flexible framework for ancestral genome reconstruction in clades where traditional approaches lose resolution. LINGUINE and GARLIC are open source and available in GitHub (https://github.com/MetazoaPhylogenomicsLab/Vargas-Chavez-Fernandez_2026_LINGUINE, and https://github.com/MetazoaPhylogenomicsLab/Vargas-Chavez-Fernandez_2026_GARLIC).

evolutionary biology↗

bioRxiv2026

Lungfish comparative genomics reveals ancient gene networks co-opted for life on land

The transition from water to land was a defining event in vertebrate evolution, requiring major changes in physiology and gene regulation. Lungfish, the closest extant relatives of tetrapods, offer a unique window into this process through their capacity for estivation, a physiological state that mirrors key demands of terrestrial life. Here, we constructed and compared gene co-expression networks across five vertebrate species using multi-tissue transcriptomic data. Focusing on estivating lungfish tissues, we identified conserved modules enriched in core functions, including metabolic regulation, RNA processing, and protein turnover. We further show that a subset of retained ohnologs from the vertebrate 2R-WGD act as network hubs under directional selection in key phylogenetic branches. These genes, involved in membrane trafficking, cytoskeletal regulation, water balance, and stress response, illustrate how duplicated, dosage-sensitive genes were co-opted to meet the physiological demands of terrestrial adaptation. Together, our findings support a model in which ancient whole-genome duplications supplied raw material later shaped by selection and network rewiring to enable extreme physiological adaptations such as estivation. TeaserAncient duplicated gene networks in lungfish estivation reveal how vertebrates repurposed genomic toolkits to adapt to land.

evolutionary biology↗

bioRxiv2025

Independent genomic trajectories shape adaptation to life on land across animal lineages

How animals repeatedly adapted to life on land is a central question in evolutionary biology. While terrestrialisation occurred independently across animal phyla, it remains unclear whether shared genomic mechanisms underlie these transitions. Here, we combine large-scale comparative genomics, machine learning, and multi-omics data, including proteomics and transcriptomics from stress experiments relevant to terrestrial environmental challenges in 17 species, to investigate the genomic basis of animal terrestrial adaptation. Gene co-expression networks reveal that genes relevant to stress are largely lineage-specific, yet converge in function through the co-option of gene families pre-dating terrestrialisation events. Phylogenomic and machine learning analyses support a dominant role for early-evolving genes, enriched in stress-related functions, paired with a higher gene loss than gain at terrestrialisation nodes. Our findings support a model of lineage-specific genomic changes involving mostly conserved genes that converged at the functional level during the independent transitions to terrestrial life.

evolutionary biology↗

bioRxiv2025

Genomic exaptation and regulatory landscape shifts as key mechanisms enabling flatworm terrestrialization

Understanding the genomic toolkit that facilitated animal terrestrialization--the transition from aquatic to terrestrial environments--is crucial for unravelling the evolutionary processes behind the origin and diversification of terrestrial biodiversity. Despite its significance, the genomic foundations driving the physiological and metabolic adaptations required for life on land remain largely unexplored across most terrestrial animal phyla. Planarians (phylum Platyhelminthes) represent an ideal model for studying terrestrialization, as only one terrestrial lineage, the family Geoplanidae (order Tricladida) is known to exist. Here, we used an integrative approach combining genomics, transcriptomics, and proteomics to investigate the genetic underpinnings potentially facilitating adaptation to terrestrial environments. Our analysis revealed a significant burst of gene gain preceding the diversification of terrestrial planarians and their split from freshwater relatives, in the branch leading to Tricladida. Upon exposure to abiotic stress, terrestrial and freshwater planarians exhibited distinct genetic toolkits: most differentially expressed genes emerged in orthologous groups gained specifically in the branch leading to Tricladida, over half of which showed signs of strong directional selection in terrestrial flatworms, indicating their adaptive importance for land colonization. Transcriptomic analyses further revealed contrasting stress responses: terrestrial planarians upregulated ancient genes whose origin predates the Geoplanidae lineage to cope with abiotic stress, while freshwater planarians downregulated a separate set of ancestral genes. Our genomic, transcriptomic, and proteomic data consistently show that the genetic toolkit for abiotic stress response in terrestrial planarians is highly differentiated from that of their freshwater counterparts, with significant regulatory shifts as well. Overall, our findings suggest a burst of gene gain in the Tricladida lineage, with co-option of these genes, rather than clade-specific innovations, playing a critical role in the origin and diversification of terrestrial flatworms. This underscores genomic exaptation and regulatory landscape shifts as key mechanisms enabling terrestrialization within Platyhelminthes. This study offers the first genome-wide insight into the genetic toolkit underlying flatworm terrestrialization and contributes broadly to understanding the genomic basis of animal terrestrialization.

