Biology subjects

Roy, S. W.

Publications and source records attributed to Roy, S. W..

17 recordsLinked to original sources

bioRxiv2026

A sex-specific regulator expands the embryonic ocular field to generate a novel visual system

Morphological novelties often emerge through the redeployment of conserved developmental programs, but how such programs become activated in new developmental contexts remains poorly understood. We investigated the evolutionary origin of the turbanate eyes (TurbEyes) of mayflies, a male-specific additional visual system. Using single-cell transcriptomics, chromatin accessibility profiling and functional genetics, we show that this novelty develops through deployment of the ancestral retinal determination gene network (RDGN). We identify a novel, male-specific paralog of the sex determination transcription factor Doublesex, DsxM, that regulates the eye-specification gene eyeless/Pax6 and promotes the expansion of the embryonic ocular field. Functional assays impairing dsxM activity reduce this male-specific expansion and causes defects in TurbEye development. Our findings reveal a developmental mechanism by which a sex-specific regulator generates a new developmental territory, enabling the spatial redeployment of a conserved developmental program and to generate a novel male-specific visual system.

evolutionary biology↗

bioRxiv2025

Evidence for an ancient master sex determination gene in Hymenoptera

The vast majority of Hymenopterans determine sex by haplodiploidy, in which males and females develop from haploid unfertilized and diploid fertilized eggs, respectively. At the molecular level, the majority of Hymenoptera are thought to determine sex by so-called Complementary Sex Determination (CSD). Under CSD, sex is determined by the feminizing effects of one or more allele-rich loci, in which the feminizing function is imparted by the interactions of functionally distinct alleles. Because of high allelic diversity, most diploids are heterozygous and develop as females, whereas haploid individuals develop as males, as do rare homozygous diploids. Despite diverse empirical results suggesting that CSD is widespread in Hymenopterans, and substantial theoretical and empirical study of the consequences of CSD, the molecular biology of CSD has received little attention outside of the honeybee, Apis mellifera. Available evidence provides support for divergent perspectives ranging from a single (nearly) universally-conserved CSD locus or a pattern dominated by evolutionary turnover with different genes serving as the CSD gene(s) in different lineages. Recently, a novel non-coding RNA gene named ANTSR was shown to serve as a CSD gene in different ant lineages, and the authors suggested that ANTSR might serve as a more broadly-conserved CSD gene. To assess the role of ANTSR role in CSD across diverse Hymenoptera, we studied syntenic conservation and polymorphism patterns in the broad ANTSR locus, genome-wide sequence from available male and female diploid Formica ants, and data from a sibling cross for Bombus terrestris. We find evidence that ANTSR is a conserved CSD gene across diverse Aculeata, the largest group of Hymenoptera, and provide preliminary evidence that Formica may have multiple CSD loci including ANTSR.

genetics↗

bioRxiv2024

Prevalence and Diversity of Haemosporidian-Associated Matryoshka RNA Viruses in a Natural Population of Wild Birds

Matryoshka RNA viruses (MaRNAV) have previously been detected using bioinformatics and limited PCR approaches. They are associated with haemosporidian parasite infections, yet their prevalence and diversity in wild bird populations remains largely unknown. To investigate the prevalence of MaRNAV, we examined blood samples collected from wild passerine birds and raptors in the San Francisco Bay Area. Samples were first screened for haemosporidian infections followed by RNA sequencing (RNAseq) and reverse transcriptase (RT) PCR to detect MaRNAV. Our analyses identified two novel MaRNAV (MaRNAV-5 and -6) infecting various bird species harboring diverse Haemoproteus and Leucocytozoon species and lineages. MaRNAV-5, associated with Haemoproteus, exhibited 71.3% amino acid identity to MaRNAV-4, also associated with Haemoproteus, and was found across 15 different passerine species. MaRNAV-6, linked to Leucocytozoon, shared 72.9% identity with Leucocytozoon-associated MaRNAV-3 and was exclusively found in 4 raptor species. Prevalence was 44.79% for MaRNAV-5 in haemosporidian-infected passerines and 22.22% for MaRNAV-6 in haemosporidian-infected raptors. These viruses were not found in uninfected birds similarly tested via RNAseq and RT-PCR and were consistently only found in birds infected with haemosporidia. Sanger sequencing revealed high similarity of viral sequences across different bird species, even of different orders. Our findings indicate a high prevalence of MaRNAV among local wild birds, as well as their potential specificity to haemosporidia genera, suggesting potential impacts on their health and ecology. We propose a potential life-cycle model for this group of viruses where the insect vector is the primary host, and the haemosporidian parasite acts as the virus "vector" to reach its next host. Further research is needed to determine the impact of these viruses in avian systems.

