Biology subjects

Hoffmann, F. G.

Publications and source records attributed to Hoffmann, F. G..

At least 19 recordsLinked to original sources

bioRxiv2026

Differential Gene Expression in the Tropical House Cricket and Its Iridovirus in Healthy versus Diseased Specimens

The tropical house cricket, Gryllodes sigillatus, is a mass-produced insect that is used as a protein source for pets and livestock. However, intensive mass-rearing conditions, coupled with high genetic relatedness, create an ideal environment for the spread of pathogenic microbes that severely impact production. Cricket iridovirus (CrIV) is a pathogen that impedes cricket growth and causes significant losses for cricket farmers. Interestingly, recent studies have shown that CrIV is often present asymptomatically, yet the molecular basis of the emergence of disease symptoms remains unknown. To address this, we sampled healthy and diseased crickets and examined differences in cricket and CrIV gene expression via RNAseq. Using differential gene expression analysis and functional enrichment analysis, we found significant differences in host and viral gene expression between healthy and diseased crickets, including genes involved in immunity. Interestingly, while we observed high CrIV gene expression across the entire CrIV genome in sick populations, healthy asymptomatic populations showed elevated expression at a single viral locus. Our results shed light not only on the cricket immune response to CrIV infection but also identify a viral gene that is highly expressed during covert infections, suggesting its potential role in suppressing the hosts immune response. These findings enhance our understanding of how CrIV interacts with our cricket host, providing essential insights for developing targeted strategies to manage CrIV outbreaks in cricket mass-rearing facilities.

bioinformatics↗

bioRxiv2025

A Deep Dive into the Globin Superfamily of Sharks, Skates, and Rays: Contrasting patterns of gene loss and retention relative to bony vertebrates

The globin gene superfamily encodes oxygen-binding proteins that are present in all domains of life. Hemoglobins and myoglobins of jawed vertebrates are among the most well-studied proteins in the context of structure-function relationships and evolution after gene duplication. However, these studies have primarily focused on bony vertebrates, and research on globin gene evolution in cartilaginous fish has been limited by a lack of genomic resources. In this study, we leverage newly available cartilaginous fish genomes to investigate globin gene family evolution across skates, rays, sharks, and sawfish. We found that, when present, most globin genes are in a single copy, with androglobin, globin-Y, and myoglobin present in all cartilaginous fish, while the two globin-X genes were differentially retained between the Holocephali and sharks, skates, and rays. Neuroglobin appears to have been lost at the common ancestor of all cartilaginous fish. The - and {beta}-globin gene subfamilies underwent independent expansions in different lineages of cartilaginous fish. Most cartilaginous fish globins have conserved synteny with other jawed vertebrates except myoglobin. Additionally, NPRL3, which directly flanks the hemoglobin clusters of other jawed and jawless vertebrates and regulates hemoglobin gene expression, is on a separate chromosome from the hemoglobin clusters of cartilaginous fish. When we examined globin gene expression patterns across cartilaginous fish tissues and developmental stages, we found that most globins are expressed as expected compared to other jawed vertebrates. However, hemoglobin paralogs are more widely expressed in embryonic tissues compared to later-stage tissues in cases where many copies exist. Our results reveal similar and contrasting patterns of globin gene evolution between cartilaginous and bony vertebrates and shed light on the early stages of globin gene evolution in gnathostomes. Significance StatementThe evolution of the globin gene family in jawed vertebrates is of significant interest; however, most studies have been limited to bony vertebrates. With the influx of new publicly available cartilaginous fish genomes, we conducted the most comprehensive analysis of globin gene evolution in cartilaginous fish to date using phylogenetic, structural, and transcriptomic analyses. Our results shed light on similar and contrasting patterns of globin-gene evolution between cartilaginous and bony vertebrates and provide insight into the early evolution of globins in jawed vertebrates. Key-words: Globins, Cartilaginous Fish, Chondrichthyes, Gene Family Evolution

