Biology subjects

Ament-Velasquez, S. L.

Publications and source records attributed to Ament-Velasquez, S. L..

12 recordsLinked to original sources

bioRxiv2026

Female-biased sex ratios despite stable genetic sex determination across a climatic gradient in a marine fish

Adult sex ratio (ASR) is a fundamental parameter shaping population dynamics and evolutionary trajectories. In theory, ASR is governed by the sex determination (SD) system and sex-specific mortality. Yet, ASR is often hard to predict in natural populations because of ecological effects on its determinants. We address this ecological complexity by investigating the drivers of ASR across a steep climatic gradient in Scandinavian populations of the two-spotted goby Pomatoschistus flavescens. Demographic surveys accounting for over 25000 fish in 30 locations, spanning 10{degrees} of latitude, revealed a general female-bias of the ASR, ca. 75%. To assess the contribution of SD, we combined reduced representation sequencing of 180 adults with our novel long-read male genome assembly. We characterised the genetic architecture of an XX/XY SD system, and identified a male-specific duplicate from the TGF-{beta} signaling pathway, amhr2y, as a candidate sex-determining gene. Subsequent genotyping of eggs and juveniles showed consistently unbiased sex ratios across latitudes, implying that the female-biased arises at later life stages. Interpreted in the light of historical data, our findings allow us to reject environmental sex determination and sex-biased mortality as important drivers of ASR bias in this species. We propose instead that the female bias originates from sex-specific patterns of habitat distribution, which could result from ecological conditions interacting with the distinct reproductive strategies of females and males. Our results underscore the need to go beyond primary theoretical expectations to understand fundamental demographic parameters within their relevant ecological context.

evolutionary biology↗

bioRxiv2025

A recent shift in centromere size and DNA content in Podospora pseudocomata co-occurs with the loss of a fungal genome defense system

The centromere of the eukaryotic chromosome is necessary for the accurate segregation during cell division. Yet, centromeric DNA is highly variable and rapidly evolving. In fungi, centromeres range from point- to regional centromeres, some of which are hundreds of thousands of base pairs long and filled with transposable elements. As fungi have evolved several specialized defense mechanisms against transposable elements, these regional centromeres are intriguing sites for investigating the connection between genome defense and centromere evolution. Here, we investigated the structure of the centromeres of seven species of the Podospora anserina species complex, which is made up of closely related filamentous ascomycetes that diverged less than 1 MYA. We discovered that one species in the complex, P. pseudocomata, lacks the genomic signature of the specialized genome defense mechanism called Repeat Induced Point mutations (RIP). We identified the centromeric regions in P. anserina and P. pseudocomata using chromatin immunoprecipitation targeting the centromere-specific histone variant cenH3, and using comparative genomics we inferred the size of centromeric regions in the other species. We found that while the centromere structure in the complex is generally well conserved, the centromeric regions of P. pseudocomata has gone through a rapid change. Specifically, the size of the centromeres in P. pseudocomata are 35-46 kb, which is significantly smaller than those of the other species (44-90 kb), and the DNA-transposon discoglosse is the most abundant TE family instead of the typical LTR-retrotransposon crapaud. Taken together, our data strongly indicates a link between genome defense and centromere evolution in fungi.

genomics↗

bioRxiv2025

NOD-like receptor genes evolve under diversity-enhancing mechanisms in a fungal species complex

Fungi harbor diverse arrays of genes encoding NOD-like receptors (NLRs), key intracellular immune proteins found in plants, animals, and bacteria. Some fungal NLRs are known to control regulated cell death (RCD) in the context of allorecognition, the capacity to recognize conspecific nonself. However, the function of most fungal NLR genes remains unknown. Here, we characterize the evolution of the NLR repertoire in the Podospora anserina species complex. We show that the vast majority of the NLRs display effector domains known to be involved in RCD execution. Moreover, NLRs undergo more rapid gene turnover than random genes, show higher dN/dS values, and faster evolutionary rates. A subgroup of NLRs, distinguished by superstructure-forming repeats with very high sequence identity (high internal conservation, HIC), evolved independently multiple times. We found that HIC NLRs are more associated with transposable elements, exhibit higher nucleotide diversity partially driven by repeat-induced point mutation (RIP), and show elevated Tajimas D values indicative of balancing selection. Furthermore, HIC NLR phylogenies do not recapitulate species relationships, which we determined is caused by both balancing selection and introgression. In addition, we identified cases of repeat exchange between distinct HIC NLR genes, implying that novel binding specificities may evolve through repeat shuffling, thereby increasing allelic diversity. Finally, we determined that NLR-like genes with HIC repeats exist outside of the fungal realm, arguing for similar dynamics in other taxa. Overall, these findings suggest that fungal NLRs evolve under diversity-enhancing mechanisms and display selective signatures consistent with a general immune function.

