Biology subjects

Unckless, R. L.

Publications and source records attributed to Unckless, R. L..

At least 19 recordsLinked to original sources

bioRxiv2026

Tropism of Drosophila innubila Nudivirus in Cell Culture and in Tissues

Most viruses are successful because they can infect and exploit specific host tissues for reproduction and transmission. As a result, we often classify viruses by their ability to infect different tissues: respiratory, reproductive and gut, for example. Thus, knowing the tissue and cellular tropism of a virus may elucidate aspects of its biology including routes of transmission and virulence. We studied tropism of the Drosophila innubila Nudivirus (DiNV) in cells and infected hosts. DiNV is a nudivirus, a family of viruses related to the baculoviruses that are relatively large (150-200 nm), contain large double-stranded DNA genomes, and infect different host tissues. Cultured cells stained with an antibody against the DiNV nucleocapsid demonstrated punctate staining in the cytoplasm by confocal microscopy. Electron micrographs of infected cells, on the other hand demonstrated that virions are present in the nucleus. After purification, DiNV was often associated with multimembrane-like vesicles as described for Oryctes rhinoceros nudivirus. We examined tropism in hosts first by sagittal section and found most virus associated with the gut and, to a lesser extent, reproductive tissues. Upon dissection and electron microscopy, we found that DiNV in the gut is primarily in the visceral muscle of the gut and not the lumen as might be expected for a virus if transmitted fecal-orally.

microbiology↗

bioRxiv2026

Fly Viral Atlas: A single-nucleus transcriptomic atlas of RNA viruses and transposable elements (TEs) in Drosophila melanogaster

Drosophila RNA viruses often persist in wild and lab populations, yet their tissue and cellular tropism is poorly understood. In the Fly Cell Atlas (a comprehensive Drosophila single-nucleus transcriptome) data, we detected four RNA virus infections: Nora virus, Drosophila A virus, Drosophila C virus, and Newfield virus. Nora and Drosophila A virus were the most abundant and widespread across tissues and cell types, while Drosophila C virus and Newfield virus RNA transcript were only found in oenocyte and fat body tissues. We found transcriptional changes associated with viral infection in canonical viral immunity genes (e.g. Vago, vir-1). Additionally, we observed that during persistent viral infections, transposable element (TE) transcripts were upregulated in somatic cells. TEs are traditionally associated with the germline, but recent studies and our data suggest they are also expressed in somatic cells. Using the Fly Cell Atlas data, we found that distinct somatic cell types express specific TE subtypes, indicating regulated and cell-type specific TE activity often overlooked in transcriptomic studies. We present Fly Viral Atlas (https://flyviralatlas.shinyapps.io/home/), a single-nucleus level atlas of RNA viruses and TE expressions in Drosophila, providing new insights into viral tropism and TE dynamics across cell types and tissues.

genomics↗

bioRxiv2026

Persistent viral infection in the Drosophila fat body is associated with immune activation at the single-cell level

BackgroundViruses are ubiquitous and can spread in two main ways: vertically, which involves transmission through or associated with gametes, and horizontally, which occurs through direct contact, airborne transmission, or indirect contact, such as through ingestion. Vertically transmitted, low virulence viruses can go undetected by both the immune system and researchers, and cause chronic, asymptomatic infections. In many Drosophila studies, researchers are unaware or ambivalent about the fact that the flies used may be infected with persistent viruses. Although they often have minimal or no observable fitness costs in laboratory fly samples, recent studies suggest that an increase in viral titer is associated with a decrease in lifespan. ResultsIn this study, we explored changes in expression occurring during these cryptic virus infections. To achieve this, we utilized publicly accessible single-nuclear RNA sequencing (snRNA-seq) data of the Drosophila fat body, where we detected persistent infections of Nora and Drosophila A virus. We observed that Nora virus and Drosophila A virus exhibit broad cell-type tropism in the Drosophila fat body, and when coinfected, Drosophila A virus showed higher viral titer and cell infection rate. Transcriptomic analysis revealed substantial immune pathway alterations: Nora virus is broadly associated with upregulation of immune pathways (IMD, Toll), whereas Drosophila A virus is associated with downregulation of specific Toll pathway effector genes. Additionally, the expression of somatic transposable element (TE) transcripts was associated with viral infection, showing mating status-dependent patterns with downregulation in Nora virus-infected virgin flies and upregulation in mated flies for both viruses. ConclusionsOverall, our results indicate that cryptic and persistent viral infections in Drosophila elicit transcriptional changes in the fat body, including activation of immune responses, and are associated with dysregulation of TE activity in somatic fat body cells.