evolutionary biology↗

bioRxiv2025

Historical Contingency Shapes Toxin Resistance in a Specialist Avian Predator

Adaptations to toxic diets can cascade through ecosystems, altering physiology, species interactions, and trophic dynamics. To uncover the molecular basis of toxin resistance in the black-headed grosbeak (Pheucticus melanocephalus), a specialist predator of cardiotonic steroid-defended monarch butterflies (Danaus plexippus), we investigated the evolution of target-site insensitivity in the toxins molecular target - the Na,K-ATPase. Functional assays of engineered Na,K-ATPases revealed that resistance in grosbeaks arises from a non-additive interaction between a substitution at position 111 (Q111E) and up to six nearby amino acid changes in the first extracellular loop of the protein. Using resurrected ancestral proteins, we show that the earliest of these six substitutions to evolve (V113L) altered the functional effects of Q111E, such that Q111E alone became maladaptive. Only after the accumulation of additional permissive substitutions could Q111E confer resistance, highlighting how intramolecular epistatic interactions and historical contingency constrained the evolutionary path to adaptation. Our phylogenetic analysis of Na,K-ATPase sequences from 360 birds further revealed that several of the specific grosbeak substitutions--particularly at sites 112, 114, and 116--show strong signatures of co-evolution with changes at site 111 across the avian tree, supporting the hypothesis that resistance evolves through repeated, interacting changes. Together, these results reveal the molecular mechanisms of convergent evolution of toxin resistance and demonstrate how genetic background can shape evolutionary outcomes across trophic levels.

evolutionary biology↗

bioRxiv2024

Temperature and Pressure Shaped the Evolution of Antifreeze Proteins in Polar and Deep Sea Zoarcoid Fishes

Antifreeze proteins (AFPs) have enabled teleost fishes to repeatedly colonize polar seas. Four AFP types have convergently evolved in several fish lineages. AFPs inhibit ice crystal growth and lower cellular freezing point. In lineages with AFPs, species inhabiting colder environments may possess more AFP copies. Elucidating how differences in AFP copy number evolve is challenging due to the genes tandem array structure and consequently poor resolution of these repetitive regions. Here we explore the evolution of type III AFPs (AFP III) in the globally distributed suborder Zoarcoidei, leveraging six new long-read genome assemblies. Zoarcoidei has fewer genomic resources relative to other polar fish clades while it is one of the few groups of fishes adapted to both the Arctic and Southern Oceans. Combining these new assemblies with additional long-read genomes available for Zoarcoidei, we conducted a comprehensive phylogenetic test of AFP III evolution and modeled the effects of thermal habitat and depth on AFP III gene family evolution. We confirm a single origin of AFP III via neofunctionalization of the enzyme sialic acid synthase B and show that AFP copies expanded under low temperature, but also decreased with depth, which reduces freezing point via pressure. Associations between the environment and AFP III copy number were driven by duplications of paralogs that were translocated out of the ancestral locus at which Zoarcoidei AFP arose. Our results reveal novel environmental effects on AFP evolution and demonstrate the value of high-quality genomic resources for studying how structural genomic variation shapes convergent adaptation.

evolutionary biology↗

bioRxiv2024

Horizontally transferred glycoside hydrolase 26 may aid hemipteran insects in plant tissue digestion

Glycoside hydrolases are enzymes that break down complex carbohydrates into simple sugars by catalyzing the hydrolysis of glycosidic bonds. There have been multiple instances of adaptive horizontal gene transfer of genes belonging to various glycoside hydrolase families from microbes to insects, as glycoside hydrolases can metabolize constituents of the carbohydrate-rich plant cell wall. In this study, we characterize the horizontal transfer of a gene from the glycoside hydrolase family 26 (GH26) from bacteria to insects of the order Hemiptera. Our phylogenies trace the horizontal gene transfer to the common ancestor of the superfamilies Pentatomoidea and Lygaeoidea, which include stink bugs and seed bugs. After horizontal transfer, the gene was assimilated into the insect genome as indicated by the gain of an intron, and a eukaryotic signal peptide. Subsequently, the gene has undergone independent losses and expansions in copy number in multiple lineages, suggesting an adaptive role of GH26s in some insects. Finally, we measured tissue-level gene expression of multiple stink bugs and the large milkweed bug using publicly available RNA-seq datasets. We found that the GH26 genes are highly expressed in tissues associated with plant digestion, especially in the principal salivary glands of the stink bugs. Our results are consistent with the hypothesis that this horizontally transferred GH26 was co-opted by the insect to aid in plant tissue digestion and that this HGT event was likely adaptive.

