Gene Content Research Articles

Whole-Genome Sequencing and Phenotyping Reveal Specific Adaptations of Lachancea thermotolerans to the Winemaking Environment.

Adaptation to the environment plays an essential role in yeast evolution as a consequence of selective pressures. Lachancea thermotolerans, a yeast related to fermentation and one of the current trends in wine technology research, has undergone an anthropisation process, leading to a notable genomic and phenomic differentiation. Using whole-genome sequencing, of 145 L. thermotolerans strains, we identified six well-defined groups primarily delineated by their ecological origin and exhibiting high levels of genetic diversity. Anthropised strains showed lower genetic diversity due to the selective pressure imposed by the winemaking environment. Strong evidence of anthropisation and adaptation to the wine environment through modification of gene content was also found. Differences in genes involved in the assimilation of alternative carbon and nitrogen sources, such as the MAL31 and DAL5 genes, which confer greater fitness in the winemaking environment, were observed. Additionally, we found that phenotypic traits considered domestication hallmarks are present in anthropised strains. Among these, increased fitness in the presence of ethanol and sulphites, assimilation of non-fermentable carbon sources, and lower levels of residual fructose under fermentative conditions highlight. We hypothesise that lactic acid production in the Saccharomyces-Lachancea lineage is an anthropisation signature linked to winemaking, resulting from the loss of respiratory chain complex I and the evolutionary preference for fermentation over respiration, even in the presence of oxygen. Overall, the results of this work provide valuable insight into the anthropisation process in L. thermotolerans and demonstrate how fermentation environments give rise to similar adaptations in different yeast species.

Reduced efficacy of selection on a young Z chromosome region of Schistosoma japonicum

Abstract Sex-linked and autosomal loci experience different selective pressures and evolutionary dynamics. X (or Z) chromosomes are often hemizygous in males (or females), as Y (or W) chromosomes often degenerate. Such hemizygous regions can be under greater efficacy of selection, as recessive mutations are immediately exposed to selection in the heterogametic sex leading to faster adaptation and faster divergence on the X chromosome (the so-called Faster-X or Faster-Z effect). However, in young non-recombining regions, Y/W chromosomes often have many functional genes, and many X/Z-linked loci are therefore diploid. The sheltering of recessive mutations on the X/Z by the Y/W homolog is expected to drive slower adaptation for diploid X/Z loci, i.e. a reduction in the efficacy of selection. While the Faster-X effect has been studied extensively, much less is known empirically about the evolutionary dynamics of diploid X or Z chromosomes. Here, we took advantage of published population genomic data in the female-heterogametic human parasite Schistosoma japonicum to characterize the gene content and diversity levels of the diploid and hemizygous regions of the Z chromosome. We used different metrics of selective pressures acting on genes to test for differences in the efficacy of selection in hemizygous and diploid Z regions, relative to autosomes. We found consistent patterns suggesting reduced Ne, and reduced efficacy of purifying selection, on both hemizygous and diploid Z regions. Moreover, relaxed selection was particularly pronounced for female-biased genes on the diploid Z, as predicted by recent theoretical work.

Pervasive mitochondrial tRNA gene loss in the clade B of haplosclerid sponges (Porifera, Demospongiae)

Abstract Mitochondrial tRNA gene loss and cytosolic tRNA import are two common phenomena in mitochondrial biology, but their importance is often under-appreciated in animals. This is because the mitochondrial DNA (mtDNA) of most bilaterally symmetrical animals (Bilateria) encodes a complete set of tRNAs required for mitochondrial translation. By contrast, the mtDNA of non-bilaterian animals (phyla Cnidaria, Ctenophora, Porifera, and Placozoa) often contains a reduced set of tRNA genes, necessitating tRNA import from the cytosol. Interestingly, in many non-bilaterian lineages, tRNA gene content appears to be set early in evolution and remains conserved thereafter. Here, we report that Clade B of Haplosclerid Sponges (CBHS) represents an exception to this pattern, displaying considerable variation in tRNA gene content even among relatively closely related species. We determined mt-genome sequences for eight CBHS species and analyzed them in conjunction with six previously available sequences. Additionally, we sequenced mt-genomes for two species of haplosclerid sponges outside the CBHS and used eight previously available sequences as outgroups. We found that tRNA gene content varied widely within CBHS, ranging from three in an undescribed Haliclona species (Haliclona sp. TLT785) to 25 in Xestospongia muta and X. testudinaria. Furthermore, we found that all CBHS species outside the genus Xestospongia lacked the atp9 gene, with some also lacking atp8. Analysis of nuclear sequences from Niphates digitalis revealed that both atp8 and atp9 had transferred to the nuclear genome, while the absence of mt-tRNA genes indicated their genuine loss. We argue that CBHS can serve as a valuable system for studying mt-tRNA gene loss, mitochondrial import of cytosolic tRNAs, and the impact of these processes on mitochondrial evolution.