evolutionary biology↗

bioRxiv2025

Reconstructing NOD-like receptor alleles with high internal conservation in Podospora anserina using long-read sequencing

NOD-like receptors (NLRs) are intracellular immune receptors that detect pathogen-associated cues and trigger defense mechanisms, including regulated cell death. In filamentous fungi, some NLRs mediate heterokaryon incompatibility, a self/non-self recognition process that prevents the vegetative fusion of genetically distinct individuals, reducing the risk of parasitism. The het-d and het-e NLRs in Podospora anserina are highly polymorphic incompatibility genes (het genes) whose products recognize different alleles of the het-c gene via a sensor domain composed of WD40 repeats. These repeats display unusually high sequence identity maintained by concerted evolution. However, some sites within individual repeats are hypervariable and under diversifying selection. Despite extensive genetic studies, inconsistencies in the reported WD40 domain sequence have hindered functional and evolutionary analyses. Here we demonstrate that the WD40 domain can be accurately reconstructed from long-read sequencing (Oxford Nanopore and PacBio) data, but not from Illumina-based assemblies. Functional alleles are usually formed by 11 highly conserved repeats, with different repeat combinations underlying the same phenotypic het-d and het-e incompatibility reactions. Protein structure models suggest that their WD40 domain folds into two 7-blade {beta}-propellers composed of the highly conserved repeats, as well as three cryptic divergent repeats at the C-terminus. We additionally show that one particular het-e allele does not have an incompatibility reaction with common het-c alleles, despite being 11-repeats long. Our findings provide a robust foundation for future research into the molecular mechanisms and evolutionary dynamics of het NLRs, while also highlighting both the fragility and the flexibility of {beta}-propellers as immune sensor domains.

genomics↗

bioRxiv2024

Multipartite complexity of the lichen symbiosis revealed by metagenome and transcriptome analysis of Xanthoria parietina

Lichens are composite symbiotic associations of fungi, algae, and bacteria that result in large, anatomically complex organisms adapted to many of the worlds most challenging environments. How such intricate, self-replicating lichen architectures develop from simple microbial components remains unknown because of their recalcitrance to experimental manipulation. Here we report a metagenomic and metatranscriptomic analysis of the lichen Xanthoria parietina at different developmental stages. We identified 168 genomes of symbionts and lichen-associated microbes within a lichen thallus, including representatives of green algae, three different classes of fungi, and 14 bacterial phyla. By analyzing occurrence of individual species across lichen thalli from diverse environments, we defined both substrate-specific and core microbial components of the lichen. Meta-transcriptomic analysis of the principal fungal symbiont from three different developmental stages of a lichen, compared to axenically grown fungus, revealed differential gene expression profiles indicative of lichen-specific transporter functions, specific cell signalling, transcriptional regulation and secondary metabolic capacity. Putative immunity-related proteins and lichen-specific structurally conserved secreted proteins resembling fungal pathogen effectors were also identified, consistent with a role for immunity modulation in lichen morphogenesis.

bioinformatics↗

bioRxiv2023

het-B allorecognition in Podospora anserina is determined by pseudo-allelic interaction of genes encoding a HET and lectin fold domain protein and a PII-like protein

