PANNZER-A practical tool for protein function prediction

Molecular features and expression characteristics of a novel tumour necrosis factor-α paralog from snubnose pompano (Trachinotus blochii)

Tumour necrosis factor alpha (TNF-α) is a pivotal cytokine in vertebrate immunity. Considering the increasing scientific interest for TNF-α in piscine biology, the paper detailed the characteristics of a novel tnf-α gene from a high-value mariculture species, Trachinotus blochii. The tbtnf-α complementary DNA (cDNA) of 1385 bp encoded an open reading frame of 762 bp, 3' untranslated region (3' UTR) of 484 bp and 5' UTR of 139 bp. The deduced Tbtnf-α1 showed the highest sequence identity to that of Seriola dumerili (∼83%). The comparative phylogenetics identified the protein as the TNF-α paralog 1. Tbtnf-α1 displayed all the hallmark features of other teleost TNF-α, suggesting similar immune-related functions. However, the Tbtnf-α1 was predicted to be more acidic and less thermostable. The study generated the three-dimensional (3-D) structure model of Tbtnfα-1 based on the protein sequence that can be applied in future research. The genomic organization of tbtnfα-1 contained four exons and three introns. Real-time polymerase chain reaction (PCR) analysis in healthy conditions showed the constitutive expression and wide distribution of tbtnfα-1 in a tissue-specific manner, with maximum expression in the kidney. As in silico analysis predicted the biological function of the novel TNF-α as a regulator in the defence response to bacterial infection, functional validation was done through the expression analysis following exposure to a marine pathogen (Vibrio harveyi) challenge. The results showed that the expression of tbtnf-α1 in the liver, spleen, heart, gill and kidney was significantly upregulated compared to the control fish after the challenge at differential time points post-infection. The study also demonstrated the kinetics of tbtnfα-1 expression in the liver, spleen, heart, gill and kidney at 6 to 48 h post-infection, and the results showed the peak expression at 24 h in all the tissues followed by a drop in the expression. Briefly, the present study detailed the sequence, structural and functional characteristics of tnf-α1 in the immune response of silver pompano.

Comparative Genomics Points to Ecological Drivers of Genomic Divergence Among Intertidal Limpets

Comparative genomic studies of closely related taxa are important for our understanding of the causes of divergence on a changing Earth. This being said, the genomic resources available for marine intertidal molluscs are limited and currently, there are few publicly available high-quality annotated genomes for intertidal species and for molluscs in general. Here we report transcriptome assemblies for six species of Patellogastropoda and genome assemblies and annotations for three of these species (Scurria scurra, Scurria viridula and Scurria zebrina). Comparative analysis using these genomic resources suggest that and recently diverging lineages (10-20 Mya) have experienced similar amounts of contractions and expansions but across different gene families. Furthermore, differences among recently diverged species are reflected in variation in the amount of coding and noncoding material in genomes, such as amount of repetitive elements and lengths of transcripts and introns and exons. Additionally, functional ontologies of species-specific and duplicated genes together with demographic inference support the finding that recent divergence among members of the genus Scurria aligns with their unique ecological characteristics. Overall, the resources presented here will be valuable for future studies of adaptation in molluscs and in intertidal habitats as a whole.

Influence of High Temperature and Ammonia and Nitrite Accumulation on the Physiological, Structural, and Genetic Aspects of the Biology of Largemouth Bass (Micropterus salmoides)

Hyperthermia and nitrogenous pollutants like ammonia and nitrite are common risk factors that adversely affect fish health and pose significant threats to the aquaculture industry. However, the impacts of high temperatures on the accumulation of nitrogenous pollutants in the water of the aquaculture systems and their toxicity to farmed fish are not well understood. In this study, juvenile largemouth bass (Micropterus salmoides, LMB) were kept at 28 °C and 34 °C in a closed aquatic system to investigate the effects of higher temperatures on ammonia and nitrite accumulation. The fish were fed 2% of their body weight daily for a 14-day experiment. Ammonia levels gradually increased, peaking on day 7 at 34 °C and on day 9 at 28 °C, then decreased to near zero. Nitrite levels remained low initially and increased rapidly along with the reduction in ammonia levels at both temperatures. The 34 °C high temperature accelerated the accumulation of ammonia and its transformation into nitrite compared to 28 °C. Fish were sampled on day 1 (low ammonia and low nitrite, LALN), day 8 (high ammonia and low nitrite, HALN), and day 14 (low ammonia and high nitrite, LAHN) to explore toxic effects. Successive exposure to high levels of ammonia and nitrite caused oxidative stress in the liver and significant pathogenic changes in the liver and spleen, with more pronounced impacts observed at 34 °C. Significant changes in gene expression were detected in the liver and spleen of fish sampled at HALN and LAHN, compared to those at LALN, with upregulated genes primarily associated with extracellular matrix (ECM) and cytoskeleton organization. A second experiment was conducted at the same temperatures but without ammonia/nitrite accumulation. The results of this experiment confirmed the combined effects of hyperthermia and ammonia/nitrite toxicity on the expression of genes involved in ECM-receptor interaction and TGF-beta signaling. These findings are valuable for optimizing cultivation environments and promoting the health of farmed LMB.

The endophytic fungus Cosmosporella sp. VM-42 from Vinca minor is a source of bioactive compounds with potent activity against drug-resistant bacteria

Medicinal plants serve as valuable resources for the isolation of endophytic fungi. Vinca minor is a well-known producer of important vinca alkaloids and emerges as a promising source of endophytic fungi with antibacterial potential and biosynthetic capacity. In this study, we isolated an endophytic fungus from V. minor and identified it as Cosmosporella sp. VM-42. To date, relatively little is known about this fungal genus. The ethyl acetate extract of this isolate selectively inhibited Gram-positive bacteria, such as methicillin-sensitive and methicillin-resistant Staphylococcus aureus (MSSA and MRSA). Therefore, we isolated the most abundant compound from the crude extract and identified it as nectriapyrone with MIC and MBC values ranging from 125 to 62.5 µg/mL against MSSA and MRSA strains. We further sequenced and annotated the 39.07 Mb genome of the isolate, revealing that it encodes 9842 protein-coding genes, including 415 genes for carbohydrate-active enzymes and various biosynthetic gene clusters. Our untargeted metabolomic analysis shows that the fungus produces various secondary metabolites, including cyclodepsipeptides, dimeric naphtho-γ-pyrones, and macrolactones, which are known to have antifungal and antibacterial activities. In addition, we used small-molecule epigenetic modulators to activate the expression of silent biosynthetic gene clusters to broaden the chemical profile of Cosmosporella sp. VM-42. Taken together, we provide a first systematic analysis of Cosmosporella sp. VM-42, and our results show that it is a promising source of compounds with pharmacological potential against drug resistant bacteria.