genomics↗

bioRxiv2025

Drive, suppression, and escape from suppression of a selfish chromosome

Meiotic drivers are selfish chromosomes that are predicted to spark a rapid intragenomic arms-race with their suppressors. However, the long-term persistence of unsuppressed selfish chromosomes in natural populations violates these theoretical expectations. The Drosophila pseudoobscura Sex-Ratio (SR) chromosome exemplifies this problem, sometimes referred to as the "ancient gene drive paradox". Here, we reconstruct the evolutionary history of this SR chromosome and show that its genetic architecture and complexity has been shaped by a history of drive, suppression, and escape from suppression. Our results indicate that the current lack of resistance to the SR chromosome represents a transient condition awaiting the emergence of new suppressors. SIGNIFICANCEIntragenomic arms races triggered by selfish chromosomes are expected to drive rapid evolution through cycles of drive, suppression, and escape from suppression. Despite these expectations, some selfish chromosomes such as the D. pseudoobscura Sex-Ratio (SR) chromosome exist unsuppressed for extended periods of time. Despite the absence of suppression, we uncover currently segregating suppressors against the ancestral version and evidence of recent dynamic evolution on the SR chromosome. Todays SR chromosome thus represents a transient state in a surprisingly slow arms race. Taken together, the lack of suppressors against this selfish chromosome can be explained by mutational limits for the emergence of suppressors.

evolutionary biology↗

bioRxiv2025

The study of the Drosophila innubila Nudivirus in cells and flies

2.Species of the fruit fly, Drosophila, are essential models for investigating host/virus interactions. Research aimed at understanding how hosts mount immune defenses against viruses and how viruses evade those immune defenses relies on host/virus pairs that have evolved together overtime, thus necessitating a need for a DNA virus model system for Drosophila with a virus that naturally infects the host. The Drosophila innubila Nudivirus (DiNV) is an emerging model system poised to take on the role as the DNA virus model for Drosophila. In this paper we describe the development of the DiNV model system with animal and cellular resources. We describe the development of new Drosophila cell lines, virus titration assays, anti-nucleocapsid antibodies, and injection-based DiNV infections in Drosophila innubila. We find that D. innubila cells can be used to grow DiNV for use in further experiments, and that DiNV is highly virulent when injected into adult D. innubila. The resources we have developed enable substantial future research on the DiNV-D. innubila system. 3. Impact statementDNA viruses are the cause of several important and challenging human diseases including hepatitis B, mononucleosis, respiratory disease, gastroenteritis, herpes and chickenpox. Recently there has even been a resurgence of many viral infections due to decreasing rates of vaccination, so to develop better therapeutics and intervention strategies, we must better understand the dynamics of how hosts and DNA viruses interact. The development of a natural DNA virus model in Drosophila creates the opportunity to better understand host/DNA virus interaction. 4. Data summaryAll data and code are available at in our Github repository: available upon publication