Filamentous fungi display allorecognition genes that trigger regulated cell death (RCD) when strains of unlike genotype fuse. Podospora anserina is one of several model species for the study of this allorecognition process termed heterokaryon or vegetative incompatibility. Incompatibility restricts transmission of mycoviruses between isolates. In P. anserina, genetic analyses have identified nine incompatibility loci, termed het loci. Here we set out to clone the genes controlling het-B incompatibility. het-B displays two incompatible alleles, het-B1 and het-B2. We find that the het-B locus encompasses two adjacent genes, Bh and Bp that exist as highly divergent allelic variants (Bh1/Bh2 and Bp1/Bp2) in the incompatible haplotypes. Bh encodes a protein with an N-terminal HET domain, a cell death inducing domain bearing homology to Toll/interleukin-1 receptor (TIR) domains and a C-terminal domain with a predicted lectin fold. The Bp product is homologous to PII-like proteins, a family of small trimeric proteins acting as sensors of adenine nucleotides in bacteria. We show that although the het-B system appears genetically allelic, incompatibility is in fact determined by the non-allelic Bh1/Bp2 interaction while the reciprocal Bh2/Bp1 interaction plays no role in incompatibility. The highly divergent C-terminal lectin fold domain of BH determines recognition specificity. Population studies and genome analyses indicate that het-B is under balancing selection with trans-species polymorphism, highlighting the evolutionary significance of the two incompatible haplotypes. In addition to emphasizing anew the central role of TIR-like HET domains in fungal RCD, this study identifies novel players in fungal allorecognition and completes the characterization of the entire het gene set in that species. Author summaryMany cellular life forms display genetic systems that protect individuality and discriminate conspecific self from non-self. In filamentous fungi, cell fusion events between strains are under check by specific allorecognition genes that trigger regulated cell death upon detection of non-self. The role of incompatibility is to restrict mycovirus transmission and conspecific parasitism. Podospora anserina, a good model for the study of this form of allorecognition, harbors nine incompatibility het loci. Previous studies have revealed that these genes can be homologous to genes with immune functions in other phyla including bacteria, plants and animals. We have cloned het-B, the last of the nine het genes that remained to be identified and found that it is a complex locus comprising two adjacent genes Bh and Bp. BH displays an N-terminal HET domain (related to TIR domains) and a C-terminal domain with a predicted lectin fold. BP is homologous to PII-like proteins, known bacterial metabolite sensors. Intriguingly, despite apparent genetic allelism, incompatibility is dictated by the non-allelic Bh/Bp interaction. This study stresses the reoccurring involvement of HET domains in fungal RCD and signs completion of the characterization of the entire set of het loci in that species, enabling a comparative analysis of the different genetic architectures underlying allorecognition.

genetics↗

bioRxiv2023

High-quality genome assemblies of four members of the Podospora anserina species complex

The filamentous fungus Podospora anserina is a model organism used extensively in the study of molecular biology, senescence, prion biology, meiotic drive, mating-type chromosome evolution, and plant biomass degradation. It has recently been established that P. anserina is a member of a complex of seven, closely related species. In addition to P. anserina, high-quality genomic resources are available for two of these taxa. Here we provide chromosome-level annotated assemblies of the four remaining species of the complex, as well as a comprehensive dataset of annotated assemblies from a total of 28 Podospora genomes. We find that all seven species have genomes of around 35 Mbp arranged in seven chromosomes that are mostly collinear and less than 2% divergent from each other at genic regions. We further attempt to resolve their phylogenetic relationships, finding significant levels of phylogenetic conflict as expected from a rapid and recent diversification. SignificanceHere we provide a dataset of 28 annotated genomes from the P. anserina species complex, including chromosome-level assemblies of four species that lacked a reference genome. With this dataset in hand, biologists can take advantage of the molecular tools available for P. anserina to study evolutionary dynamics at the interphase between micro- and macroevolution, with particular emphasis on trait evolution, genome architecture, and speciation.

genomics↗

bioRxiv2022

The dynamics of adaptation to stress from standing genetic variation and de novo mutations

Adaptation from standing genetic variation is an important process underlying evolution in natural populations but we rarely get the opportunity to observe the dynamics of fitness changes in real time. Here, we used the power of microbial experimental evolution and whole population sequencing to track the phenotypic and genomic changes of genetically diverse yeast populations in environments with different stress levels. We found that populations rapidly and in parallel increased in fitness in stressful environments. The founders genetic diversity was quickly depleted, however, not to the same degree in all populations and environments. Some populations fixed all ancestral variation in < 30 generations while others maintained diversity across hundreds of generations. We also observed parallelism at the gene and pathway level. Specifically, we detected up to seven genes harbouring multiple independent mutations in different populations, and a general enrichment for mutations affecting downstream effectors of the high-osmolarity-glycerol pathway in three out of four environments. Adaptation to the most stressful environment was characterised by the fast evolution of functional haploidy, likely driven by standing genetic variation. Almost 40% of all populations contained aneuploidies (losses or gains of chromosomes) at least once during experimental evolution. Some aneuploidies were maintained for hundreds of generations in parallel in different replicates, suggesting they were adaptive. This work shows that experimental evolution is a great tool to address the interplay between standing variation and the influx of de novo mutations, leading to a better understanding of the demographic and environmental drivers and constraints of a populations capacity to adapt to environmental change.

evolutionary biology↗

bioRxiv2020

The plot thickens: haploid and triploid-like thalli, hybridization, and biased mating type ratios in Letharia