Shifts in sex-specific immune gene expression in a beetle with parental care

Males and females generally differ in resource investment strategies in order to maximise reproductive output. These strategies involve the control of important systemic processes such as self-maintenance and immune activity, which in turn could be traded-off against aspects of reproduction in a sex-specific manner. While some aspects of this immunomodulation have been previously shown in domestic animals, sex-specific immune modulation using repeated sampling over the breeding period has rarely been tested in the wild. Here we used Lethrus apterus, a sexually dimorphic beetle with parental care, to investigate the association between sex roles (e.g. offspring provisioning) and sex-specific immune gene expression. By determining the immune gene activation of males and females at five successive moments within the active season, we found that their sex-specific immune gene expression varies substantially across the active season, alternating between male bias to female bias and vice versa. Though, when pooling all sampling dates together, there was no overall difference in the number of up-regulated immune genes between the sexes. Sex roles in this beetle are associated with energetically demanding behaviours that could potentially explain our results. We highlight the importance of successive sampling protocols to understand ecological dynamics in the wild.

Independent origins and non-parallel selection signatures of triclabendazole resistance in Fasciola hepatica

Triclabendazole (TCBZ) is the primary treatment for fascioliasis, a global foodborne zoonosis caused by Fasciola hepatica. Widespread resistance to TCBZ (TCBZ-R) in livestock and a rapid rise in resistant human infections are significant concerns. To understand the genetic basis of TCBZ-R, we sequenced the genomes of 99 TCBZ-sensitive (TCBZ-S) and 210 TCBZ-R adult flukes from 146 bovine livers in Cusco, Peru. We identify genomic regions of high differentiation (FST outliers above the 99.9th percentile) that encod genes involved in the EGFR-PI3K-mTOR-S6K pathway and microtubule function. Transcript expression differences are observed in microtubule-related genes between TCBZ-S and -R flukes, both without drug treatment and in response to treatment. Using only 30 SNPs, it is possible to differentiate between TCBZ-S and -R parasites with ≥75% accuracy. Our outlier loci are distinct from the previously reported TCBZ-R-associated QTLs in the UK, suggesting an independent evolution of resistance alleles. Effective genetics-based TCBZ-R surveillance must consider the heterogeneity of loci under selection across diverse geographical populations.

In Silico Functional Annotation and Structural Characterization of Hypothetical Proteins in Bacillus paralicheniformis and Bacillus subtilis Isolated from Honey

Bacillus species are ubiquitous and survive in competitive microbial communities under adverse environmental conditions. Bacillus paralicheniformis and Bacillus subtilis obtained from honey revealed a significant proportion of proteins within their genomes as uncharacterized hypothetical proteins (HPs). A total of 1007 HP sequences were evaluated, resulting in the successful annotation of 56 HPs by assigning specific functions to them. A systematic in silico approach, integrating a range of bioinformatics tools and databases to annotate functions, characterize physicochemical properties, determine subcellular localization, and study protein-protein interactions, was used. Homology and de novo models were generated for the HPs, coupled with iterative remodeling and molecular dynamics (MD) simulations. HPs having significant roles in sporulation, biofilm formation, motility, ion transportation, regulation of metabolic processes, DNA repair, replication, and transcription were identified. Classical MD simulations of globular and transducer membrane proteins, along with postprocessing analyses, refined our structural predictions and provided deeper insights into the stability and functional dynamics of the protein structures under physiological conditions. Moreover, we observed a correlation between the percentage of α helix, β sheet, and coil structures in globular proteins and transducer membrane proteins. The integration of iterative loop modeling, MD simulations, and Dictionary of Secondary Structure in Proteins analysis further validated our predicted models and facilitated the identification of regions critical for protein function, thereby enhancing the overall reliability and robustness of our functional annotations. Furthermore, annotation of these hypothetical proteins aids in identifying novel proteins within bacterial cells, ultimately contributing to a deeper understanding of bacterial cell biology and their use for biotechnological purposes.

Profiling trace organic chemical biotransformation genes, enzymes and associated bacteria in microbial model communities

Microbial biotransformation of trace organic chemicals (TOrCs) is an essential process in wastewater treatment to eliminate environmental pollution. Understanding TOrC biotransformation mechanisms, especially at their original concentrations, is important to optimize treatment performance, whereas our current knowledge is limited. Here, we investigated the biotransformation of seven TOrCs by 24 model communities. The genome-centric analyses unraveled potential biotransformation drivers concerning functional genes, enzymes, and responsible bacteria. We obtained efficient model communities for completely removing ibuprofen, caffeine, and atenolol, with transformation efficiencies between 0 % and 45 % for sulfamethoxazole, carbamazepine, trimethoprim, and gabapentin. Biotransformation performance was not fully reflected by the presence of known biotransformation genes and enzymes in the metagenomes of the communities. Functional similar homologs to existing biotransformation genes and enzymes (e.g., long-chain-fatty-acid-CoA ligase encoded by fadD and fadD13 gene) could play critical roles in TOrC metabolism. Finally, we identified previously undescribed degrading strains, e.g., Rhodococcus qingshengii for caffeine, carbamazepine, sulfamethoxazole, and ibuprofen biotransformation, and potential transformation enzymes, e.g., SDR family oxidoreductase targeting sulfamethoxazole and putative hypothetical proteins for caffeine, atenolol and gabapentin biotransformation. This study provides fundamental insights into naturally assembled low-complexity degrader communities that can help to identify and tackle the current research gaps on biotransformation.