Prophage dynamics in gastric and enterohepatic environments: unraveling ecological barriers and adaptive transitions

Abstract Phage predation plays a critical role in shaping bacterial genetic diversity, with prophages playing a comparable role. However, the prevalence and genetic variability of prophages within the Helicobacter genus remain inadequately studied. Helicobacter species are clinically significant and occupy distinct digestive system regions, with gastric species (e.g., Helicobacter pylori) residing in the gastric mucosa and enterohepatic species colonizing the liver and intestines of various vertebrates. Here, we address this knowledge gap by analyzing prophage presence and diversity across 343 non-pylori Helicobacter genomes, mapping their distribution, comparing genomic features between gastric and enterohepatic prophages, and exploring their evolutionary relationships with hosts. We identified and analyzed a catalogue of 119 new complete and 78 incomplete prophages. Our analysis reveals significant differences between gastric and enterohepatic species. Gastric prophages exhibit high synteny, and cluster in a few groups, indicating a more conserved genetic structure. In contrast, enterohepatic prophages show greater diversity in gene order and content, reflecting their adaptation to varied host environments. Helicobacter cinaedi stands out, harboring a large number of prophages among the enterohepatic species, forming a distinct cohesive group. Phylogenetic analyses reveal a co-evolutionary relationship between several prophages and their bacterial hosts, though exceptions, such as the enterohepatic prophages from H. canis, Helicobacter equorum, H. jaachi, and the gastric prophage from H. himalayensis, suggesting more complex co-evolutionary dynamics like host jumps, recombination and horizontal gene transfer. The insights gained from this study enhance our understanding of prophage dynamics in Helicobacter, emphasizing their role in bacterial adaptation, virulence, and host specificity.

Single-cell sequencing provides clues about the developmental genetic basis of evolutionary adaptations in syngnathid fishes

Seahorses, pipefishes, and seadragons are fishes from the family Syngnathidae that have evolved extraordinary traits including male pregnancy, elongated snouts, loss of teeth, and dermal bony armor. The developmental genetic and cellular changes that led to the evolution of these traits are largely unknown. Recent syngnathid genome assemblies revealed suggestive gene content differences and provided the opportunity for detailed genetic analyses. We created a single-cell RNA sequencing atlas of Gulf pipefish embryos to understand the developmental basis of four traits: derived head shape, toothlessness, dermal armor, and male pregnancy. We completed marker gene analyses, built genetic networks, and examined the spatial expression of select genes. We identified osteochondrogenic mesenchymal cells in the elongating face that express regulatory genes bmp4, sfrp1a, and prdm16. We found no evidence for tooth primordia cells, and we observed re-deployment of osteoblast genetic networks in developing dermal armor. Finally, we found that epidermal cells expressed nutrient processing and environmental sensing genes, potentially relevant for the brooding environment. The examined pipefish evolutionary innovations are composed of recognizable cell types, suggesting that derived features originate from changes within existing gene networks. Future work addressing syngnathid gene networks across multiple stages and species is essential for understanding how the novelties of these fish evolved.

Single-cell sequencing provides clues about the developmental genetic basis of evolutionary adaptations in syngnathid fishes.