microbiology↗

bioRxiv2025

Antagonistic kinesin-14s within a single chromosomal drive haplotype

In maize, there are two meiotic drive systems that operate on large tandem repeat arrays called knobs that are found on chromosome arms. One meiotic drive haplotype, Abnormal chromosome 10 (Ab10), encodes two kinesin proteins that interact with two distinct tandem repeat arrays in a sequence-specific manner to confer meiotic drive. The kinesin KINDR associates with knob180 repeats while the kinesin TRKIN associates with TR-1 repeats. Prior data show that meiotic drive is conferred primarily by the KINDR/knob180 system, with the TRKIN/TR-1 system having little or no role. The second meiotic drive haplotype, K10L2, shows low levels of meiotic drive and only encodes the TRKIN/TR-1 system. Here we used long-read sequencing to assemble the K10L2 haplotype and showed that it has strong homology to an internal portion of the Ab10 haplotype. We also carried out CRISPR mutagenesis of Trkin to test the role of Trkin on Ab10 and K10L2. The data indicate that the Trkin gene on Ab10 does not improve drive or fitness but instead has a weak deleterious effect when paired with a normal chromosome 10. The deleterious effect is more severe when Ab10 is paired with K10L2: in this context functional Trkin on either chromosome nearly abolishes Ab10 drive. We modeled the effect of Trkin on Ab10 and found it should not persist in the population. We conclude that Trkin either confers an advantage to Ab10 in untested circumstances or that it is in the process of being purged from the Ab10 population. ARTICLE SUMMARYMendels first law states that paired chromosomes are transmitted through meiosis at equal frequencies. Some chromosome variants, however, are transmitted at higher frequencies in a process called meiotic drive. We wanted to know the function of a motor protein called TRKIN that is encoded on a maize meiotic drive chromosome. Surprisingly, we found that TRKIN provides no advantage to the meiotic driver and instead seems to be deleterious, suggesting it had a function in a wild ancestor but is now being purged from the population. The results illustrate how genomes are shaped by often-conflicting forces of selection and selfish genetic elements.

evolutionary biology↗

bioRxiv2023

Meiotic drive, postzygotic isolation, and the Snowball Effect

AO_SCPLOWBSTRACTC_SCPLOWAs populations diverge, they accumulate incompatibilities which reduce gene flow and facilitate the formation of new species. Simple models suggest that the genes that cause Dobzhansky-Muller incompatibilities should accumulate at least as fast as the square of the number of substitutions between taxa, the so-called snowball effect. We show, however, that in the special-- but possibly common-- case in which hybrid sterility is due primarily to cryptic meiotic (gametic) drive, the number of genes that cause postzygotic isolation may increase nearly linearly with the number of substitutions between species.

evolutionary biology↗

bioRxiv2023

Germline novelty through recurrent copy-number, protein, and regulatory evolution of the synaptonemal complex

The synaptonemal complex (SC) is a protein-rich structure essential for meiotic recombination and faithful chromosome segregation. Acting like a zipper to paired chromosomes during early prophase, the complex consists of central elements bilaterally tethered by the transverse filaments to the lateral elements anchored on either side to the homologous chromosome axes. Despite being found in most major eukaryotic taxa implying a deeply conserved evolutionary origin, several components of the complex exhibit unusually high rates of sequence turnover. This is puzzlingly exemplified by the SC of Drosophila, where the central elements and transverse filaments display no identifiable homologs outside of the genus. Here, we exhaustively examine the evolutionary history of the SC in Drosophila taking a comparative phylogenomic approach with high species density to circumvent obscured homology due to rapid sequence evolution. Contrasting starkly against other genes involved in meiotic chromosome pairing, SC significantly shows elevated rates of coding evolution due to a combination of relaxed constraint and recurrent, widespread positive selection. In particular, the central element cona and transverse filament c(3)G have diversified through tandem and retro-duplications, repeatedly generating paralogs that likely have novel germline functions. In a striking case of molecular convergence, c(3)G paralogs that independently arose in distant lineages evolved under positive selection to have convergent truncations to the protein termini and elevated testes expression. Surprisingly, the expression of SC genes in the germline is exceedingly prone to change suggesting recurrent regulatory evolution which, in many species, resulted in high testes expression even though Drosophila males are achiasmic. Overall, our study recapitulates the poor conservation of SC components, and further uncovers that the lack of conservation extends to other modalities including copy number, genomic locale, and germline regulation. Considering the elevated testes expression in many Drosophila species and the common ancestor, we suggest that the function of SC genes in the male germline, while still poorly understood, may be a prime target of constant evolutionary pressures driving repeated adaptations and innovations. SummaryThe synaptonemal complex (SC) is essential for meiotic recombination and faithful chromosome segregation across eukaryotes, yet components of the SC are often poorly conserved. Here we show that across the Drosophila phylogeny several SC genes have evolved under recurrent positive selection resulting in orthologs that are barely recognizable. This is partly driven duplications repeatedly generating paralogs that may have adopted novel germline functions, often in the testes. Unexpectedly, while most SC genes are thought to be dispensable in the male germline where recombination is absent in Drosophila, elevated testes expression appears to be the norm across the genus and likely the ancestral state. The evolutionary lability of SC genes in Drosophila is likely a repeated source of adaptive innovations in the germline.