Spatial proteomics of Onchocerca volvulus with pleomorphic neoplasms shows local and systemic dysregulation of protein expression

Onchocerca volvulus is the agent of onchocerciasis (river blindness) and targeted by WHO for elimination though mass drug administration with ivermectin. A small percentage of adult female worms develop pleomorphic neoplasms (PN) which occur more frequently after ivermectin treatment. Worms with PN have a lower life expectancy and improved understanding of proteins expressed in PN and their impact on different tissues could help elucidate the mechanisms of macrofilaricidal activity of ivermectin. Within paraffin embedded nodules removed after ivermectin treatment, we detected 24 (5.6%) O. volvulus females with PN. To assess the protein inventory of the PN and identify proteins potentially linked with tumor development, we used laser capture microdissection and highly sensitive mass spectrometry analysis. Three female worms were used to compare the protein profiles of three tissue types (body wall, uterus, and intestine) to the PN, and then to healthy female worms without PN. The healthy females showed all normal embryogenesis. In PN worms, 151 proteins were detected in the body wall, 215 proteins in the intestine, 47 proteins in the uterus and 1,577 proteins in the PN. Only the uterus of one PN female with some stretched intrauterine microfilariae had an elevated number of proteins (601) detectable, while in the uteri of the healthy females 1,710 proteins were detected. Even in tissues that were not directly affected by PN (intestine, body wall), fewer proteins were detected compared to the corresponding tissue of the healthy controls. Immunolocalization of calcium binding protein OvDig-1 (OVOC8391), which was identified through mass spectrometry as one of the proteins with the highest spectral counts in the PN tissue triplicates, allowed us to confirm the results using an independent method. In conclusion we identified proteins that are potentially linked to the development of PN, and systemic dysregulation of protein expression may contribute to worm mortality.

Improvement in genomic prediction of maize with prior gene ontology information depends on traits and environmental conditions

Classical genomic prediction approaches rely on statistical associations between traits and markers rather than their biological significance. Biologically informed selection of genomic regions can help prioritize polymorphisms by considering underlying biological processes, making prediction models robust and accurate. Gene ontology (GO) terms can be used for this purpose, and the information can be integrated into genomic prediction models through marker categorization. It allows likely causal markers to account for a certain portion of genetic variance independently from the remaining markers. We systematically tested a list of 5110 GO terms for their predictive performance for physiological (platform traits) and productivity traits (field grain yield) in a maize (Zea mays L.) panel using genomic features best linear unbiased prediction (GFBLUP) model. Predictive abilities were compared to the classical genomic best linear unbiased prediction (GBLUP). Predictive gains with categorizing markers based on a given GO term strongly depend on the trait and on the growth conditions, as a term can be useful for a given trait in a given condition or somewhat similar conditions but not useful for the same trait in a different condition. Overall, results of all GFBLUP models compared to GBLUP show that the former might be less efficient than the latter. Even though we could not identify a prior criterion to determine which GO terms can offer benefit to a given trait, we could a posteriori find biological interpretations of the results, meaning that GFBLUP could be helpful if more about the gene functions and their relationships with the growth conditions was known.

Exploring the principles behind antibiotics with limited resistance

Antibiotics that target multiple cellular functions are anticipated to be less prone to bacterial resistance. Here we hypothesize that while dual targeting is crucial, it is not sufficient in preventing resistance. Only those antibiotics that simultaneously target membrane integrity and block another cellular pathway display reduced resistance development. To test the hypothesis, we focus on three antibiotic candidates, POL7306, Tridecaptin M152-P3 and SCH79797, all of which fulfill the above criteria. Here we show that resistance evolution against these antibiotics is limited in ESKAPE pathogens, including Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa, while dual-target topoisomerase antibiotics are prone to resistance. We discover several mechanisms restricting resistance. First, de novo mutations result in only a limited elevation in resistance, including those affecting the molecular targets and efflux pumps. Second, resistance is inaccessible through gene amplification. Third, functional metagenomics reveal that mobile resistance genes are rare in human gut, soil and clinical microbiomes. Finally, we detect rapid eradication of bacterial populations upon toxic exposure to membrane targeting antibiotics. We conclude that resistance mechanisms commonly found in natural bacterial pathogens provide only limited protection to these antibiotics. Our work provides guidelines for the future development of antibiotics.

High-quality genome assembly and annotation of Thalassiosira rotula (synonym of Thalassiosira gravida)

Diatoms are unicellular eukaryotic microorganisms thriving in most aquatic environments thanks to the expression of biosynthetic pathways for secondary metabolites involved in defence and adaptation to environmental changes. The sequencing of the transcriptome of the cosmopolitan diatom Thalassiosira rotula Meunier 1910 (synonym of Thalassiosira gravida Cleve 1896) and of the metagenome of its associated microbiome revealed the presence of biosynthetic pathways synthesising molecules and compounds useful for the algae survival and with potential biotechnological applications. Here we present the genome of a Neapolitan T. rotula strain, which is 672 Mbp in size due to a high proportion of repetitive elements (63.59%) and segmental duplications (14%), while the number of predicted genes resulted to be comparable to that of smaller diatom genomes. DNA methylation was predominantly located in transposable elements.

Chromosome-level genome assembly of Phytoseiulus persimilis Athias-Henriot

As a globally recognized predatory mite, Phytoseiulus persimilis Athias-Henriot is known for its highly effective control of pest mites. Also, as a model species in Phytoseiidae, P. persimilis possesses unique biological characteristics, such as the first offspring developing into a male with a strict sex sequence. However, the genetic mechanisms have not been fully unrevealed yet. To lay the groundwork for genetic research, we presented a high-quality chromosomal genome of P. persimilis with PacBio HiFi and Hi-C data. The total length of genome is 214.23 Mb, of which 190.48 (88.91%) is anchored on 4 chromosomes. The scaffold N50 is 57.95 Mb and the BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness is 98.3%. Repeat elements comprise 27.59% (59.10 Mb) of the genome. The genome contained 15,847 predicted protein-coding genes, 12,344 of which were annotated for function. This high-quality genome of P. persimilis would allow us to explore the genetic mechanism underlying the biological characteristics of the Phytoseiidae species, and provide possibilities for the industrial optimization of commercial predatory mites in the future.

Genome assembly of Hawaiian flower thrips Thrips hawaiiensis (Thysanoptera: Thripidae)

The Hawaiian flower thrips, Thrips hawaiiensis, is a common flower inhabiting pest of various horticultural plant species. It damages flowers and fruits by puncturing. T. hawaiiensis shows a rapidly developed resistance to chemical control. The lack of a high-quality reference genome limits our understanding of the genetics of T. hawaiiensis. Here, we sequenced the genome of T. hawaiiensis using Oxford Nanopore sequencing technology, Illumina, and Hi-C technology, yielding a genome assembly of 287.59 Mb with scaffold N50 of 13.84 Mb. BUSCO analysis demonstrated the T. hawaiiensis genome assembly has a high-level completeness of 98.7%. In total, 18,289 protein-coding genes were annotated and 26.69% of the genome were annotated as repeats. Our study presents the first high-quality genome assembly of T. hawaiiensis and lays the foundation for further studies on thrips genetic characteristics and pest management.