molecular biology↗

bioRxiv2022

A phylogenetic approach to studying the roles of within-host evolution and between-host transmission of resistance for clinical Escherichia coli infections

Bacterial antibiotic resistance represents a public health concern that will remain relevant for the foreseeable future. Antibiotic resistant bacterial infections can occur in two ways: (1) a host is infected by a resistant bacterial strain (due to between-host transmission of resistance), or (2) a host is infected infection by a susceptible strain, followed by the de novo evolution or acquisition of resistance (due to within-host evolution of resistance). While both are critical to understanding how the evolution of resistance happens in natural settings, the relative rate at which they occur is unclear. Here, we employ phylogenetic comparative methods to examine the evolutionary dynamics of resistance in Escherichia coli for multiple common antibiotics. We report evolutionary patterns consistent with common de novo evolution of resistance for some antibiotics and sustained transmission of resistant strains for others. For example, we observe 79 putative de novo resistance evolution events for resistance to Cefuroxime but only 31 for resistance to Ciprofloxacin, despite similar numbers of observed infections (239 and 267 respectively). We find that clusters of resistance are generally larger for Ciprofloxacin, Ceftazidima and AmoxiClav, which suggests that for these drugs, resistance is often transmitted from patient to patient. In contrast, we find that cluster sizes for resistance are generally smaller for PipTaz, Cefuroxime and Gentamicin, suggesting that resistance to these drugs is less often transmitted from patient to patient and instead evolves de novo. In addition to differences between drugs, we also find that cluster sizes were generally larger in phylogroup B2 compared to the other phylogroups, suggesting that transmission of resistant strains is more common in this phylogroup compared to the others. Our study proposes new approaches for determining the importance of de novo evolution or acquisition (within-host evolution) from resistance from infection with an already resistant strain (between-host transmission). Significantly, this work also bridges an important gap between evolutionary genomics and epidemiology, opening up a range of opportunities for studying the evolutionary dynamics of bacterial antibiotic resistance.

evolutionary biology↗

bioRxiv2022

Where the Minor Things Are: A Survey of Minor Spliceosomal Introns in Thousands of Eukaryotic Genomes

Spliceosomal introns are gene segments removed ("spliced") from RNA transcripts by large ribonucleoprotein machineries called spliceosomes. In some eukaryotes a second spliceosome (the minor/ U12-type) is responsible for processing a tiny minority of introns. Despite its seemingly modest role, minor splicing has persisted for roughly 1.5 billion years of eukaryotic evolution. Identifying and cataloging minor introns in > 3000 eukaryotic genomes, we report diverse evolutionary histories including surprisingly high numbers of minor introns in some fungi and green algae, repeated massive loss, as well as several general biases in the positional and genic distributions of minor introns. We estimate that ancestral minor intron densities were comparable to those of the most minor intron-rich species, suggesting a trend of long-term stasis. Finally, three findings suggest a major role for neutral processes in minor intron evolution. First, we find highly similar patterns of minor and major intron evolution, in contrast to the predictions of both functionalist and deleterious models. Second, we find that observed functional biases among minor intron-containing genes are largely explained by these genes greater ages. Third, we find no association of intron splicing with cell proliferation in a minor intronrich fungus, suggesting that regulatory roles are lineage-specific and thus cannot offer a general explanation for minor splicings persistence. These data constitute the most comprehensive view to date of modern minor introns, their evolutionary history, and the forces shaping minor splicing, and provide a foundation for future studies of these remarkable genomic elements.

bioinformatics↗

bioRxiv2022

Genomic analysis in Entamoeba reveals intron gain and unbiased intron loss, transformed splicing signals, and a coevolved snRNA.

The intron-exon structures of nuclear genes show striking diversity across eukaryotes. Several independent lineages have undergone convergent evolution including widespread loss of introns and transformed cis splicing signals. The causes and mechanisms of these changes remain mysterious: (i) transformation of splicing signals could reflect either selective loss of suboptimal introns or coevolution of introns and splicing machinery; and (ii) corresponding changes in the splicing machinery remain poorly characterized. A promising model to study these questions is Entamoeba. Analysis of five Entamoeba species revealed low intron densities, nearly universal atypical 5 splice sites and 3 intronic sequences. A flexible search for U1 snRNA genes revealed a modified 5-AACAAAC-3 recognition sequence, affording complete Watson-Crick basepairing potential with the atypical 5 splice site and extended basepairing potential. A U1 candidate in the related species Mastigamoeba balumuthi revealed a separate modification complimenting a different atypical consensus splice site. Genome-wide study of intron loss and gain revealed that introns with suboptimal splicing motifs were no more likely to be lost, suggesting against genome-wide homogenization of intron splicing motifs by selective intron loss. Unexpectedly, this analysis also revealed widespread intron gain in Entamoeba invadens. In total, the current analyses: (i) provide the most direct available evidence of coevolution of spliceosomal introns and splicing machinery; (ii) illuminate the evolutionary forces responsible for concerted intron loss and splicing motif transformation; and (iii) reveal widespread intron gain in an otherwise highly reduced lineage.