Seahorses, pipefishes, and seadragons are fishes from the family Syngnathidae that have evolved extraordinary traits including male pregnancy, elongated snouts, loss of teeth, and dermal bony armor. The developmental genetic and cellular changes that led to the evolution of these traits are largely unknown. Recent syngnathid genome assemblies revealed suggestive gene content differences and provided the opportunity for detailed genetic analyses. We created a single-cell RNA sequencing atlas of Gulf pipefish embryos to understand the developmental basis of four traits: derived head shape, toothlessness, dermal armor, and male pregnancy. We completed marker gene analyses, built genetic networks, and examined the spatial expression of select genes. We identified osteochondrogenic mesenchymal cells in the elongating face that express regulatory genes bmp4, sfrp1a, and prdm16. We found no evidence for tooth primordia cells, and we observed re-deployment of osteoblast genetic networks in developing dermal armor. Finally, we found that epidermal cells expressed nutrient processing and environmental sensing genes, potentially relevant for the brooding environment. The examined pipefish evolutionary innovations are composed of recognizable cell types, suggesting that derived features originate from changes within existing gene networks. Future work addressing syngnathid gene networks across multiple stages and species is essential for understanding how the novelties of these fish evolved.

Alteration of intestinal microbiota-intestinal barrier interaction interferes with intestinal health after microcystin-LR exposure in Lithobates catesbeianus tadpoles.

There remains uncertainty regarding the influence of microcystin-leucine arginine (MC-LR) on amphibian intestinal health, specifically how MC-LR interferes with intestinal microbiota following exposure to environmental concentrations. In this study, Lithobates catesbeianus tadpoles were exposed to varying MC-LR concentrations (0, 0.5, and 2 µg/L) over a 30-day period. The aim was to investigate how altered interactions between tadpole intestinal microbiota and the intestinal barrier influence intestinal health following MC-LR exposure. Following exposure to the MC-LR at low ambient concentrations, tadpole intestinal tissue was damaged. It had increased permeability, reduced pathogen inhibition capacity, and impaired digestive function. Additionally, there was a significant increase in lipopolysaccharide content and upregulation of downstream response genes, including TLR4, MyD88, and NF-κB, within the intestinal tissue. Therefore, eosinophils' count and pro-inflammatory cytokines' expression increased. In addition, MC-LR exposure induced oxidative stress and mitochondrial structural damage by increasing the levels of reactive oxygen species in intestinal tissue. CytoC and Bax transcription, as well as caspase 9 and caspase 3 activities, increased significantly. Significant downregulation of Bcl-2 transcription promoted apoptosis in tadpole intestinal cells. MC-LR exposure disrupted intestinal microbiota and metabolism in tadpoles. Correlation analysis revealed a strong association between intestinal microbiota and oxidative stress, inflammation, immunity, and tissue damage in the intestine. Conclusively, this study provides the first demonstration that MC-LR significantly affects amphibian intestinal microbiota, highlighting tadpoles' susceptibility to environmental risks posed by MC-LR.

Transcriptome analysis unveils the mechanisms of oxidative stress, immunotoxicity and neurotoxicity induced by benzotriazole UV stabilizer-328 in zebrafish embryos.

As an emerging pollutant, ultraviolet stabilizer-328 (UV-328) has been frequently detected in aquatic environments and attracted great attention. Nevertheless, the toxicity and mechanisms of UV-328 to aquatic organisms are still not fully understood. In particular, the immunotoxicity and neurotoxicity of UV-328 to aquatic organisms and their mechanisms have not been reported yet. In this experiment, the developmental toxicity, oxidative stress, apoptosis, immunotoxicity and neurotoxicity in zebrafish embryos exposed to UV-328 with concentrations of 0.01, 0.1, 1, 10 and 100 µg/L for 120 h were studied. By measuring the growth and developmental indices, production of ROS, enzyme activities, MDA content and expression of genes related to oxidative, immune and nerve, and histopathological analysis, it was found that UV-328 had developmental toxicity to zebrafish larvae, and could induce oxidative stress, immunotoxicity and neurotoxicity to zebrafish larvae even at environmental concentrations with concentration-dependent effects. Moreover, the results of transcriptome analysis and qRT-PCR validation suggested that immune and nerve disorders were caused by UV-328 in zebrafish larvae through regulating the RIG-I-like receptor signaling pathway and neuroactive ligand-receptor interaction, respectively. In addition, transcriptome analysis further revealed that UV-328 could mediate the RIG-I to induce oxidative stress through p38-MAPK/p53 signaling pathway, leading to apoptosis and oxidative damage. In addition, the p38-MAPK signaling pathway enhanced ROS production and activated inflammatory cytokines to induce immunotoxicity. The results of the present work provided important information for understanding the toxicity of UV-328 to aquatic organisms and evaluating its ecological risk in aquatic environment.