Chromosome-Level Genome Assembly and Annotation of Corallium rubrum: A Mediterranean Coral Threatened by Overharvesting and Climate Change

Reference genomes are key resources in biodiversity conservation. Yet, sequencing efforts are not evenly distributed across the tree of life raising concerns over our ability to enlighten conservation with genomic data. Good-quality reference genomes remain scarce in octocorals while these species are highly relevant targets for conservation. Here, we present the first annotated reference genome in the red coral, Corallium rubrum (Linnaeus, 1758), a habitat-forming octocoral from the Mediterranean and neighboring Atlantic, impacted by overharvesting and anthropogenic warming-induced mass mortality events. Combining long reads from Oxford Nanopore Technologies (ONT), Illumina paired-end reads for improving the base accuracy of the ONT-based genome assembly, and Arima Hi-C contact data to place the sequences into chromosomes, we assembled a genome of 532 Mb (20 chromosomes, 309 scaffolds) with contig and scaffold N50 of 1.6 and 18.5 Mb, respectively. Fifty percent of the sequence (L50) was contained in seven superscaffolds. The consensus quality value of the final assembly was 42, and the single and duplicated gene completeness reported by BUSCO was 86.4% and 1%, respectively (metazoa_odb10 database). We annotated 26,348 protein-coding genes and 34,548 noncoding transcripts. This annotated chromosome-level genome assembly, one of the first in octocorals and the first in Scleralcyonacea order, is currently used in a project based on whole-genome resequencing dedicated to the conservation and management of C. rubrum.

ESKAPE pathogens rapidly develop resistance against antibiotics in development in vitro

Despite ongoing antibiotic development, evolution of resistance may render candidate antibiotics ineffective. Here we studied in vitro emergence of resistance to 13 antibiotics introduced after 2017 or currently in development, compared with in-use antibiotics. Laboratory evolution showed that clinically relevant resistance arises within 60 days of antibiotic exposure in Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa, priority Gram-negative ESKAPE pathogens. Resistance mutations are already present in natural populations of pathogens, indicating that resistance in nature can emerge through selection of pre-existing bacterial variants. Functional metagenomics showed that mobile resistance genes to antibiotic candidates are prevalent in clinical bacterial isolates, soil and human gut microbiomes. Overall, antibiotic candidates show similar susceptibility to resistance development as antibiotics currently in use, and the corresponding resistance mechanisms overlap. However, certain combinations of antibiotics and bacterial strains were less prone to developing resistance, revealing potential narrow-spectrum antibacterial therapies that could remain effective. Finally, we develop criteria to guide efforts in developing effective antibiotic candidates.

An updated reference genome of Barbatula barbatula (Linnaeus, 1758)

The stone loach Barbatula barbatula is a benthic fish species widely distributed throughout Europe, primarily inhabiting stony upper sections of stream networks. This study presents an updated genome assembly of B. barbatula, contributing to the species' available genomic resources for downstream applications such as conservation genetics. The draft assembly was 550 Mbp in size, with an N50 of 11.21 Mbp. We used the species' available chromosome scaffolds to finish the genome. The final assembly had a BUSCO score of 96.7%. We identified 23270 protein-coding genes, and the proteome exhibited high completeness with BUSCO (93.1%) and OMArk (90.81%). Despite using multiple approaches to reduce duplicate contigs, we observed a relatively high duplicate ratio of 6.1% (BUSCO) and 8.52% (OMArk) in the annotations. We aimed to find microsatellite loci present in both the species' publicly available genome and the new assembly to aid marker development for downstream analyses. This dataset serves as a reference for genomic analysis and is useful for developing markers to study the species' biodiversity and support conservation efforts.

Evaluating the advancements in protein language models for encoding strategies in protein function prediction: a comprehensive review

Protein function prediction is crucial in several key areas such as bioinformatics and drug design. With the rapid progress of deep learning technology, applying protein language models has become a research focus. These models utilize the increasing amount of large-scale protein sequence data to deeply mine its intrinsic semantic information, which can effectively improve the accuracy of protein function prediction. This review comprehensively combines the current status of applying the latest protein language models in protein function prediction. It provides an exhaustive performance comparison with traditional prediction methods. Through the in-depth analysis of experimental results, the significant advantages of protein language models in enhancing the accuracy and depth of protein function prediction tasks are fully demonstrated.

Adaptive evolution of stress response genes in parasites aligns with host niche diversity

BACKGROUND

Stress responses are key the survival of parasites and, consequently, also the evolutionary success of these organisms. Despite this importance, our understanding of the evolution of molecular pathways dealing with environmental stressors in parasitic animals remains limited. Here, we tested the link between adaptive evolution of parasite stress response genes and their ecological diversity and species richness. We comparatively investigated antioxidant, heat shock, osmoregulatory, and behaviour-related genes (foraging) in two model parasitic flatworm lineages with contrasting ecological diversity, Cichlidogyrus and Kapentagyrus (Platyhelminthes: Monopisthocotyla), through whole-genome sequencing of 11 species followed by in silico exon bait capture as well as phylogenetic and codon analyses.

RESULTS

We assembled the sequences of 48 stress-related genes and report the first foraging (For) gene orthologs in flatworms. We found duplications of heat shock (Hsp) and oxidative stress genes in Cichlidogyrus compared to Kapentagyrus. We also observed positive selection patterns in genes related to mitochondrial protein import (Hsp) and behaviour (For) in species of Cichlidogyrus infecting East African cichlids-a host lineage under adaptive radiation. These patterns are consistent with a potential adaptation linked to a co-radiation of these parasites and their hosts. Additionally, the absence of cytochrome P450 and kappa and sigma-class glutathione S-transferases in monogenean flatworms is reported, genes considered essential for metazoan life.

CONCLUSIONS

This study potentially identifies the first molecular function linked to a flatworm radiation. Furthermore, the observed gene duplications and positive selection indicate the potentially important role of stress responses for the ecological adaptation of parasite species.

Introduction to Integrated Proteogenomic Pipeline for Dealing with Pathogenic Missense SNPs

Proteogenomics is a multi-omics setup combining mass spectrometry and next-generation sequencing (NGS) technologies (using genomics and/or transcriptomics) with main aims of improving genome annotation and facilitating characterization of proteo-isoforms. However, working with proteogenomic approach is a very challenging task as it is generating multi-omics data and integrating these data for interpretation of results for biological or clinical implications. There is an urgent need for the development of protocols for integrated proteogenomics approaches. Genome resequencing yields massive data for missense single-nucleotide polymorphisms (SNP), and SNPs are yet not fully covered for their pathogenic nature using proteogenomic approaches. In this chapter, we present such a protocol for dealing with pathogenic missense SNPs using an integrated proteogenomics pipeline combining several steps: DNA-Seq, RNA-Seq, mass spectroscopy (MS), making customized databases of produced datasets, and screening and filtering for useful MS spectrums. This protocol also provides users with tricks and tips for the modifications, based on the requirements of the projects.