evolutionary biology↗

bioRxiv2024

Detection of known and novel virus sequences in the black solider fly and expression of host antiviral pathways

Mass rearing of animals in close quarters can be highly conducive to microbe transmission, including pathogens. This has been shown multiple times in the case of important industrial insects such as crickets, silkworms, and honeybees. One industrial insect of increasing importance is the black soldier fly (Diptera: Hermetia illucens), as it can convert organic waste into high quality protein and fatty acids. Along with this, they take up far less space than traditional protein sources, as millions of black soldier flies can be reared in a relatively small facility. Because of this, there is a growing interest in the pathogens that could impact black soldier fly rearing efforts. So far, only three black soldier fly-associated viruses have been identified. We used metatranscriptomic sequencing to survey black soldier fly guts, frass, and diet for viruses. We detected sequences from two novel viruses. One, which we name Hermetia illucens sigma-like virus 1, is phylogenetically related to viruses of the genus Sigmavirus, which have been highly studied in Drosophila. The other novel virus, which we name Hermetia illucens toti-like virus 2, is the second toti-like virus to be described in the black soldier fly. We also detected two black soldier fly-associated viruses previously identified by our group: BSF nairo-like virus, and BSF uncharacterized bunya-like virus. Consistent with our previous study, these two viruses are found primarily in frass samples and occur together more often than expected at random. When analyzing host transcription, we found significant differences in gene expression for eight candidate antiviral genes in black soldier fly when comparing samples with and without viral sequences. Our results suggest that black soldier fly-virus interactions are ongoing, and they could be of interest to black soldier fly producers.

bioinformatics↗

bioRxiv2024

Under the radar: differential responses of bed bugs to an entomopathogen, environmental bacteria, and a human pathogen

BackgroundBed bugs (Hemiptera: Cimicidae) are a widely distributed, obligately blood-feeding insect, but they have never been linked to pathogen transmission in humans. Most other hematophagous insects that frequently bite humans transmit pathogens, and it is unclear why bed bugs do not. One hypothesis is that bed bugs have evolved a highly robust immune system because their mating system, traumatic insemination, exposes females to consistent wounding and bacterial infections. Although this has been proposed, very little is known about the bed bug immune system and how bed bugs respond to microbial challenges. Understanding the bed bug immune system could give insight to why bed bugs are not known to transmit disease and under what circumstances they could, while also facilitating biological control efforts involving microbes. MethodsTo investigate the immune response of bed bugs to bacterial challenges, we exposed female bed bugs to three bacterial challenges. 1.) Pseudomonas fluorescens, an entomopathogen known to have harmful effects to bed bugs, 2.) bacteria cultured from a bed bug enclosure likely encountered during traumatic insemination, and 3.) Borrelia duttoni, a human vector-borne pathogen that causes relapsing fever. We compared the transcriptomes of infected bed bugs with uninfected bed bugs, focusing on immune-related genes. We also conducted phylogenetic analyses to understand patterns of gene duplication and function of potentially immune-related genes. ResultsWe found many known immune effector genes upregulated in response to P. fluorescens and traumatic insemination-associated bacteria, but interestingly, not in response to B. duttoni. Furthermore, we found significant overlap in the genes differentially expressed in response to P. fluorescens and the traumatic insemination associated bacteria, and between P. fluorescens and B. duttoni, but no significant overlap between traumatic insemination bacteria and B. duttoni. We also show that bed bug diptericin-like antimicrobial peptides underwent a lineage-specific gene duplication, and that they may have further functional specialization. Finally, we identify previously overlooked candidates for future study of immune function in bed bugs, including some putative cuticle-associated genes, a laccase-like gene, and a mucin-like gene. ConclusionsBy taking comprehensive transcriptomic approach, our study is an important step in understanding how bed bugs respond to diverse immune challenges.