The study of the reproductive biology of lichen fungal symbionts has been traditionally challenging due to their complex and symbiotic lifestyles. Against the common belief of haploidy, a recent genomic study found a triploid-like signal in Letharia. Here, we used genomic data from a pure culture and from thalli, together with a PCR survey of the MAT locus, to infer the genome organization and reproduction in Letharia. We found that the read count variation in the four Letharia specimens, including the pure culture derived from a single sexual spore of L. lupina, is consistent with haploidy. By contrast, the L. lupina read counts from a thallus metagenome are triploid-like. Characterization of the mating-type locus revealed a conserved heterothallic configuration across the genus, along with auxiliary genes that we identified. We found that the mating-type distributions are balanced in North America for L. vulpina and L. lupina, suggesting widespread sexual reproduction, but highly skewed in Europe for L. vulpina, consistent with predominant asexuality. Taken together, we propose that Letharia fungi are heterothallic and typically haploid, and provide evidence that triploid-like individuals are rare hybrids between L. lupina and an unknown Letharia lineage, reconciling classic systematic and genetic studies with recent genomic observations.

evolutionary biology↗

bioRxiv2020

Invasion and maintenance of spore killing in ascomycete fungi

Meiotic drivers are selfish genetic elements that are able to become over-represented among the products of meiosis. This transmission advantage makes it possible for them to spread in a population even when they impose fitness costs on their host organisms. Whether a meiotic driver can invade a population, and subsequently reach fixation or coexist in a stable polymorphism, depends on the one hand on the biology of the host organism, including its life-cycle, mating system, and population structure, and on the other hand on the specific fitness effects of the driving allele on the host. Here, we present a population genetic model for spore killing, a type of drive specific to fungi. We show how ploidy level, rate of selfing, and efficiency of spore killing affect the invasion probability of a driving allele and the conditions for its stable coexistence with the non-driving allele. Our model can be adapted to different fungal life-cycles, and is applied here to two well-studied genera of filamentous ascomycetes known to harbor spore killing elements, Neurospora and Podospora. We discuss our results in the light of recent empirical findings for these two systems.

evolutionary biology↗

bioRxiv2020

The Enterprise: A massive transposon carrying Spok meiotic drive genes

The genomes of eukaryotes are full of parasitic sequences known as transposable elements (TEs). Most TEs studied to date are relatively small (50 - 12000 bp), but can contribute to very large proportions of genomes. Here we report the discovery of a giant tyrosine-recombinase-mobilized DNA transposon, Enterprise, from the model fungus Podospora anserina. Previously, we described a large genomic feature called the Spok block which is notable due to the presence of meiotic drive genes of the Spok gene family. The Spok block ranges from 110 kb to 247 kb and can be present in at least four different genomic locations within P. anserina, despite what is an otherwise highly conserved genome structure. We have determined that the reason for its varying positions is that the Spok block is not only capable of meiotic drive, but is also capable of transposition. More precisely, the Spok block represents a unique case where the Enterprise has captured the Spoks, thereby parasitizing a resident genomic parasite to become a genomic hyperparasite. Furthermore, we demonstrate that Enterprise (without the Spoks) is found in other fungal lineages, where it can be as large as 70 kb. Lastly, we provide experimental evidence that the Spok block is deleterious, with detrimental effects on spore production in strains which carry it. In contrast to the selfish role of the Enterprise in P. anserina, we hypothesize that the mobility of the Enterprise may also play an adaptive role in fungi when Enterprise undergoes horizontal transfer while carrying metabolic genes. This union of meiotic drivers and a transposon has created a selfish element of impressive size in Podospora, challenging our perception of how TEs influence genome evolution and broadening the horizons in terms of what the upper limit of transposition may be.

genomics↗

bioRxiv2019

Combinations of Spok genes create multiple meiotic drivers in Podospora

Meiotic drive is the preferential transmission of a particular allele at a given locus during sexual reproduction. The phenomenon is observed as spore killing in a variety of fungal lineages, including Podospora. In natural populations of Podospora anserina, seven spore killers (Psks) have been identified through classical genetic analyses. Here we show that the Spok gene family underlie the Psk spore killers. The combination of the various Spok genes at different chromosomal locations defines the spore killers and creates a killing hierarchy within the same population. We identify two novel Spok homologs that are located within a complex region (the Spok block) that reside in different chromosomal locations in given natural strains. We confirm that the individual SPOK proteins perform both the killing and resistance functions and show that these activities are dependent on distinct domains, a nuclease and a kinase domain respectively. Genomic data and phylogenetic analysis across ascomycetes suggest that the Spok genes disperse via cross-species transfer, and evolve by duplication and diversification within several lineages.

genetics↗