Proteomic characterization and comparison of the infective and adult life stage secretomes from Necator americanus and Ancylostoma ceylanicum

More than 470 million people globally are infected with the hookworms Ancylostoma ceylanicum and Necator americanus, resulting in an annual loss of 2.1 to 4 million disability-adjusted-life-years. Current infection management approaches are limited by modest drug efficacy, the costs associated with frequent mass drug administration campaigns, and the risk of reinfection and burgeoning drug resistance. Subunit vaccines based on proteins excreted and secreted (ES) by hookworms that reduce worm numbers and associated disease burden are a promising management strategy to overcome these limitations. However, studies on the ES proteomes of hookworms have mainly described proteins from the adult life stage which may preclude the opportunity to target the infective larva. Here, we employed high resolution mass spectrometry to identify 103 and 57 ES proteins from the infective third larvae stage (L3) as well as 106 and 512 ES proteins from the adult N. americanus and A. ceylanicum respectively. Comparisons between these developmental stages identified 91 and 41 proteins uniquely expressed in the L3 ES products of N. americanus and A. ceylanicum, respectively. We characterized these proteins based on functional annotation, KEGG pathway analysis, InterProScan signature and gene ontology. We also performed reciprocal BLAST analysis to identify orthologs across species for both the L3 and adult stages and identified five orthologous proteins in both life stages and 15 proteins that could be detected only in the L3 stage of both species. Last, we performed a three-way reciprocal BLAST on the L3 proteomes from both hookworm species together with a previously reported L3 proteome from the rodent hookworm Nippostrongylus brasiliensis, and identified eight L3 proteins that could be readily deployed for testing using well established rodent models. This novel characterization of L3 proteins and taxonomic conservation across hookworm species provides a raft of potential candidates for vaccine discovery for prevention of hookworm infection and disease.

Structural characterization and proteomic profiling of oviposition secretions across three rice planthopper species

Insect oviposition secretions play crucial roles during the reproductive process, yet systematic studies on their structural characterization and protein compositions remain limited. This study investigated the oviposition secretions of three major rice pests: the brown planthopper (Nilaparvata lugens, BPH), small brown planthopper (Laodelphax striatella, SBPH), and white-backed planthopper (Sogatella furcifera, WBPH). Ultrastructural observation revealed differences in the oviposition secretions of them. The eggs of BPH and SBPH were adhered to rice tissue by abundant secretions, while WBPH eggs were embedded deeper within the leaf sheath with less secretions. Proteomic analysis identified 111, 98, and 66 oviposition secretion proteins (OSPs) in BPH, SBPH, and WBPH, respectively. 4 common protein subgroups were shared among them, along with varying numbers of shared subgroups between species pairs. Notably, the majority of OSPs were exclusively found in one species, indicating the existence of both similar and specialized functions unique to each planthopper species. The functions of 4 uncharacterized OSPs (Nl.chr07.0363, Nl.chr12.078, Nl.chr11.716, Nl.scaffold.0714) that were uniquely identified in the BPH were studied by maternal RNAi. Downregulation of each of these 4 protein-coding genes led to a significant decrease in egg production and hatchability. Moreover, knockdown of Nl.chr12.078 or Nl.chr07.0363 also disrupt the secretory function of the lateral oviduct. In conclusion, this study provides insights into the structural characteristics and protein components of the oviposition secretions of BPH, SBPH, and WBPH, which could serve as potential targets for RNAi-based pest control and lay a foundation for future studies on insect-plant interactions mediated by oviposition secretions.

A comprehensive review on probiotics and their use in aquaculture: Biological control, efficacy, and safety through the genomics and wet methods

Probiotics, defined as viable microorganisms that enhance host health when consumed through the diet, exert their effects through mechanisms such as strengthening the immune system, enhancing resistance to infectious diseases, and improving tolerance to stressful conditions. Driven by a growing market, research on probiotics in aquaculture is a burgeoning field. However, the identification of new probiotics presents a complex challenge, necessitating careful consideration of both the safety and efficacy of the microorganisms employed. This review aims to delineate the most utilized and effective methods for identifying probiotics. The most effective approach currently combines in silico analysis of genomic sequences with in vitro and in vivo experiments. Two main categories of genetic traits are analyzed using bioinformatic tools: those that could harm the host or humans (e.g., toxin production, antibiotic resistance) and those that offer benefits (e.g., production of helpful compounds, and enzymes). Similarly, in vitro experiments allow us to examine the safety of a probiotic but also its effectiveness (e.g., ability to adhere to epithelia). Finally, in vivo experiments allow us to study the effect of probiotics on fish growth and health, including the ability of the probiotic to manipulate the host's microbiota and the ability to mitigate the infections. This review comprehensively analyzes these diverse aspects, with a particular focus on the potential of studying the interaction between bacterial pathogens and probiotics through these integrated methods.

Vaccination with OprB porin, and its epitopes offers protection against A. baumannii infections in mice

A. baumannii is a deadly antimicrobial resistance pathogen that acquires drug resistance through different mechanisms. Therefore, it is necessary to investigate all its virulence factors and design effective vaccines against it. For this purpose, OprB, an outer membrane porin, was investigated in this study, and its secondary and tertiary structures, physicochemical properties, and B-T epitopes were determined. The vaccine potential of this protein and its linear, non-continuous, and chimeric epitopes were also in-vivo analyzed. Based on the results, two surface epitopes and one non-continuous epitope were identified. Surface contiguous epitopes were produced recombinantly and non-continuous epitope sequences were synthesized and then produced. The chimeric epitope was also produced via the SOE-PCR technique. Active and passive immunization of mice with the whole OprB protein, non-continuous epitope, contiguous epitopes, two epitopes in chimeric form, as well as the mixture of two purified epitopes showed that the survival level and total IgG titer of the mice compared to non-vaccinated mice or mice that were vaccinated with an internal fragment increased significantly. The bacterial load in the immunized mice's lung, liver, kidney, and spleen was much lower than in the control groups, and the TNF-α, IFN-γ, and IL-6 cytokines levels were also lower in these groups and were similar to the naive mice. On the other hand, subunit vaccines showed acceptable safety and due to their minimal cross-activity, their use is much safer.