molecular biology↗

bioRxiv2024

Evolutionary analysis of genome-specific duplications in flatworm genomes

Platyhelminthes, also known as flatworms, is a phylum of bilaterian invertebrates infamous for their parasitic representatives. The classes Cestoda, Monogenea, and Trematoda comprise parasitic helminths inhabiting multiple hosts, including fishes, humans, and livestock, and are responsible for considerable economic damage and burden on human health. As in other animals, the genomes of flatworms have a wide variety of paralogs, genes related via duplication, whose origins could be mapped throughout the evolution of the phylum. Through in-silico analysis, we studied inparalogs, i.e., genome-specific duplications, focusing on their biological functions, expression changes, and evolutionary rate. These genes are assumed to be key players in the adaptation process of species to each particular niche. Our results showed that genes associated with specific functions, such as response to stress, ion binding, oxidoreductase activity, and peptidase, are overrepresented among inparalogs. This trend is conserved among species from different classes, including free-living species. Available expression data from Schistosoma mansoni, a parasite from the trematode class, demonstrated high conservation of the expression patterns between inparalogs, but with notable exceptions, which also display evidence of rapid evolution. We discuss how natural selection may operate to maintain these genes and the particular duplication models that fit better to the observations. Our results support the critical role of gene duplication in the evolution of flatworms.

evolutionary biology↗

bioRxiv2023

Comparative genomics and the salivary transcriptome of the redbanded stink bug shed light on its high damage potential to soybean

The redbanded stink bug, Piezodorus guildinii (Westwood) (Hemiptera: Pentatomidae), is a significant soybean pest in the Americas, inflicting more physical damage on soybean than other native stink bugs. Studies suggest that its heightened impact is attributed to the aggressive digestive properties of its saliva. Despite its agricultural importance, the factors driving its greater ability to degrade plant tissues have remained unexplored in a genomic evolutionary context. In this study, we hypothesized that lineage-specific gene family expansions have increased the dosage of digestive genes expressed in the salivary glands. To investigate this, we annotated a previously published genome assembly of the redbanded stink bug and performed a comparative genomic analysis on 11 hemipteran species and reconstructed patterns of gene duplication, gain, and loss in the redbanded stink bug. We also performed RNA-seq on the redbanded stink bugs salivary tissues, along with the rest of the body without salivary glands. We identified hundreds of differentially expressed salivary genes, including a subset lost in other stink bug lineages but retained and expressed in the redbanded stink bugs salivary glands. These genes were significantly enriched with protein families involved in proteolysis, potentially explaining the redbanded stink bugs heightened damage to soybeans. Contrary to our hypothesis, we found no support for an increased dosage of digestive genes in the salivary glands of the redbanded stink bug. Nonetheless, these results provide insight into the evolution of this important crop pest, establishing a link between its genomic history and its agriculturally important physiology. SIGNIFICANCE STATEMENTThe redbanded stink bug, an important soybean pest in the Americas, inflicts greater damage to soybean due to higher salivary digestion. We employed comparative genomics and analyses of the salivary transcriptome to explore this and found that the differential retention of ancestral salivary genes may explain this phenomenon better than gene gains or duplications in the redbanded stink bug genome. We identify a distinct set of genes in the salivary gland that were differentially retained and expressed in the redbanded stink bug lineage, demonstrating enrichment in proteolytic function. This discovery offers a potential explanation for the redbanded stink bugs elevated damage to soybean crops.

genomics↗

bioRxiv2023

The genome and transcriptome of the snail Biomphalaria sudanica s.l.: Immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