Assessing the authenticity and purity of a commercial Bacillus thuringiensis bioinsecticide through whole genome sequencing and metagenomics approaches

Biopesticides, biological agents for pest control in plants, are becoming increasingly prevalent in agricultural practices. However, no established methodology currently exists to assess their quality, and there are currently no publicly available authenticity and purity evaluations of commercial products. This lack of data may represent risks because of their widespread dispersal in the environment. We evaluated the potential of whole genome sequencing (WGS) and metagenomics approaches, including nanopore long-read sequencing, to verify both authenticity (i.e., the labeled strain) and biological purity (i.e., the absence of any undesired genetic material) of commercial Bacillus thuringiensis bioinsecticides. Four commercially available bioinsecticidal products containing Bacillus thuringiensis serovar kurstaki strain HD-1 were collected from the European market as a case study. Two sequencing approaches were employed: WGS of isolates and metagenomics sequencing of all genetic material in a product. To assess authenticity, isolate WGS data were compared against the publicly available reference genome of the expected strain. Antimicrobial resistance gene content, insecticidal gene content, and single nucleotide polymorphism differences were characterized to evaluate similarity to the reference genome. To assess purity, metagenomic sequencing data were analyzed using read classification and strain differentiation methods. Additionally, long- and short-read data were used to assess potential large-scale structural variations. Our results confirmed all investigated products to be authentic and pure. With the increasing usage of biopesticides, it is crucial to have adequate quality control methods. Our proposed approach could be adapted for other biopesticides, and similar products, providing a standardized and robust approach to contribute to biopesticide safety.

Rapid expansion and specialization of the TAS2R bitter taste receptor family in amphibians.

TAS2Rs are a family of G protein-coupled receptors that function as bitter taste receptors in vertebrates. Mammalian TAS2Rs have historically garnered the most attention, leading to our understanding of their roles in taste perception relevant to human physiology and behaviors. However, the evolution and functional implications of TAS2Rs in other vertebrate lineages remain less explored. Here, we identify 9,291 TAS2Rs from 661 vertebrate genomes. Large-scale phylogenomic analyses reveal that frogs and salamanders contain unusually high TAS2R gene content, in stark contrast to other vertebrate lineages. In most species, TAS2R genes are found in clusters; compared to other vertebrates, amphibians have additional clusters and more genes per cluster. We find that vertebrate TAS2Rs have few one-to-one orthologs between closely related species, although total TAS2R count is stable in most lineages. Interestingly, TAS2R count is proportional to the receptors expressed solely in extra-oral tissues. In vitro receptor activity assays uncover that many amphibian TAS2Rs function as tissue-specific chemosensors to detect ecologically important xenobiotics.

P-2112. Development and Validation of a Cheap, Portable Assay to Rapidly Profile Bacterial Infections of the Bloodstream

Abstract Background Antimicrobial resistant (AMR) bacterial infections pose a significant and growing health threat worldwide, and their burden is most severe in lower income areas where diagnostic infrastructure is lacking. The development of cost-effective and accessible diagnostic tools for the rapid identification of resistant infections in low-resource settings is crucial. Specific High-sensitivity Enzymatic Reporter Unlocking, or SHERLOCK, is a promising CRISPR-based system that can aid in the diagnosis of infections and support clinical decision making. Here, we present an assay termed BADLOCK (Bacteria and AMR Detection by SHERLOCK) that uses this technology to rapidly identify bacterial species and AMR genes on blood cultures. BADLOCK workflow demonstrating simplicity of approach and rapid turnaround. Methods We combine isothermal amplification of targets with CRISPR/Cas13-based detection into a single step, allowing for a streamlined workflow and a total time-to-identification of less than two hours from positive cultures using lateral flow strips (Fig. 1). The assay primarily targets topA for species identification, a highly conserved gene within species with sufficient variability between them to enable species-level typing. A panel of clinically important AMR genes, including the ESBL blaCTX-M-15, three major carbapenemases, and the GPC resistance genes mecA and vanA, is also included. Pilot study assessing assay performance. A) each column represents a different isolate while each row represents a different CRISPR gene target, which are enumerated at the bottom. Each species name refers to the topA gene sequence unique to that species. The top box shows the expected gene content based on prior sequencing, while the bottom box shows the results of each assay. The blue shading shows relative fluorescence intensity of the generated signal. B) Basic test characteristics for each target gene. Results In addition to the AMR resistance genes, we have validated a panel of 9 gram-negative rods, 6 staphylococci, 2 enterococci, and 2 streptococcal species with further targets being developed, and have performed a laboratory pilot study on a subset of these (Fig. 2). We have additionally collected over 600 sequential positive blood cultures and are in the process of performing a large clinical validation study on patient samples, thereby elucidating the precise test characteristics of our assay. Conclusion We have developed an assay capable of rapidly detecting bacterial species causing bloodstream infections and their major epidemic AMR genes on low-cost paper strips. Our work has the potential to improve the diagnostic landscape for resistant infections in low-and-middle-income countries and serve as an adjunctive diagnostic to traditional approaches in highly resourced setting, which would represent a major step forward in infectious disease diagnostics. Disclosures All Authors: No reported disclosures