Employing Machine Learning Techniques to Detect Protein Function: A Survey, Experimental, and Empirical Evaluations

This review article delves deeply into the various machine learning (ML) methods and algorithms employed in discerning protein functions. Each method discussed is assessed for its efficacy, limitations, potential improvements, and future prospects. We present an innovative hierarchical classification system that arranges algorithms into intricate categories and unique techniques. This taxonomy is based on a tri-level hierarchy, starting with the methodology category and narrowing down to specific techniques. Such a framework allows for a structured and comprehensive classification of algorithms, assisting researchers in understanding the interrelationships among diverse algorithms and techniques. The study incorporates both empirical and experimental evaluations to differentiate between the techniques. The empirical evaluation ranks the techniques based on four criteria. The experimental assessments rank: (1) individual techniques under the same methodology sub-category, (2) different sub-categories within the same category, and (3) the broad categories themselves. Integrating the innovative methodological classification, empirical findings, and experimental assessments, the article offers a well-rounded understanding of ML strategies in protein function identification. The paper also explores techniques for multi-task and multi-label detection of protein functions, in addition to focusing on single-task methods. Moreover, the paper sheds light on the future avenues of ML in protein function determination.

Aerobic adaptation and metabolic dynamics of Propionibacterium freudenreichii DSM 20271: insights from comparative transcriptomics and surfaceome analysis

Propionibacterium freudenreichii (PFR) DSM 20271T is a bacterium known for its ability to thrive in diverse environments and to produce vitamin B12. Despite its anaerobic preference, recent studies have elucidated its ability to prosper in the presence of oxygen, prompting a deeper exploration of its physiology under aerobic conditions. Here, we investigated the response of DSM 20271T to aerobic growth by employing comparative transcriptomic and surfaceome analyses alongside metabolite profiling. Cultivation under controlled partial pressure of oxygen (pO2) conditions revealed significant increases in biomass formation and altered metabolite production, notably of vitamin B12, pseudovitamin-B12, propionate, and acetate, under aerobic conditions. Transcriptomic analysis identified differential expression of genes involved in lactate metabolism, tricarboxylic acid cycle, and electron transport chain, suggesting metabolic adjustments to aerobic environments. Moreover, surfaceome analysis unveiled growth environment-dependent changes in surface protein abundance, with implications for adaptation to atmospheric conditions. Supplementation experiments with key compounds highlighted the potential for enhancing aerobic growth, emphasizing the importance of iron and α-ketoglutarate availability. Furthermore, in liquid culture, FeSO4 supplementation led to increased heme production and reduced vitamin B12 production, highlighting the impact of oxygen and iron availability on the metabolic pathways. These findings deepen our understanding of PFR's physiological responses to oxygen availability and offer insights for optimizing its growth in industrial applications.

IMPORTANCE

The study of the response of Propionibacterium freudenreichii to aerobic growth is crucial for understanding how this bacterium adapts to different environments and produces essential compounds like vitamin B12. By investigating its physiological changes under aerobic conditions, we can gain insights into its metabolic adjustments and potential for enhanced growth. These findings not only deepen our understanding of P. freudenreichii's responses to oxygen availability but also offer valuable information for optimizing its growth in industrial applications. This research sheds light on the adaptive mechanisms of this bacterium, providing a foundation for further exploration and potential applications in various fields.

Spatial proteomics of Onchocerca volvulus with pleomorphic neoplasms shows local and systemic dysregulation of protein expression

Onchocerca volvulus is the agent of onchocerciasis (river blindness) and targeted by WHO for elimination though mass drug administration with ivermectin. A small percentage of adult worms develop pleomorphic neoplasms (PN) that are positively associated with the frequency of ivermectin treatment. Worms with PN have a lower life expectancy and a better understanding about the proteins expressed in PN, and how PN affect protein expression in different tissues could help to elucidate the mechanisms of macrofilaricidal activity of ivermectin. Within a clinical trial of drug combinations that included ivermectin, we detected 24 (5.6%) O. volvulus females with PN by histology of paraffin embedded nodules. To assess the protein inventory of the neoplasms and to identify proteins that may be associated with tumor development, we used laser capture microdissection and highly sensitive mass spectrometry analysis. Neoplasm tissue from three female worms was analyzed, and compared to normal tissues from the body wall, uterus and intestine from the same worms, and to tissues from three females without PN. The healthy females showed all intact embryogenesis. In PN worms, 151 proteins were detected in the body wall, 215 proteins in the intestine, 47 proteins in the uterus and 1,577 proteins in the neoplasms. Only the uterus of one PN female with some stretched intrauterine microfilariae had an elevated number of proteins (601) detectable, while in the uteri of the healthy females 1,710 proteins were detected. Even in tissues that were not directly affected by PN (intestine, body wall), fewer proteins were detected compared to the corresponding tissue of the healthy controls. Immunolocalization of the calcium binding protein OvDig-1 (OVOC8391) confirmed the detection in PN by mass spectrometry. In conclusion we identified proteins that are potentially linked to the development of PN, and systemic dysregulation of protein expression may contribute to worm mortality.

Widespread distribution of the DyP-carrying bacteria involved in the aflatoxin B1 biotransformation in Proteobacteria and Actinobacteria

Aflatoxin is one of the most notorious mycotoxins, of which aflatoxin B1 (AFB1) is the most harmful and prevalent. Microbes play a crucial role in the environment for the biotransformation of AFB1. In this study, a bacterial consortium, HS-1, capable of degrading and detoxifying AFB1 was obtained. Here, we combined multi-omics and cultivation-based techniques to elucidate AFB1 biotransformation by consortium HS-1. Co-occurrence network analysis revealed that the key taxa responsible for AFB1 biotransformation in consortium HS-1 mainly belonged to the phyla Proteobacteria and Actinobacteria. Moreover, metagenomic analysis showed that diverse microorganisms, mainly belonging to the phyla Proteobacteria and Actinobacteria, carry key functional enzymes involved in the initial step of AFB1 biotransformation. Metatranscriptomic analysis indicated that Paracoccus-related bacteria were the most active in consortium HS-1. A novel bacterium, Paracoccus sp. strain XF-30, isolated from consortium HS-1, contains a novel dye-decolorization peroxidase (DyP) enzyme capable of effectively degrading AFB1. Taxonomic profiling by bioinformatics revealed that DyP, which is involved in the initial biotransformation of AFB1, is widely distributed in metagenomes from various environments, primarily taxonomically affiliated with Proteobacteria and Actinobacteria. The in-depth examination of AFB1 biotransformation in consortium HS-1 will help us to explore these crucial bioresources more sensibly and efficiently.