evolutionary biology↗

bioRxiv2024

A punctuated burst of massive genomic rearrangements by chromosome shattering and the origin of non-marine annelids

The genomic basis of cladogenesis and adaptive evolutionary change has intrigued biologists for decades. Here, we show that the tectonics of genome evolution in clitellates, a clade composed of most freshwater and all terrestrial species of the phylum Annelida, is characterised by extensive genome-wide scrambling that resulted in a massive loss of macrosynteny between marine annelids and clitellates. These massive rearrangements included the formation of putative neocentromeres with newly acquired transposable elements and preceded a further period of genome-wide reshaping events, potentially triggered by the loss of genes involved in genome stability and homeostasis of cell division. Notably, while these rearrangements broke short-range interactions observed between Hox genes in marine annelids, they were reformed as long-range interactions in clitellates. Our findings reveal extensive genomic reshaping in clitellates at both the linear (2D) and three-dimensional (3D) levels, suggesting that, unlike in other animal lineages where synteny conservation constrains structural evolution, clitellates exhibit a remarkable tolerance for chromosomal rearrangements. Our study thus suggests that the genomic landscape of Clitellata resulted from a rare burst of genomic changes that ended a long period of stability that persists across large phylogenetic distances.

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↗

bioRxiv2024

MATEdb2, a collection of high-quality metazoan proteomes across the Animal Tree of Life to speed up phylogenomic studies

Recent advances in high throughput sequencing have exponentially increased the number of genomic data available for animals (Metazoa) in the last decades, with high-quality chromosome-level genomes being published almost daily. Nevertheless, generating a new genome is not an easy task due to the high cost of genome sequencing, the high complexity of assembly, and the lack of standardized protocols for genome annotation. The lack of consensus in the annotation and publication of genome files hinders research by making researchers lose time in reformatting the files for their purposes but can also reduce the quality of the genetic repertoire for an evolutionary study. Thus, the use of transcriptomes obtained using the same pipeline as a proxy for the genetic content of species remains a valuable resource that is easier to obtain, cheaper, and more comparable than genomes. In a previous study, we presented the Metazoan Assemblies from Transcriptomic Ensembles database (MATEdb), a repository of high-quality transcriptomic and genomic data for the two most diverse animal phyla, Arthropoda and Mollusca. Here, we present the newest version of MATEdb (MATEdb2) that overcomes some of the previous limitations of our database: (1) we include data from all animal phyla where public data is available, (2) we provide gene annotations extracted from the original GFF genome files using the same pipeline. In total, we provide proteomes inferred from high-quality transcriptomic or genomic data for almost 1000 animal species, including the longest isoforms, all isoforms, and functional annotation based on sequence homology and protein language models, as well as the embedding representations of the sequences. We believe this new version of MATEdb will accelerate research on animal phylogenomics while saving thousands of hours of computational work in a plea for open, greener, and collaborative science.

evolutionary biology↗

bioRxiv2023

The genome sequence of the Montseny horsehair worm, Gordionus montsenyensis sp. nov., a key resource to investigate Ecdysozoa evolution