evolutionary biology↗

bioRxiv2023

Modeling the Evolution of Populations with Multiple Killer Meiotic Drivers

Meiotic drivers are selfish genetic loci that can be transmitted to more than half of the viable gametes produced by a heterozygote. This biased transmission gives meiotic drivers an evolutionary advantage that can allow them to spread over generations until all members of a population carry the driver. This evolutionary power can also be exploited to modify natural populations using synthetic drivers known as gene drives. Recently, it has become clear that natural drivers can spread within genomes to birth multicopy gene families. To understand intragenomic spread of drivers, we model the evolution of two distinct meiotic drivers in a population. We employ the wtf killer meiotic drivers from Schizosaccharomyces pombe, which are multicopy in all sequenced isolates, as models. We find that a duplicate wtf driver identical to the parent gene can spread in a population unless, or until, the original driver is fixed. When the duplicate driver diverges to be distinct from the parent gene, we find that both drivers spread to fixation under most conditions. Finally, we show that stronger drivers make weaker drivers go extinct in most, but not all, polymorphic populations with absolutely linked drivers. These results reveal the strong potential for natural meiotic drive loci to duplicate and diverge within genomes. Our findings also highlight duplication potential as a factor to consider in the design of synthetic gene drives.

evolutionary biology↗

bioRxiv2023

Wolbachia enhances the survival of Drosophila infected with fungal pathogens

Wolbachia bacteria of arthropods are at the forefront of basic and translational research on multipartite host-symbiont-pathogen interactions. These microbes are vertically inherited from mother to offspring via the cytoplasm. They are the most widespread endosymbionts on the planet due to their infamous ability to manipulate the reproduction of their hosts to spread themselves in a population, and to provide a variety of fitness benefits to their hosts. Importantly, some strains of Wolbachia can inhibit viral pathogenesis within and between arthropod hosts. Mosquitoes carrying the wMel Wolbachia strain of Drosophila melanogaster have a greatly reduced capacity to spread viruses like dengue and Zika to humans. Therefore, Wolbachia are the basis of several global vector control initiatives. While significant research efforts have focused on viruses, relatively little attention has been given to Wolbachia-fungal interactions despite the ubiquity of fungal entomopathogens in nature. Here, we demonstrate that Wolbachia increase the longevity of their Drosophila melanogaster hosts when challenged with a spectrum of yeast and filamentous fungal pathogens. We find that this pattern can vary based on host genotype, sex, and fungal species. Further, Wolbachia correlates with higher fertility and reduced pathogen titers during initial fungal infection, indicating a significant fitness benefit. This study demonstrates Wolbachias role in diverse fungal pathogen interactions and determines that the phenotype is broad, but with several variables that influence both the presence and strength of the phenotype. These results enhance our knowledge of the strategies Wolbachia uses that likely contribute to such a high global symbiont prevalence. ImportanceWolbachia bacteria of arthropods are at the forefront of global initiatives to fight arthropod-borne viruses. Despite great success in using the symbiont to fight viruses, little research has focused on Wolbachia-fungal interactions. Here, we find that Wolbachia of Drosophila melanogaster, the same strain widely used in antiviral initiatives, can also increase the longevity of flies systemically infected with a panel of yeast and filamentous fungal pathogens. The symbiont also partially increases host fertility and reduces fungal titers during early infection, indicating a significant fitness benefit. This represents a major step forward in Wolbachia research since its pathogen blocking abilities can now be extended to a broad diversity of another major branch of microbial life. This discovery may inform basic research on pathogen blocking and has potential translational applications in areas including biocontrol in agriculture.