Biodegradation of microcystins by microbiota of duckweed Spirodelapolyrhiza

Cyanobacteria-produced allelochemicals, including hepatotoxic microcystins (MCs), exert an inhibitory effect on macrophyte growth. However, the role of macrophyte-associated bacteria and algae (macrophyte microbiota) in mitigating these immediate negative effects of cyanotoxins remains poorly understood. In this paper, we analyzed the biodegradation of microcystin-RR, MC-LR, and MC-LF by microbiota of the macrophyte Spirodela polyrhiza. The biodegradation of two MC variants was observed and LC-MS/MS analysis allowed identifying the degradation products of MC-RR (m/z 1011, 984, 969, 877, 862, 820, and 615) and MC-LR (m/z 968 and 953), including eight previously unreported products. No degradation products of MC-LF were detected, suggesting its stability and resistance under experimental conditions. NGS-based profiling of microbial consortia revealed no major differences in bacterial community composition across experimental treatments. Taxa previously reported as capable of MC degradation have been found in S. polyrhiza microbiota. Furthermore, the presence of genes encoding putative microcystinase homologues and the formation of new linear intermediates suggest a biochemical pathway that is similar, but not identical to previously reported. The ability of aquatic plant microbiota to biodegrade MCs holds environmental significance, and further studies in this field are required.

Chromosome-level genome assembly of the planthopper Nilaparvata muiri

The Nilaparvata muiri (Hemiptera: Delphacidae) is a sibling species of a destructive rice insect pest, the brown planthopper (BPH), Nilaparvata lugens. Here, we generated a high-quality chromosome-level genome assembly of N. muiri using a combination of the PacBio HiFi sequencing, Illumina short-read sequencing and Hi-C scaffolding technologies. The genome assembly (524.9 Mb) is anchored to 15 pseudochromosomes, with a scaffold N50 of 43.3 Mb and 99.1% BUSCO completeness. It contains 188.1 Mb repeat sequences and 13204 protein-coding genes. As a closely related species within the same genus as the significant pest, N. lugens, the chromosome-level genome assembly of N. muiri will provide important support for the better analysis of pathogenicity mechanisms of N. lugens based on comparative genomics.

PRONTO-TK: a user-friendly PROtein Neural neTwOrk tool-kit for accessible protein function prediction

Associating one or more Gene Ontology (GO) terms to a protein means making a statement about a particular functional characteristic of the protein. This association provides scientists with a snapshot of the biological context of the protein activity. This paper introduces PRONTO-TK, a Python-based software toolkit designed to democratize access to Neural-Network based complex protein function prediction workflows. PRONTO-TK is a user-friendly graphical interface (GUI) for empowering researchers, even those with minimal programming experience, to leverage state-of-the-art Deep Learning architectures for protein function annotation using GO terms. We demonstrate PRONTO-TK's effectiveness on a running example, by showing how its intuitive configuration allows it to easily generate complex analyses while avoiding the complexities of building such a pipeline from scratch.

Trans2express - de novo transcriptome assembly pipeline optimized for gene expression analysis

BACKGROUND

As genomes of many eukaryotic species, especially plants, are large and complex, their de novo sequencing and assembly is still a difficult task despite progress in sequencing technologies. An alternative to genome assembly is the assembly of transcriptome, the set of RNA products of the expressed genes. While a bunch of de novo transcriptome assemblers exists, the challenges of transcriptomes (the existence of isoforms, the uneven expression levels across genes) complicates the generation of high-quality assemblies suitable for downstream analyses.

RESULTS

We developed Trans2express - a web-based tool and a pipeline of de novo hybrid transcriptome assembly and postprocessing based on rnaSPAdes with a set of subsequent filtrations. The pipeline was tested on Arabidopsis thaliana cDNA sequencing data obtained using Illumina and Oxford Nanopore Technologies platforms and three non-model plant species. The comparison of structural characteristics of the transcriptome assembly with reference Arabidopsis genome revealed the high quality of assembled transcriptome with 86.1% of Arabidopsis expressed genes assembled as a single contig. We tested the applicability of the transcriptome assembly for gene expression analysis. For both Arabidopsis and non-model species the results showed high congruence of gene expression levels and sets of differentially expressed genes between analyses based on genome and based on the transcriptome assembly.

CONCLUSIONS

We present Trans2express - a protocol for de novo hybrid transcriptome assembly aimed at recovering of a single transcript per gene. We expect this protocol to promote the characterization of transcriptomes and gene expression analysis in non-model plants and web-based tool to be of use to a wide range of plant biologists.

Metagenome-assembled microbial genomes from Parkinson's disease fecal samples

The human gut microbiome composition has been linked to Parkinson's disease (PD). However, knowledge of the gut microbiota on the genome level is still limited. Here we performed deep metagenomic sequencing and binning to build metagenome-assembled genomes (MAGs) from 136 human fecal microbiomes (68 PD samples and 68 control samples). We constructed 952 non-redundant high-quality MAGs and compared them between PD and control groups. Among these MAGs, there were 22 different genomes of Collinsella and Prevotella, indicating high variability of those genera in the human gut environment. Microdiversity analysis indicated that Ruminococcus bromii was statistically significantly (p < 0.002) more diverse on the strain level in the control samples compared to the PD samples. In addition, by clustering all genes and performing presence-absence analysis between groups, we identified several control-specific (p < 0.05) related genes, such as speF and Fe-S oxidoreductase. We also report detailed annotation of MAGs, including Clusters of Orthologous Genes (COG), Cas operon type, antiviral gene, prophage, and secondary metabolites biosynthetic gene clusters, which can be useful for providing a reference for future studies.

Selection and Gene Duplication Associated With High-Elevation Diversification in Pristimantis, the Largest Terrestrial Vertebrate Genus

The genus Pristimantis diversified in the tropical Andes mountains and is the most speciose genus of terrestrial vertebrates. Pristimantis are notable among frogs in that they thrive at high elevations (>2,000 m) and are direct developers without a tadpole stage. Despite their ecological significance, little is known about the genetic and physiological traits enabling their success. We conducted transcriptomic analysis on seven Pristimantis species sampled across elevations in the Ecuadorean Andes to explore three hypotheses for their success: (i) unique genes are under selection relative to all other frogs, (ii) common selection occurs across all direct developers, or (iii) common selection occurs across all high-elevation frog clades. Comparative analysis with 34 frog species revealed unique positive selection in Pristimantis genes related to aerobic respiration, hemostasis, signaling, cellular transportation of proteins and ions, and immunity. Additionally, we detected positive selection across all direct developers for genes associated with oxygenase activity and metal ion binding. While many genes under selection in Pristimantis were not positively selected in other high-elevation frog species, we identified some shared genes and pathways linked to lipid metabolism, innate immunity, and cellular redox processes. We observed more positive selection in duplicated- versus single-copy genes, while relaxed purifying selection was prevalent in single-copy genes. Notably, copy number of an innate immunity complement gene was positively correlated with Pristimantis species elevation. Our findings contribute novel insights into the genetic basis of adaptation in Pristimantis and provide a foundation for future studies on the evolutionary mechanisms leading to direct development and coping with high elevations.