Nematomorpha, also known as Gordiacea or Gordian worms, are a phylum of parasitic organisms that belong to the Ecdysozoa, a clade of invertebrate animals characterized by molting. They are one of the less scientifically studied animal phyla, and many aspects of their biology and evolution are still unknown, partially due to the lack of genomic resources for this phylum. As part of the European Reference Genome Atlas pilot effort to generate reference genomes for European biodiversity, we present the taxonomic description and chromosome-level genome assembly of a newly described species of Nematomorpha (Gordionus montsenyensis Schmidt-Rhaesa & Fernandez sp. nov.). The final assembly has a total length of 288 Mb in 396 scaffolds with an N50 of 64.4 Mb, 97% of which is scaffolded into 5 pseudochromosomes. The circular mitochondrial genome was also assembled into a 15-kilobases sequence. Gene annotation predicted 10,320 protein-coding genes in the nuclear genome. In this study, we contribute a key genomic resource to not only explore the evolution of Ecdysozoa, but also to further our understanding on the genomic basis of parasitic lifestyles. In addition, we describe a species new to science from this enigmatic animal phyla.

evolutionary biology↗

bioRxiv2022

MATEdb, a data repository of high-quality metazoan transcriptome assemblies to accelerate phylogenomic studies

AO_SCPLOWBSTRACTC_SCPLOWWith the advent of high throughput sequencing, the amount of genomic data available for animals (Metazoa) species has bloomed over the last decade, especially from transcriptomes due to lower sequencing costs and easier assembling process compared to genomes. Transcriptomic data sets have proven useful for phylogenomic studies, such as inference of phylogenetic interrelationships (e.g., species tree reconstruction) and comparative genomics analyses (e.g., gene repertoire evolutionary dynamics). However, these data sets are often analyzed following different analytical pipelines, particularly including different software versions, leading to potential methodological biases when analyzed jointly in a comparative framework. Moreover, these analyses are computationally expensive and not affordable for a large part of the scientific community. More importantly, assembled transcriptomes are usually not deposited in public databases. Furthermore, the quality of these data sets is hardly ever taken into consideration, potentially impacting subsequent analyses such as orthology and phylogenetic or gene repertoire evolution inference. To alleviate these issues, we present Metazoan Assemblies from Transcriptomic Ensembles (MATEdb), a curated database of 335 high-quality transcriptome assemblies from different animal phyla analyzed following the same pipeline. The repository is composed, for each species, of (1) a de novo transcriptome assembly, (2) its candidate coding regions within transcripts (both at the level of nucleotide and amino acid sequences), (3) the coding regions filtered using their contamination profile (i.e., only metazoan content), (4) the longest isoform of the amino acid candidate coding regions, (5) the gene content completeness score as assessed against the BUSCO database, and (6) an orthology-based gene annotation. We complement the repository with gene annotations from high-quality genomes, which are often not straightforward to obtain from individual sequencing projects, totalling 423 high-quality genomic and transcriptomic data sets. We invite the community to provide suggestions for new data sets and new annotation features to be included in subsequent versions, that will be analyzed following the same pipeline and be permanently stored in public repositories. We believe that MATEdb will accelerate research on animal phylogenomics while saving thousands of hours of computational work in a plea for open and collaborative science.

evolutionary biology↗

bioRxiv2021

The genome sequence of the cereal pest Sitophilus oryzae: an unprecedented transposable element content

BackgroundThe rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. ResultsWe sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 Kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino-acids required for insect development and cuticle biosynthesis. ConclusionsHere we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.

genomics↗

bioRxiv2021

Coordination between growth and stress responses by DELLA in the liverwort Marchantia polymorpha