microbiology↗

bioRxiv2023

A single amino acid polymorphism in natural Metchnikowin alleles of Drosophila results in systemic immunity and life history tradeoffs

Antimicrobial peptides (AMPs) are at the interface of interactions between hosts and microbes and are therefore expected to be fast evolving in a coevolutionary arms race with pathogens. In contrast, previous work demonstrated that one AMP, Metchikowin (Mtk), has a single residue that segregates as either proline (P) or arginine (R) in populations of four different Drosophila species, some of which diverged more than 10 million years ago. The recurrent finding of this polymorphism regardless of geography or host species, coupled with evidence of balancing selection in Drosophila AMPs, suggest there is a distinct functional importance to each allele. The most likely hypotheses involve alleles having specificity to different pathogens or the more potent allele conferring a cost on the host. To assess their functional differences, we created D. melanogaster lines with the P allele, R allele, or Mtk null mutation using CRISPR/Cas9 genome editing. Here, we report results from experiments assessing the two hypotheses using these lines. In males, testing of systemic immune responses to a repertoire of bacteria and fungi demonstrated that the R allele performs as well or better than the P and null alleles with most infections. With some pathogens, however, females show results in contrast with males where Mtk alleles either do not contribute to survival or where the P allele outperforms the R allele. In addition, measurements of life history traits demonstrate that the R allele is more costly in the absence of infection for both sexes. These results provide strong in vivo evidence that differential fitness with or without infection and sex-based functional differences in alleles may be adaptive mechanisms of maintaining immune gene polymorphisms in contrast with expectations of rapid evolution. Therefore, a complex interplay of forces including pathogen species and host sex may lead to balancing selection for immune genotypes. Strikingly, this selection may act on even a single amino acid polymorphism in an AMP.

genetics↗

bioRxiv2022

The genetic basis of variation immune defense against Lysinibacillus fusiformis infection in Drosophila melanogaster

The genetic causes of phenotypic variation often differ depending on the population examined, particularly if the populations were founded by relatively small numbers of genotypes. Similarly, the genetic causes of phenotypic variation among similar traits (resistance to different xenobiotic compounds or pathogens) may also be completely different or only partially overlapping. Differences in genetic causes for variation in the same trait among populations suggests considerable context dependence for how selection might act on those traits. Similarities in the genetic causes of variation for different traits, on the other hand, suggests pleiotropy which also would influence how natural selection would shape variation in a trait. We characterized immune defense against a natural Drosophila pathogen, the Gram-positive Lysinibacillus fusiformis, in three different populations and found almost no overlap in the genetic architecture of variation in survival post infection. However, when comparing our results to a similar experiment with the fungal pathogen, B. bassiana, we found a convincing shared QTL peak for both pathogens. This peak contains the Bomanin cluster of Drosophila immune effectors. RNAi knockdown experiments confirms a role of some of these genes in immune defense against both pathogens. This suggests that natural selection may act on the entire cluster of Bomanin genes (and the linked region under the QTL) or specific peptides for specific pathogens. Author SummaryLike most traits, the way individuals respond to infection vary among individuals within a population. Some of this variation is caused by genetic differences in the host organism. Over the past decade, two prominent resources were developed to assess genetic variation for complex traits of the fruit fly, Drosophila melanogaster and map the genetic variants responsible. We recently described a strain of Lysinibacillus fusiformis bacteria, which was isolated from fruit flies and is moderately virulent when flies are infected. We mapped genetic variation in resistance L. fusiformis using these mapping resources. We find that among the resources, different changes were associated with immune defense. However, we also found that within a resource, the same region of the genome was associated with resistance to both L. fusiformis and a fungal pathogen. These results suggest that different populations adapt differently to the same pathogens, but two distinct pathogens share similar causes of genetic variation within a single population.

genetics↗

bioRxiv2022

Hoisted with his own petard: how sex-ratio meiotic drive in Drosophila affinis creates resistance alleles that limit its spread