Plastid genome comparison and phylogenetic analyses of the Chinese group of medicinal species and related taxa within Asparagus genus

BackgroundAsparagus L. is a large genus widely distributed across the continents of the Old World. Among its members, approximately 14 species found in China are recognized as popular herbal medicines. However, accurate authentication of these medicinal species and their phylogenetic relationships with related taxa remains unresolved.MethodsTo identify simple sequence repeats (SSRs) and divergence hotspot regions appropriate for future authentication studies, as well as to infer the phylogenetic relationships among Asparagus species, we employed a plastid genome (plastome) dataset consisting of 25 Asparagus species (21 newly sequenced and four retrieved from GenBank), encompassing 12 Chinese medicinal species, for comparative and phylogenetic analyses.ResultsAll Asparagus plastomes displayed a typical quadripartite structure with sizes ranging from 155,948 bp to 157,128 bp and harbored 114 unique genes (80 protein-coding genes, 30 tRNA genes, and four rRNA genes). IRscope and Mauve analyses indicated minimal structural variation among Asparagus plastomes. We detected between 79 to 95 SSRs across the plastomes; most were located in the large single-copy (LSC) region and primarily consisted of mono-nucleotide repeat sequences (especially A and T repeats). The genus displayed mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide repeats, but with variations in types and numbers among different species. Additionally, we identified 12 special SSR motifs and seven divergent hotspot regions that may serve as potential molecular markers for future identification efforts. Phylogenetic analyses yielded a robust phylogeny for Asparagus taxa, which were split into Clades I, II, and III. Notably, medicinal Asparagus species were mainly found in Clade III. Although the phylogenetic relationships of most Asparagus species aligned with previous study findings, the phylogenetic positions of A. munitus, A. subscandens, A. gobicus, and A. dauricus were newly determined.ConclusionsThe plastomes of Asparagus are largely conserved in terms of genome structure, size, gene content, and arrangement. Nevertheless, SSRs analyses revealed significant interspecific polymorphism within Asparagus. In addition, special SSR motifs and divergent hotspot regions identified from Asparagus plastomes provided reference for subsequent identification investigations. The plastome-based phylogeny provided preliminary insights into the relationships among the Chinese group of medicinal species and related taxa within Asparagus. Overall, this study offers a wealth of informative genetic resources pertinent to Asparagus, thereby enhancing our understanding of its evolution and laying a foundation for species identification, assessment of genetic population diversity, as well as the exploration and conservation of germplasm resources.

Intraspecific Variation and Recent Loss of Ancient, Conserved Effector Genes in the Sudden Oak Death Pathogen Phytophthora ramorum.

Members of the Phytophthora genus are responsible for many important diseases in agricultural and natural ecosystems. Phytophthora ramorum causes devastating diseases of oak, and tanoak stands in US forests and larch in the UK. The four evolutionary lineages involved express different virulence phenotypes on plant hosts, and characterization of gene content is foundational to understanding the basis for these differences. Recent discovery of P. ramorum at its candidate center of origin in Asia provides a new opportunity for investigating the evolutionary history of the species. We assembled, high-quality genome sequences of six P. ramorum isolates representing three lineages from Asia and three causing epidemics in western US forests. The six genomes were assembled into 13 putative chromosomes. Analysis of structural variation revealed multiple chromosome fusion and fission events. Analysis of putative virulence genes revealed variations in effector gene composition among the sequenced lineages. We further characterized their evolutionary history and inferred a contraction of crinkler-encoding genes in the subclade of Phytophthora containing P. ramorum. There were losses of multiple families and a near complete loss of paralogs in the largest core crinkler family in the ancestor of P. ramorum and sister species P. lateralis. Secreted glycoside hydrolase enzymes showed a similar degree of variation in abundance among genomes of P. ramorum lineages as that observed among several Phytophthora species. We found plasticity among genomes from multiple lineages in a Phytophthora species and provide insights into the evolutionary history of a class of anciently conserved effector genes.