Plant survival depends on the optimal use of resources under variable environmental conditions. Among the mechanisms that mediate the balance between growth, differentiation and stress responses, the regulation of transcriptional activity by DELLA proteins stands out. In angiosperms, DELLA accumulation promotes defense against biotic and abiotic stress and represses cell division and expansion, while loss of DELLA function is associated with increased plant size and sensitivity towards stress1. Given that DELLA protein stability is dependent on gibberellin (GA) levels2, and GA metabolism is influenced by the environment3, this pathway is proposed to relay environmental information to the transcriptional programs that regulate growth and stress responses in angiosperms4,5. However, DELLA genes are also found in bryophytes, whereas canonical GA receptors appeared only in vascular plants6-10. Thus, it is not clear whether these regulatory functions of DELLA predated or emerged with typical GA signaling. Here we show that, as in vascular plants, the only DELLA in the liverwort Marchantia polymorpha also participates in the regulation of growth and key developmental processes, and promotes the tolerance towards oxidative stress. Moreover, part of these effects is likely caused by the conserved physical interaction with the MpPIF transcription factor. Therefore, we suggest that the role in the coordination of growth and stress responses was already encoded in DELLA from the common ancestor of land plants, and the importance of this function is justified by its conservation over the past 450 M years.

plant biology↗

bioRxiv2020

Impact of transposable elements on the genome of the urban malaria vector Anopheles coluzzii

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSAnopheles coluzzii is one of the primary vectors of human malaria in sub-Saharan Africa. Recently, it has colonized the main cities of Central Africa threatening vector control programs. The adaptation of An. coluzzii to urban environments is partly due to an increased tolerance to organic pollution and insecticides. While some of the molecular mechanisms for ecological adaptation, including chromosome rearrangements and introgressions, are known, the role of transposable elements (TEs) in the adaptive processes of this species has not been studied yet. To assess the role of TEs in rapid urban adaptation, the first step is to accurately annotate TE insertions in the genomes of natural populations collected in urban settings. ResultsWe sequenced using long-reads six An. coluzzii genomes from natural breeding sites in two major Central Africa cities. We de novo annotated the complete set of TEs in these genomes and in an additional high-quality An. coluzzii genome available and identified 64 previously undescribed TE families. TEs were non-randomly distributed throughout the genome with significant differences in the number of insertions of several superfamilies across the studied genomes. We identified seven putatively active families with insertions near genes with functions related to vectorial capacity. Moreover, we identified several TE insertions providing promoter and transcription factor binding sites to insecticide resistance and immune-related genes. ConclusionsThe analysis of multiple genomes sequenced using long-read technologies allowed us to generate the most comprehensive TE annotations in this species to date. We identified several TE insertions that could potentially impact both genome architecture and the regulation of functionally relevant genes in An. coluzzii. These results provide a basis for future studies of the impact of TEs on the biology of An. coluzzii.

genomics↗

bioRxiv2019

Genomic adaptations to aquatic and aerial life in mayflies and the origin of wings in insects

The first winged insects underwent profound morphological and functional transformations leading to the most successful animal radiations in the history of earth. Despite this, we still have a very incomplete picture of the changes in their genomes that underlay this radiation. Mayflies (Ephemeroptera) are one of the extant sister groups of all other winged insects and therefore are at a key phylogenetic position to understand this radiation. Here, we describe the genome of the cosmopolitan mayfly Cloeon dipterum and study its expression along development and in specific organs. We discover an expansion of odorant-binding proteins, some expressed specifically in the breathing gills of aquatic nymphs, suggesting a novel sensory role for gills. In contrast, as flying adults, mayflies make use of an enlarged set of opsins and utilise these visual genes in a sexually dimorphic manner, with some opsins expressed only in males. Finally, to illuminate the origin of wings, we identify a core set of deeply conserved wing-specific genes at the root of the pterygote insects. Globally, this is the first comprehensive study of the structure and expression of the genome of a paleopteran insect and shows how its genome has kept a record of its functional adaptations.

evolutionary biology↗