BackgroundControl and elimination of schistosomiasis is an arduous task, with current strategies proving inadequate to break transmission. Exploration of genetic approaches to interrupt Schistosoma mansoni transmission, the causative agent for human intestinal schistosomiasis in sub-Saharan Africa and South America, has led to genomic research of the snail vector hosts of the genus Biomphalaria. Few complete genomic resources exist, with African Biomphalaria species being particularly underrepresented despite this being where the majority of S. mansoni infections occur. Here we generate and annotate the first genome assembly of Biomphalaria sudanica sensu lato, a species responsible for S. mansoni transmission in lake and marsh habitats of the African Rift Valley. Supported by whole-genome diversity data among five inbred lines, we describe orthologs of immune-relevant gene regions in the South American vector B. glabrata and present a bioinformatic pipeline to identify candidate novel pathogen recognition receptors (PRRs). ResultsDe novo genome and transcriptome assembly of inbred B. sudanica originating from the shoreline of Lake Victoria (Kisumu, Kenya) resulted in a haploid genome size of [~]944.2 Mb (6732 fragments, N50=1.067 Mb), comprising 23,598 genes (BUSCO=93.6% complete). The B. sudanica genome contains orthologues to all described immune genes/regions tied to protection against S. mansoni in B. glabrata. The B. sudanica PTC2 candidate immune genomic region contained many PRR-like genes across a much wider genomic region than has been shown in B. glabrata, as well as a large inversion between species. High levels of intra-species nucleotide diversity were seen in PTC2, as well as in regions linked to PTC1 and RADres orthologues. Immune related and putative PRR gene families were significantly over-represented in the sub-set of B. sudanica genes determined as hyperdiverse, including high extracellular diversity in transmembrane genes, which could be under pathogen-mediated balancing selection. However, no overall expansion in immunity related genes were seen in African compared to South American lineages. ConclusionsThe B. sudanica genome and analyses presented here will facilitate future research in vector immune defense mechanisms against pathogens. This genomic/transcriptomic resource provides necessary data for the future development of molecular snail vector control/surveillance tools, facilitating schistosome transmission interruption mechanisms in Africa.

genomics↗

bioRxiv2023

Do bed bugs transmit human viruses, or do humans transmit bed bug viruses? A worldwide survey of the bed bug RNA virosphere

Bed bugs (Hemiptera: Cimicidae) are a globally distributed hematophagous pest that routinely feed on humans. Unlike many blood-sucking arthropods, they have never been linked to disease transmission in a natural setting, and despite interest in their role as disease vectors, little is known about the viruses that bed bugs naturally harbor. Here, we present a global-scale survey of the bed bug RNA virosphere. We sequenced the metatranscriptomes of 22 individual bed bugs (Cimex lectularius and Cimex hemipterus) from 8 locations around the world. We detected sequences from two known bed bug viruses (Shuangao bedbug virus 1 and Shuangao bedbug virus 2) which extends their geographical range and the host range of Shuangao bedbug virus 1 to Cimex lectularius. We identified three novel bed bug virus sequences from a tenui-like virus (Bunyavirales), a toti-like virus (Ghabrivirales), and a luteo-like virus (Tolivirales). Interestingly, some of the bed bug viruses branch near to insect-transmitted plant-infecting viruses, opening questions regarding the evolution of plant virus infection. When we analyzed the putative viral sequences by their hosts collection location, we found unexpected patterns of geographical diversity that may reflect humans role in bed bug dispersal. Additionally, we investigated the effect that Wolbachia, the primary bed bug endosymbiont, may have on viral abundance and found that Wolbachia infection neither promotes nor inhibits viral infection. Finally, our results provide no evidence that bed bugs transmit any known human pathogenic viruses.

bioinformatics↗

bioRxiv2023

Bioinformatic Surveillance Leads to Discovery of Two Novel Putative Bunyaviruses Associated with Black Soldier Fly

The black soldier fly (Hermetia illucens, BSF) has emerged as an industrial insect of high promise because of its ability to convert organic waste into nutritious feedstock, making it an environmentally sustainable alternative protein source. As global interest rises, rearing efforts are also upscaled, which is highly conducive to pathogen transmission. Viral epidemics have stifled mass-rearing efforts of other insects of economic importance, such as crickets, silkworms, and honeybees, but little is known about the viruses that associate with BSF. Although it is thought that BSF are unusually resistant to pathogens because of their expansive antimicrobial gene repertoire, surveillance techniques could be useful to identify emerging pathogens and common BSF microbes. In this study, we used high-throughput sequencing data to survey BSF larvae and frass samples, and we identified two novel bunyavirus-like sequences. Our phylogenetic analyses grouped one in the family Nairoviridae, and the other with two unclassified bunyaviruses. We describe these putative novel viruses as BSF Nairovirus-like 1 and BSF uncharacterized bunyavirus-like 1. We identified candidate segments for the full BSF Nairovirus-like 1 genome using a technique based on transcript co-occurrence, and only a partial genome for BSF uncharacterized bunyavirus-like 1. These results emphasize the value of routine BSF colony surveillance and add to the number of viruses associated with BSF.