molecular biology↗

bioRxiv2022

Transposable elements drive intron gain in diverse eukaryotes

There is massive variation in intron numbers across eukaryotic genomes, yet the major drivers of intron content during evolution remain elusive. Rapid intron loss and gain in some lineages contrasts with long term evolutionary stasis in others. Episodic intron gain could be explained by recently discovered specialized transposons called Introners, but so far introners are only known from a handful of species. Here, we performed a systematic search across 3,325 eukaryotic genomes and identified 27,563 Introner-derived introns in 175 genomes (5.2%). Species with introners span remarkable phylogenetic diversity, from animals to basal protists, representing lineages whose last common ancestor dates to over 1.7 billion years ago. Marine organisms were 6.5 times more likely to contain Introners than their terrestrial counterparts. Introners exhibit mechanistic diversity but most are consistent with DNA transposition, indicating that Introners have evolved convergently hundreds of times from autonomous transposable elements. Transposable elements and marine taxa are associated with high rates of horizontal gene transfer, suggesting that this combination of factors may explain the punctuated and biased diversity of species containing Introners. More generally our data suggest that Introners may explain the episodic nature of intron gain across the eukaryotic tree of life. These results illuminate the major source of ongoing intron creation in eukaryotic genomes.

genomics↗

bioRxiv2021

Novel RNA viruses associated with avian haemosporidian parasites

Avian haemosporidian parasites can cause malaria-like symptoms in their hosts and have been implicated in the demise of some bird species. The newly described Matryoshka RNA viruses (MaRNAV1 and MaRNAV2) infect parasites that in turn infect their vertebrate hosts. MaRNAV2 was the first RNA virus discovered associated with parasites of the genus Leucocytozoon. By analyzing metatranscriptomes from the NCBI SRA database with local sequence alignment tools, we detected two novel RNA viruses; we describe them as MaRNAV3 associated with Leucocytozoon and MaRNAV4 associated with Parahaemoproteus. These had ~40-60% amino acid identity to the RNA-dependent RNA-polymerase (RdRp) of MaRNAV1 and 2, respectively. These findings lead us to hypothesize that MaRNAV_like viruses are widespread and tightly associated with the order Haemosporida since they have been described in human Plasmodium vivax, and now two genera of avian haemosporidians.

microbiology↗

bioRxiv2021

Evolutionary rates of testes-expressed genes differ between monogamous and promiscuous Peromyscus species

Reproductive proteins, including those expressed in the testes, are among the fastest evolving proteins across the tree of life. Sexual selection on traits involved in sperm competition is thought to be a primary driver of testes gene evolution and is expected to differ between promiscuous and monogamous species due to intense competition between males to fertilize females in promiscuous lineages and lack thereof in monogamous ones. Here, we employ the rodent genus Peromyscus as a model to explore differences in evolutionary rates between testes-expressed genes in monogamous and promiscuous species. We find candidate genes that may be associated with increased sperm production in promiscuous species and gene ontology categories that show patterns of molecular convergence associated with phenotypic convergence in independently evolved monogamous species. Overall, our results highlight the possible molecular consequences of differences in mating system, likely due to differences in selective pressures.

evolutionary biology↗

bioRxiv2021

Coupling of spliceosome complexity to intron diversity

We determined that over 40 spliceosomal proteins are conserved between many fungal species and humans but were lost during the evolution of S. cerevisiae, an intron-poor yeast with unusually rigid splicing signals. We analyzed null mutations in a subset of these factors, most of which had not been investigated previously, in the intron-rich yeast Cryptococcus neoformans. We found they govern splicing efficiency of introns with divergent spacing between intron elements. Importantly, most of these factors also suppress usage of weak nearby cryptic/alternative splice sites. Among these, orthologs of GPATCH1 and the helicase DHX35 display correlated functional signatures and copurify with each other as well as components of catalytically active spliceosomes, identifying a conserved G-patch/helicase pair that promotes splicing fidelity. We propose that a significant fraction of spliceosomal proteins in humans and most eukaryotes are involved in limiting splicing errors, potentially through kinetic proofreading mechanisms, thereby enabling greater intron diversity.