Comparative Chloroplast Genomes and Phylogenetic Relationships of True Mangrove Species Brownlowia tersa and Brownlowia argentata (Malvaceae)

Brownlowia tersa and Brownlowia argentata are two true mangroves in the genus Brownlowia in Malvaceae, and they are a near-threatened and a data-deficient species, respectively. However, the genomic resources of Brownlowia have not been reported for studying their phylogeny and evolution. Here, we report the chloroplast genomes of B. tersa and B. argentata based on stLFR data that were 159,478 and 159,510 base pairs in length, respectively. Both chloroplast genomes contain 110 unique genes and one infA pseudogene. Sixty-eight RNA-editing sites were detected in 26 genes in B. argentata. A comparative analysis with related species showed similar genome sizes, genome structures, and gene contents as well as high sequence divergence in non-coding regions. Abundant SSRs and dispersed repeats were identified. Five hotspots, psbI-trnS, trnR-atpA, petD-rpoA, rpl16-rps3, and trnN-ndhF, were detected among four species in Brownlowioideae. One hotspot, rps14-psaB, was observed in the two Brownlowia species. Additionally, phylogenetic analysis supported that the Brownlowia species has a close relationship with Pentace triptera. Moreover, rpoC2 was a candidate gene for adaptive evolution in the Brownlowia species compared to P. triptera. Thus, these chloroplast genomes present valuable genomic resources for further evolutionary and phylogenetic studies of mangroves and plant species in Malvaceae.

Therapeutic potential of s-cdcs in myocardial infarction: interactions with standard drugs

Abstract Introduction Myocardial infarction (MI) remains a leading global cause of mortality and is commonly treated with Captopril, Spironolactone, and Bisoprolol. Emerging therapies, such as the secretome derived from cardiosphere-derived cells (S-CDCs), have shown potential in reducing MI scar size. This study aims to evaluate the potential therapeutic implications of S-CDCs in MI treatment, particularly in relation to the aforementioned standard drugs. Methods CDCs (n = 4) were isolated from cardiac explants of Large White pigs and cultured in DMEM with 1% ITS and antibiotics for four days. The conditioned medium was centrifuged and ultrafiltered (3 kDa) to obtain the S-CDCs. The content of S-CDCs, including miRNAs and genes, was analysed using transcriptomic and qPCR techniques. Bioinformatics tools were used to establish the interaction network (IN) of Captopril, Bisoprolol, and Spironolactone with their target genes through the String app within Cytoscape. miRTargetLink 2.0 was used to predict miRNA-gene interactions, and FunRich analysed the gene network. Finally, the content of S-CDCs was compared with previously identified miRNAs and genes, and an interaction network was generated using Cytoscape. Results Our findings show that S-CDCs contain six miRNAs that interact with target genes of Captopril and Spironolactone. Additionally, S-CDCs harbor genes that interact with those affected by the drugs, with a predominant influence from Spironolactone. Conclusion S-CDCs may mimic the effects of Captopril and Spironolactone, potentially simplifying MI treatment. However, further studies are necessary to validate these findings.

P0036 NRG1, a gene significantly detected from intestinal mucosa eccDNA, may predict therapeutic response in Inflammatory Bowel Disease