bioinformatics↗

bioRxiv2022

Evolution and molecular basis of a novel allosteric property of crocodilian hemoglobin

Understanding the evolution of novel protein functions requires data on the mechanistic effects of causative mutations and the extent of coupling between the gain of new function and loss of ancestral function. Here, we use ancestral protein resurrection and directed mutagenesis to dissect the molecular basis of a novel mode of allosteric regulation in crocodilian hemoglobin. We discovered that regulation of Hb-O2 affinity via allosteric binding of bicarbonate ions (a biochemical adaptation unique to crocodilians) and the concomitant loss of allosteric regulation by ATP-binding are attributable to non-overlapping sets of substitutions. Gain of bicarbonate-sensitivity involved direct effects of few replacements at key sites in combination with indirect effects of numerous replacements at structurally disparate sites. Due to the context-dependence of causative substitutions, the unique allosteric properties of crocodilian hemoglobin cannot be easily transplanted into divergent homologs of other species. Significance StatementThe extraordinary breath-hold diving capacity of crocodilians is partly attributable to a unique mode of allosterically regulating hemoglobin-oxygenation in circulating red blood cells. We investigated the origin and mechanistic basis of this novel biochemical adaptation by performing directed mutagenesis experiments on resurrected ancestral crocodilian hemoglobins. Our results revealed that evolved changes in allosteric regulation involved the direct effect of few amino acid substitutions at key sites in combination with indirect effects of numerous other substitutions at structurally disparate sites. Such indirect interaction effects suggest that the evolution of novel protein functions may often depend on neutral mutations that produce no adaptive benefit when they first arise, but which contribute to a permissive background for subsequent function-altering mutations at other sites.

evolutionary biology↗

bioRxiv2021

Deterministic shifts in molecular evolution correlate with convergence to annualism in killifishes

The repeated evolution of novel life histories correlating with ecological variables offer opportunities to test scenarios of convergence and determinism in genetic, developmental, and metabolic features. Here we leverage the diversity of aplocheiloid killifishes, a clade of teleost fishes that contains over 750 species on three continents. Nearly half of these are "annual" or seasonal species that inhabit bodies of water that desiccate and are unfeasible for growth, reproduction, or survival for weeks to months at a time. We present a large-scale phylogenomic reconstruction of aplocheiloid killifish evolution using newly sequenced transcriptomes from all major clades. We show that developmental dormancy (diapause) and annualism have up to seven independent origins in Africa and America. We then measure evolutionary rates of orthologous genes and show that annual life history is correlated with higher dN/dS ratios. Many of these fast-evolving genes in annual species constitute key developmental genes and nuclear-encoded metabolic genes that control oxidative phosphorylation. Lastly, we compare these fast-evolving genes to genes associated with developmental dormancy and metabolic shifts in killifishes and other vertebrates and thereby identify molecular evolutionary signatures of repeated evolutionary transitions to extreme environments.

evolutionary biology↗

bioRxiv2020

Evolved increases in hemoglobin-oxygen affinity and Bohr effect coincided with the aquatic specialization of penguins.

Dive capacities of air-breathing vertebrates are dictated by onboard O2 stores, suggesting that physiological specializations of diving birds like penguins may have involved adaptive changes in convective O2 transport. It has been hypothesized that increased hemoglobin (Hb)-O2 affinity improves pulmonary O2 extraction and enhance capacities for breath-hold diving. To investigate evolved changes in Hb function associated with the aquatic specialization of penguins, we integrated comparative measurements of whole-blood and purified native Hbs with protein engineering experiments based on site-directed mutagenesis. We reconstructed and resurrected ancestral Hbs representing the common ancestor of penguins and the more ancient ancestor shared by penguins and their closest nondiving relatives (order Procellariiformes, which includes albatrosses, shearwaters, petrels, and storm petrels). These two ancestors bracket the phylogenetic interval in which penguin-specific changes in Hb function would have evolved. The experiments revealed that penguins evolved a derived increase in Hb-O2 affinity and a greatly augmented Bohr effect (reduced Hb-O2 affinity at low pH). Although an increased Hb-O2 affinity reduces the gradient for O2 diffusion from systemic capillaries to metabolizing cells, this can be compensated by a concomitant enhancement of the Bohr effect, thereby promoting O2 unloading in acidified tissues. We suggest that the evolved increase in Hb-O2 affinity in combination with the augmented Bohr effect maximizes both O2 extraction from the lungs and O2 unloading from the blood, allowing penguins to fully utilize their onboard O2 stores and maximize underwater foraging time.