molecular biology↗

bioRxiv2021

ExOrthist: a tool to infer exon orthologies at any evolutionary distance

Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes among species. However, no existing tool allows the detection of orthologous/paralogous exons. Here, we present ExOrthist, a fully reproducible Nextflow-based software enabling to (i) infer exon homologs and orthogroups, (ii) visualize evolution of exon-intron structures, and (iii) assess conservation of alternative splicing patterns. ExOrthist not only evaluates exon sequence conservation but also considers the surrounding exon-intron context to derive genome-wide multi-species exon homologies at any evolutionary distance. We demonstrate its use in various evolutionary scenarios, from whole genome duplication to convergence of alternative splicing networks.

genomics↗

bioRxiv2020

Massive intron gain in the most intron-rich eukaryotes is driven by introner-like transposable elements of unprecedented diversity and flexibility

Spliceosomal introns, which interrupt nuclear genes and are removed from RNA transcripts by machinery termed spliceosomes, are ubiquitous features of eukaryotic nuclear genes [1]. Patterns of spliceosomal intron evolution are complex, with some lineages exhibiting virtually no intron creation while others experience thousands of intron gains [2-5]. One possibility is that this punctate phylogenetic distribution is explained by intron creation by Introner-Like Elements (ILEs), transposable elements capable of creating introns, with only those lineages harboring ILEs undergoing massive intron gain [6-10]. However, ILEs have been reported in only four lineages. Here we study intron evolution in dinoflagellates. The remarkable fragmentation of nuclear genes by spliceosomal introns reaches its apex in dinoflagellates, which have some twenty introns per gene [11,12]. Despite this, almost nothing is known about the molecular and evolutionary mechanisms governing dinoflagellate intron evolution. We reconstructed intron evolution in five dinoflagellate genomes, revealing a dynamic history of intron loss and gain. ILEs are found in 4/5 studied species. In one species, Polarella glacialis, we find an unprecedented diversity of ILEs, with ILE insertion leading to creation of some 12,253 introns, and with 15 separate families of ILEs accounting for at least 100 introns each. These ILE families range in mobilization mechanism, mechanism of intron creation, and flexibility of mechanism of intron creation. Comparison within and between ILE families provides evidence that biases in so-called intron phase, the distribution of introns relative to codon periodicity, are driven by ILE insertion site requirements [9,13,14]. Finally, we find evidence for multiple additional transformations of the spliceosomal system in dinoflagellates, including widespread loss of ancestral introns, and alterations in required, tolerated and favored splice motifs. These results reveal unappreciated intron creating elements diversity and spliceosomal evolutionary capacity, and suggest complex evolutionary dependencies shaping genome structures.

genomics↗

bioRxiv2020

Expansion and transformation of the minor spliceosomal system in the slime mold Physarum polycephalum

Spliceosomal introns interrupt nuclear genes and are removed from RNA transcripts ("spliced") by machinery called spliceosomes. While the vast majority of spliceosomal introns are removed by the so-called major spliceosome, diverse eukaryotes also contain a mysterious second form, the minor spliceosome, and associated introns [1-3]. In all characterized species, minor introns are distinguished by several features, including being rare in the genome ([~]0.5% of all introns) [4-6], containing extended evolutionary-conserved splicing sites [4,5,7,8], being generally ancient [9,10] and being inefficiently spliced [11-13]. Here, we report a remarkable exception in the slime mold Physarum polycephalum. The P. polycephalum genome contains > 20,000 minor introns--25 times more than any other species--with transformed splicing signals that have co-evolved with the spliceosome due to massive gain of efficiently spliced minor introns. These results reveal an unappreciated dynamism of minor spliceosomal introns and spliceosomal introns in general.

genomics↗

bioRxiv2020

Gene-rich X chromosomes implicate intragenomic conflict in the evolution of bizarre genetic systems