Abstract Background Many patients with Inflammatory Bowel Diseases do not respond to biological therapies. Extrachromosomal circular DNA(eccDNA) has been showed to play a role in the pathophysiology of IBD, as there is a higher presence of eccDNA in the intestinal mucosa of these patients. By characterizing the gene content of eccDNA, up-regulation of certain genes is observed; one of these is NRG1 (Neuregulin 1), an EGF ligand that guides tissue repair after injury and is associated with tissue plasticity. This gene is located on chromosome 8p12 and it is expressed in macrophages, Paneth cells, and stromal mesenchymal cells of the stem cell niche. In the context of IBD, where chronic inflammation is a hallmark, NRG1 could potentially modulate the immune response to reduce inflammation and promote healing. It is important to understand whether its expression within eccDNA may correlate with a particular course of the disease. Methods eccDNA was extracted from intestinal mucosa samples derived from patients diagnosed with IBD and amplified using the Circle-Seq analysis. Following sequencing, bioinformatic interpretation of the data was performed, through which a list of gene fragments present on the circles of individual patients and their localization was obtained. Finally, the presence of the gene found up-regulated by the bioinformatic analysis was confirmed using Real Time PCR. Results Starting from 99 intestinal mucosa samples from IBD patients, whose eccDNA was sequenced, circles containing fragments of NRG1 were found in 22 of them; its presence was compared to samples of diseased mucosa biopsies versus healthy mucosa from the same IBD patient. The number of circles from NRG1 is greater in diseased mucosa samples compared to healthy ones, in both UC and CD patients. Furthermore stratifying patients by response to therapy, about 70% of responders to IBD-therapy were NRG1- , with Odds Ratio <1. Conclusion Preliminary results show that NRG1, a gene significantly detected from intestinal mucosa eccDNA, may predict therapeutic response in Inflammatory Bowel Disease. Further analysis are needed to confirm these data.

Comprehensive analysis of 111 Pleuronectiformes mitochondrial genomes: insights into structure, conservation, variation and evolution

BackgroundPleuronectiformes, also known as flatfish, are important model and economic animals. However, a comprehensive genome survey of their important organelles, mitochondria, has been limited. Therefore, we aim to analyze the genomic structure, codon preference, nucleotide diversity, selective pressure and repeat sequences, as well as reconstruct the phylogenetic relationship using the mitochondrial genomes of 111 flatfish species.ResultsOur analysis revealed a conserved gene content of protein-coding genes and rRNA genes, but varying numbers of tRNA genes and control regions across species. Various gene rearrangements were found in flatfish species, especially for the rearrangement of nad5-nad6-cytb block in Samaridae family, the swapping rearrangement of nad6 and cytb gene in Bothidae family, as well as the control region translocation and tRNA-Gln gene inversion in the subfamily Cynoglossinae, suggesting their unique evolutionary history and/or functional benefit. Codon usage showed obvious biases, with adenine being the most frequent nucleotide at the third codon position. Nucleotide diversity and selective pressure analysis suggested that different protein-coding genes underwent varying degrees of evolutionary pressure, with cytb and cox genes being the most conserved ones. Phylogenetic analysis using both whole mitogenome information and concatenated independently aligned protein-coding genes largely mirrored the taxonomic classification of the species, but showed different phylogeny. The identification of simple sequence repeats and various long repetitive sequences provided additional complexity of genome organization and offered markers for evolutionary studies and breeding practices.ConclusionsThis study represents a significant step forward in our comprehension of the flatfish mitochondrial genomes, providing valuable insights into the structure, conservation and variation within flatfish mitogenomes, with implications for understanding their evolutionary history, functional genomics and fisheries management. Future research can delve deeper into conservation biology, evolutionary biology and functional usages of variations.

Extensive transcriptional differentiation and specialization of a single-host parasite aligns with niche turnover generated by its host's metamorphosis.

Foundational theory on life cycle evolution suggests that given genetic independence, the phenotypes presented by different life stages will diverge more when they occupy more distinct niches. When divergence between stages is significant and punctual, we typically consider the life cycle complex. In parasites, the delineation between simple and complex life cycles is usually made between those that utilize single and multiple host species. However, many parasites can experience significant niche shifts in a single host. To explore the potential for a host's metamorphosis to shape divergence between stages across its parasite's life cycle, we quantified the transcriptional differentiation and specialization that the protozoan parasite Ophryocystis elektroscirrha exhibits across the metamorphosis of its host, the monarch butterfly. We found evidence that O. elektroscirrha differentiates in concordance with the ecological turnover imposed by monarch transitions to different stages, and that patterns of transcriptional decoupling across O. elektroscirrha exceeded even those of its host. However, due to its greater gene content, the monarch butterfly exhibited greater total transcriptional turnover than its parasite. These findings suggest that a deeper understanding of life cycle evolution for both free-living and parasitic lifestyles may be facilitated by more nuanced and continuous descriptions of life cycle complexity.