Meiotic drivers are selfish genetic elements that tinker with gametogenesis to bias their own transmission into the next generation of offspring. Such tinkering can have significant consequences on gametogenesis and end up hampering the spread of the driver. In Drosophila affinis, sex-ratio meiotic drive is caused by an X-linked complex that, when in males with a susceptible Y chromosome, results in broods that are typically more than 95% female. Interestingly, D. affinis males lacking a Y chromosome (XO) are fertile and males with the meiotic drive X and no Y produce only sons - effectively reversing the sex-ratio effect. Here, we show that meiotic drive dramatically increases the rate of nondisjunction of the Y chromosome (at least 750X), meaning that the driver is creating resistant alleles through the process of driving. We then model how the O might influence the spread, dynamics and equilibrium of the sex-ratio X chromosome. We find that the O can prevent the spread or reduce the equilibrium frequency of the sex-ratio X chromosome and it can even lead to oscillations in frequency. Finally, with reasonable parameters, the O is unlikely to lead to the loss of the Y chromosome, but we discuss how it might lead to sex-chromosome turnover indirectly.

evolutionary biology↗

bioRxiv2021

Induction and inhibition of Drosophila X chromosome gene expression are both impeded by the dosage compensation complex

Sex chromosomes frequently differ from the autosomes in the frequencies of genes with sexually dimorphic or tissue-specific expression. Multiple hypotheses have been put forth to explain the unique gene content of the X chromosome, including selection against male-beneficial X-linked alleles, expression limits imposed by the haploid dosage of the X in males, and interference by the dosage compensation complex (DCC) on expression in males. Here, we investigate these hypotheses by examining differential gene expression in Drosophila melanogaster following several treatments that have widespread transcriptomic effects: bacterial infection, viral infection, and abiotic stress. We found that genes that are induced (up-regulated) by these biotic and abiotic treatments are frequently under-represented on the X chromosome, but so are those that are repressed (down-regulated) following treatment. We further show that whether a gene is bound by the DCC in males can largely explain the paucity of both up- and down-regulated genes on the X chromosome. Specifically, genes that are bound by the DCC, or close to a DCC high-affinity site, are unlikely to be up- or down-regulated after treatment. This relationship, however, could partially be explained by a correlation between differential expression and breadth of expression across tissues. Nonetheless, our results suggest that DCC binding, or the associated chromatin modifications, inhibit both up- and down-regulation of X chromosome gene expression within specific contexts. We propose multiple possible mechanisms of action for the effect, including a role of Males absent on the first (Mof), a component of the DCC, as a dampener of gene expression variance in both males and females. This effect could explain why the Drosophila X chromosome is depauperate in genes with tissue-specific or induced expression, while the mammalian X has an excess of genes with tissue-specific expression.

genomics↗

bioRxiv2020

Rapid evolution and horizontal gene transfer in the genome of a male-killing Wolbachia

Wolbachia are widespread bacterial endosymbionts that infect a large proportion of insect species. While some strains of this bacteria do not cause observable host phenotypes, many strains of Wolbachia have some striking effects on their hosts. In some cases, these symbionts manipulate host reproduction to increase the fitness of infected, transmitting females. Here we examine the genome and population genomics of a male-killing Wolbachia strain, wInn, that infects Drosophila innubila mushroom-feeding flies. We compared wInn to other closely-related Wolbachia genomes to understand the evolutionary dynamics of specific genes. The wInn genome is similar in overall gene content to wMel, but also contains many unique genes and repetitive elements that indicate distinct gene transfers between wInn and non-Drosophila hosts. We also find that genes in the Wolbachia prophage and Octomom regions are particularly rapidly evolving, including those putatively or empirically confirmed to be involved in host pathogenicity. Of the genes that rapidly evolve, many also show evidence of recent horizontal transfer among Wolbachia symbiont genomes, suggesting frequent movement of rapidly evolving regions among individuals. These dynamics of rapid evolution and horizontal gene transfer across the genomes of several Wolbachia strains and divergent host species may be important underlying factors in Wolbachias global success as a symbiont.

genomics↗

bioRxiv2020

Atypical meiosis can be adaptive in outcrossed S. pombe due to wtf meiotic drivers