Haplodiploidy and paternal genome elimination (HD/PGE) are common in invertebrates, having evolved at least two dozen times, all from male heterogamety (i.e., systems with X chromosomes). However, why X chromosomes are important for the evolution of HD/PGE remains debated. The Haploid Viability Hypothesis posits that X-linked genes promote the evolution of male haploidy by facilitating purging recessive deleterious mutations. The Intragenomic Conflict Hypothesis holds that conflict between genes drives genetic system turnover; under this model, X-linked genes could promote the evolution of male haploidy due to conflicts with autosomes over sex ratios and genetic transmission. We studied lineages where we can distinguish these hypotheses: species with germline PGE that retain an XX/X0 sex determination system (gPGE+X). Because evolving PGE in these cases involves changes in transmission without increases in male hemizygosity, a high degree of X linkage in these systems is predicted by the Intragenomic Conflict Hypothesis but not the Haploid Viability Hypothesis. To quantify the degree of X linkage, we sequenced and compared 7 gPGE+X species genomes with 11 related species with typical XX/XY or XX/X0 genetic systems, representing three transitions to gPGE. We find highly increased X linkage in both modern and ancestral genomes of gPGE+X species compared to non-gPGE relatives, and recover a significant positive correlation between percent X linkage and the evolution of gPGE. These are among the first empirical results suggesting a role for intragenomic conflict in the evolution of novel genetic systems like HD/PGE. Significance StatementSex determination systems such as haplodiploidy, in which males gene transmission is haploid, are surprisingly common, however, the evolutionary paths to these systems are poorly understood. X chromosomes may play a particularly important role, either by increasing survival of males with only maternal genomes, or due to conflicts between X-chromosomal and autosomal genes. We studied X-chromosome gene richness in three arthropod lineages in which males are diploid as adults but only transmit their maternally-inherited haploid genome. We find that species with such atypical systems have far more X chromosomal genes than related diploid species. These results suggest that conflict between genetic elements within the genome drives the evolution of unusual sex determination systems.

evolutionary biology↗

bioRxiv2020

Analysis of fungal genomes reveals commonalities of intron loss/gain and functions in intron-poor species

Current evolutionary reconstructions predict that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes. However, some extant eukaryotes have few introns, raising the question as to why these few introns are retained. Here we have used recently available fungal genomes to address this question. Evolutionary reconstruction of intron presence and absence using 263 diverse fungal species support the idea that massive intron loss has occurred in multiple clades. The intron densities estimated in the fungal ancestral states differ from zero to 8.28 introns per one kbp of protein-coding gene. Massive intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts (0.01 and 0.05 introns/kbp on average, respectively), but also in diverse smuts and allies (e.g. Ustilago maydis, Meira miltonrushii and Malassezia globosa have 0.06, 0.10 and 0.20 introns/kbp, respectively). To investigate the roles of introns, we searched for their special characteristics using 1302 orthologous genes from eight intron-poor fungi. Notably, most of these introns are found close to the translation initiation codons. Our transcriptome and translatome data analyses showed that these introns are from genes with both higher mRNA expression and translation efficiency. Furthermore, these introns are common in specific classes of genes (e.g. genes involved in translation and Golgi vesicle transport), and rare in others (e.g. base-excision repair genes). Our study shows that fungal introns have a complex evolutionary history and underappreciated roles in gene expression.

evolutionary biology↗

bioRxiv2019

Reconstructing the complex evolutionary history of the fused Aco2 gene in fission yeast.

The Aco2 gene of Schizosaccharomyces pombe was formed by gene fusion between curious partners, namely genes encoding the enzyme aconitase and a mitochondrial ribosomal protein. In addition to a full-length transcript, a truncated mRNA encoding only the N-terminal aconitase domain is produced by polyadenylation at an internal site. Protein products of the gene are found in the nucleus, mitochondria and cytoplasm, consistent with the presence of multiple subcellular targeting signals. To reconstruct the evolution of this complex gene, we studied homologous genes from a range of related species. We find evidence for a dynamic history within Taphrinomycotina, including: early evolution of a nuclear localization signal; creation of a 3 intron that could be involved in regulating subcellular targeting; evolution of multiple peroxisomal targeting signals in different lineages; and recurrent gene loss. We present a likely stepwise model for the evolution of this remarkable gene and discuss alternative scenarios.

bioinformatics↗

bioRxiv2019

Updated Database and Evolutionary Dynamics of U12-Type Introns

During nuclear maturation of most eukaryotic pre-messenger RNAs and long non-coding RNAs, introns are removed through the process of RNA splicing. Different classes of introns are excised by the U2-type or the U12-type spliceosomes, large complexes of small nuclear ribonucleoprotein particles and associated proteins. We created intronIC, a program for assigning intron class to all introns in a given genome, and used it on 24 eukaryotic genomes to create the Intron Annotation and Orthology Database (IAOD). We then used the data in the IAOD to revisit several hypotheses concerning the evolution of the two classes of spliceosomal introns, finding support for the class conversion model explaining the low abundance of U12-type introns in modern genomes.

genomics↗