Global transcriptome changes during growth of a novel Penicillium coffeae isolate on the wheat stripe rust fungus, Puccinia striiformis f. sp. tritici.

Wheat stripe rust caused by the fungus Puccinia striiformis f. sp. tritici (Pst) is currently the most destructive disease of wheat. The major control methods which include the deployment of resistant wheat cultivars and application of chemical fungicides are losing efficiency as the fungus evolves. Natural antagonists of Pst may be an avenue for alternative and environmentally sustainable control of the disease in the field. Here we describe a novel fungus found growing on Pst pustules. We identified the fungus as a novel isolate of the plant endophyte Penicillium coffeae. We present a high-quality reference genome and a comparative transcriptomic analysis used to investigate how the fungus deploys its genes during growth amongst Pst spores. The gene content of the P. coffeae ANU01 genome is suggestive of a generalist that makes use of diverse substrates. An abundance of genes related to lipid, amino acid and carbohydrate metabolism indicate that P. coffeae ANU01 has evolved the ability to exploit nutrient stores in Pst urediniospores. P. coffeae ANU01 deploys a number of biosynthetic gene clusters during growth on Pst spores, potentially to inhibit urediniospores germination and halt defence responses. A number of genes encoding carbohydrate active enzymes are also highly upregulated, suggesting targeting and degradation of Pst urediniospores structures. Alongside carbohydrates, P. coffeae ANU01 appears to target spore lipids as a nutrient source, secreting several highly upregulated lipases. Our findings broaden the understanding of growth associated with rust spores as an evolutionary strategy and provide insight into the genes potentially required for this process.

Gene content of seawater microbes is a strong predictor of water chemistry across the Great Barrier Reef

BackgroundSeawater microbes (bacteria and archaea) play essential roles in coral reefs by facilitating nutrient cycling, energy transfer, and overall reef ecosystem functioning. However, environmental disturbances such as degraded water quality and marine heatwaves, can impact these vital functions as seawater microbial communities experience notable shifts in composition and function when exposed to stressors. This sensitivity highlights the potential of seawater microbes to be used as indicators of reef health. Microbial indicator analysis has centered around measuring the taxonomic composition of seawater microbial communities, but this can obscure heterogeneity of gene content between taxonomically similar microbes, and thus, microbial functional genes have been hypothesized to have more scope for predictive potential, though empirical validation for this hypothesis is still pending. Using a metagenomics study framework, we establish a functional baseline of seawater microbiomes across offshore Great Barrier Reef (GBR) sites to compare the diagnostic value between taxonomic and functional information in inferring continuous physico-chemical metrics in the surrounding reef.ResultsIntegrating gene-centric metagenomics analyses with 17 physico-chemical variables (temperature, salinity, and particulate and dissolved nutrients) across 48 reefs revealed that associations between microbial functions and environmental parameters were twice as stable compared to taxonomy-environment associations. Distinct seasonal variations in surface water chemistry were observed, with nutrient concentrations up to threefold higher during austral summer, explained by enhanced production of particulate organic matter (POM) by photoautotrophic picocyanobacteria, primarily Synechococcus. In contrast, nutrient levels were lower in winter, and POM production was also attributed to Prochlorococcus. Additionally, heterotrophic microbes (e.g., Rhodospirillaceae, Burkholderiaceae, Flavobacteriaceae, and Rhodobacteraceae) were enriched in reefs with elevated dissolved organic carbon (DOC) and phytoplankton-derived POM, encoding functional genes related to membrane transport, sugar utilization, and energy metabolism. These microbes likely contribute to the coral reef microbial loop by capturing and recycling nutrients derived from Synechococcus and Prochlorococcus, ultimately transferring nutrients from picocyanobacterial primary producers to higher trophic levels.ConclusionThis study reveals that functional information in reef-associated seawater microbes more robustly associates with physico-chemical variables than taxonomic data, highlighting the importance of incorporating microbial function in reef monitoring initiatives. Our integrative approach to mine for stable seawater microbial biomarkers can be expanded to include additional continuous metrics of reef health (e.g., benthic cover of corals and macroalgae, fish counts/biomass) and may be applicable to other large-scale reef metagenomics datasets beyond the GBR.D4ZFkyo-_x3xtsAViMg6HSVideo