Killer meiotic drivers are genetic parasites that destroy sibling gametes lacking the driver allele. The fitness costs of drive can lead to selection of unlinked suppressors. This suppression could involve evolutionary tradeoffs that compromise gametogenesis and contribute to infertility. Schizosaccharomyces pombe, an organism containing numerous gamete-killing wtf drivers, offers a tractable system to test this hypothesis. Here, we demonstrate that in scenarios analogous to outcrossing, wtf drivers generate a fitness landscape in which atypical gametes, such as aneuploids and diploids, are advantageous. In this context, wtf drivers can decrease the fitness cost of mutations that disrupt meiotic fidelity and, in some circumstances, can even make such mutations beneficial. Moreover, we find that S. pombe isolates vary greatly in their ability to make haploid gametes, with some isolates generating more than 25% aneuploid or diploid gametes. This work empirically demonstrates the potential for meiotic drivers to shape the evolution of gametogenesis.

evolutionary biology↗

bioRxiv2020

A comparative analysis of Caenorhabditis and Drosophila transcriptional changes in response to pathogen infection

Drosophila melanogaster and Caenorhabditis elegans are well-used invertebrate models for studying the innate immune system. The organisms are susceptible to bacterial pathogens that include Pseudomonas species, (entomophilia - Drosophila) or (aeruginosa - Caenorhabditis), E. faecalis and P. rettgeri, which are or are related to human pathogens. Further, the consequences of exposure to these pathogens, in terms of organismal survival, are roughly equivalent when compared. That is, worms and flies are more susceptible to infection by Pseudomonas than E. faecalis, whereas organismal survival on E. faecalis and P. rettgeri are roughly the same in both. To better understand how these organisms are coordinating their responses to these bacterial pathogens we examined transcriptomes in infected animals. We grouped our analysis based on protein orthology. Of the 3611 pairs analyzed, we found genes whose responses were conserved across the different species at a higher than expected rate for two of the three pathogens. Interestingly within the animals, genes with 1:1 orthologs between species behaved differently. Such genes were more likely to be expressed in D. melanogaster, and less likely to be expressed in C. elegans. From this analysis we found that the gene nucleobindin (nucb-1/NUCB1 in C. elegans and D. melanogaster, respectively) was upregulated in both species in response to Gram negative bacteria. We used RNAi to knock down nucb-1 and found the treated animals were more susceptible to infection by the Gram negative pathogen P. rettgeri than controls. These results provide insight into some of the conserved mechanisms of pathogen defense, but also suggest that these divergent organisms have evolved specific means to orchestrate the defense against pathogens. Article SummaryWe analyzed transcriptomic data from C. elegans and D. melanogaster to compare the expression of orthologous pairs of genes in response to bacterial pathogens. Our results indicated that only a handful of genes that are orthologous between species are differentially expressed in response to pathogens, but that the pattern of expression was different when comparing one-to-one orthologs versus those that are restricted to one of the two organisms. These results suggest that, although broad patterns of susceptibility to bacterial pathogens are conserved, the regulatory framework by which the organisms fight pathogens is less well conserved. Further our results suggest a more complete analysis of the evolutionary changes in organismal responses to pathogens is required.

genetics↗

bioRxiv2019

A Simple Deep Learning Approach for Detecting Duplications and Deletions in Next-Generation Sequencing Data

Copy number variants (CNV) are associated with phenotypic variation in several species. However, properly detecting changes in copy numbers of sequences remains a difficult problem, especially in lower quality or lower coverage next-generation sequencing data. Here, inspired by recent applications of machine learning in genomics, we describe a method to detect duplications and deletions in short-read sequencing data. In low coverage data, machine learning appears to be more powerful in the detection of CNVs than the gold-standard methods or coverage estimation alone, and of equal power in high coverage data. We also demonstrate how replicating training sets allows a more precise detection of CNVs, even identifying novel CNVs in two genomes previously surveyed thoroughly for CNVs using long read data.\n\nAvailable at: https://github.com/tomh1lll/dudeml

bioinformatics↗