evolutionary biology↗

bioRxiv2020

Phylogenetic diversification of sirtuin genes with a description of a new family member

Studying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disentangling their evolution is also critical to those who do functional/structural studies to allow a deeper and more precise interpretation of their results in an evolutionary context. The sirtuin gene family is a group of genes that are involved in a variety of biological functions mostly related to aging. Their duplicative history is an open question, as well as the definition of the repertoire of sirtuin genes among vertebrates. Our results show a well-resolved phylogeny that represents an improvement in our understanding of the duplicative history of the sirtuin gene family. We identified a new sirtuin gene family member (SIRT3.2) that was apparently lost in the last common ancestor of amniotes but retained in all other groups of jawed vertebrates. According to our experimental analyses, elephant shark SIRT3.2 protein is located in mitochondria, the overexpression of which leads to an increase in cellular levels of ATP. Moreover, in vitro analysis demonstrated it has deacetylase activity being modulated in a similar way to mammalian SIRT3. Our results indicate that there are at least eight sirtuin paralogs among vertebrates and that all of them can be traced back to the last common ancestor of the group that existed between 676 and 615 millions of years ago.

evolutionary biology↗

bioRxiv2019

Evolution of the DAN gene family in vertebrates

The DAN gene family (DAN, Differential screening-selected gene Aberrant in Neuroblastoma) is a group of genes that is expressed during development and plays fundamental roles in limb bud formation and digitation, kidney formation and morphogenesis and left-right axis specification. During adulthood the expression of these genes are associated with diseases, including cancer. Although most of the attention to this group of genes has been dedicated to understanding its role in physiology and development, its evolutionary history remains poorly understood. Thus, the goal of this study is to investigate the evolutionary history of the DAN gene family in vertebrates, with the objective of complementing the already abundant physiological information with an evolutionary context. Our results recovered the monophyly of all DAN gene family members and divide them into five main groups. In addition to the well-known DAN genes, our phylogenetic results revealed the presence of two new DAN gene lineages; one is only retained in cephalochordates, whereas the other one (GREM3) was only identified in cartilaginous fish, holostean fish, and coelacanth. According to the phyletic distribution of the genes, the ancestor of gnathostomes possessed a repertoire of eight DAN genes, and during the radiation of the group GREM1, GREM2, SOST, SOSTDC1, and NBL1 were retained in all major groups, whereas, GREM3, CER1, and DAND5 were differentially lost.

evolutionary biology↗

bioRxiv2019

The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements

Transposable elements (TEs) are genomic parasites that can propagate by inserting copies of themselves into host genomes. Mammalian genomes are typically dominated by LINE retrotransposons and their associated SINEs, and their mobilization in the germline is a challenge to genome integrity. There are genomic defenses against TE proliferation and the PIWI/piRNA defense is among the most well understood. However, the PIWI/piRNA system has been investigated largely in animals with abundant and actively mobilizing TEs and it is unclear how the PIWI/piRNA system functions in the absence of mobilizing TEs. The 13-lined ground squirrel provides an excellent opportunity to examine PIWI/piRNA and TE dynamics within the context of minimal, and possibly nonexistent, TE accumulation. We sequenced RNA and small RNAs pools from the testes of juvenile and adult squirrels and compared results to TE and PIWI/piRNA dynamics in the European rabbit and house mouse. Interestingly in squirrels, despite a lack of young insertions, TEs were still actively transcribed at higher levels compared to mouse and rabbit. All three PIWI proteins were either not expressed, or only minimally expressed, prior to P8 in squirrel testis, but there was little TE expression change with the onset of PIWI expression. We found PIWIs largely did not reduce TE transcription, and the ping-pong cycle was significantly reduced among squirrel LINEs and SINEs compared to the mouse and rabbit. We speculate that, although the PIWI/piRNA system is adaptable to novel TE threats, transcripts from TEs that are no longer threatening receive less attention from PIWI proteins.

evolutionary biology↗