Accurate prediction of protein function using statistics-informed graph networks

Understanding protein function is pivotal in comprehending the intricate mechanisms that underlie many crucial biological activities, with far-reaching implications in the fields of medicine, biotechnology, and drug development. However, more than 200 million proteins remain uncharacterized, and computational efforts heavily rely on protein structural information to predict annotations of varying quality. Here, we present a method that utilizes statistics-informed graph networks to predict protein functions solely from its sequence. Our method inherently characterizes evolutionary signatures, allowing for a quantitative assessment of the significance of residues that carry out specific functions. PhiGnet not only demonstrates superior performance compared to alternative approaches but also narrows the sequence-function gap, even in the absence of structural information. Our findings indicate that applying deep learning to evolutionary data can highlight functional sites at the residue level, providing valuable support for interpreting both existing properties and new functionalities of proteins in research and biomedicine.

Network analyses predict major regulators of resistance to early blight disease complex in tomato

BACKGROUND

Early blight and brown leaf spot are often cited as the most problematic pathogens of tomato in many agricultural regions. Their causal agents are Alternaria spp., a genus of Ascomycota containing numerous necrotrophic pathogens. Breeding programs have yielded quantitatively resistant commercial cultivars, but fungicide application remains necessary to mitigate the yield losses. A major hindrance to resistance breeding is the complexity of the genetic determinants of resistance and susceptibility. In the absence of sufficiently resistant germplasm, we sequenced the transcriptomes of Heinz 1706 tomatoes treated with strongly virulent and weakly virulent isolates of Alternaria spp. 3 h post infection. We expanded existing functional gene annotations in tomato and using network statistics, we analyzed the transcriptional modules associated with defense and susceptibility.

RESULTS

The induced responses are very distinct. The weakly virulent isolate induced a defense response of calcium-signaling, hormone responses, and transcription factors. These defense-associated processes were found in a single transcriptional module alongside secondary metabolite biosynthesis genes, and other defense responses. Co-expression and gene regulatory networks independently predicted several D clade ethylene response factors to be early regulators of the defense transcriptional module, as well as other transcription factors both known and novel in pathogen defense, including several JA-associated genes. In contrast, the strongly virulent isolate elicited a much weaker response, and a separate transcriptional module bereft of hormone signaling.

CONCLUSIONS

Our findings have predicted major defense regulators and several targets for downstream functional analyses. Combined with our improved gene functional annotation, they suggest that defense is achieved through induction of Alternaria-specific immune pathways, and susceptibility is mediated by modulating hormone responses. The implication of multiple specific clade D ethylene response factors and upregulation of JA-associated genes suggests that host defense in this pathosystem involves ethylene response factors to modulate jasmonic acid signaling.

Evolution of Orthonectida body plan

Orthonectida is an enigmatic group of animals with still uncertain phylogenetic position. Orthonectids parasitize various marine invertebrates. Their life cycle comprises a parasitic plasmodium and free-living males and females. Sexual individuals develop inside the plasmodium; after egress from the host they copulate in the external environment, and the larva, which has developed inside the female infects a new host. In a series of studied orthonectid species simplification of free-living sexual individuals can be clearly traced. The number of longitudinal and transverse muscle fibers is gradually reduced. In the nervous system, simplification is even more pronounced. The number of neurons constituting the ganglion is dramatically reduced from 200 in Rhopalura ophiocomae to 4-6 in Intoshia variabili. The peripheral nervous system undergoes gradual simplification as well. The morphological simplification is accompanied with genome reduction. However, not only genes are lost from the genome, it also undergoes compactization ensured by extreme reduction of intergenic distances, short intron sizes, and elimination of repetitive elements. The main trend in orthonectid evolution is simplification and miniaturization of free-living sexual individuals coupled with reduction and compactization of the genome.

GWAS for the identification of introgressed candidate genes of Sinapis alba with increased branching numbers in backcross lines of the allohexaploid Brassica

Plant architecture is a crucial determinant of crop yield. The number of primary (PB) and secondary branches (SB) is particularly significant in shaping the architecture of Indian mustard. In this study, we analyzed a panel of 86 backcross introgression lines (BCILs) derived from the first stable allohexaploid Brassicas with 170 Sinapis alba genome-specific SSR markers to identify associated markers with higher PB and SB through association mapping. The structure analysis revealed three subpopulations, i.e., P1, P2, and P3, in the association panel containing a total of 11, 33, and 42 BCILs, respectively. We identified five novel SSR markers linked to higher PB and SB. Subsequently, we explored the 20 kb up- and downstream regions of these SSR markers to predict candidate genes for improved branching and annotated them through BLASTN. As a result, we predicted 47 complete genes within the 40 kb regions of all trait-linked markers, among which 35 were identified as candidate genes for higher PB and SB numbers in BCILs. These candidate genes were orthologous to ANT, RAMOSUS, RAX, MAX, MP, SEU, REV, etc., branching genes. The remaining 12 genes were annotated for additional roles using BLASTP with protein databases. This study identified five novel S. alba genome-specific SSR markers associated with increased PB and SB, as well as 35 candidate genes contributing to plant architecture through improved branching numbers. To the best of our knowledge, this is the first report of introgressive genes for higher branching numbers in B. juncea from S. alba.

Haematococcus lacustris genome assembly and annotation reveal diploid genetic traits and stress-induced gene expression patterns

The green alga Haematococcus lacustris (formerly Haematococcus pluvialis) is a primary source of astaxanthin, a ketocarotenoid with high antioxidant activity and several industrial applications. Here, the Haematococcus lacustris highly repetitive genome was reconstructed by exploiting next-generation sequencing integrated with Hi-C scaffolding, obtaining a 151 Mb genome assembly in 32 scaffolds at a near-chromosome level with high continuity. Surprisingly, the distribution of the single-nucleotide-polymorphisms identified demonstrates a diploid configuration for the Haematococcus genome, further validated by Sanger sequencing of heterozygous regions. Functional annotation and RNA-seq data enabled the identification of 13,946 nuclear genes, with >5000 genes not previously identified in this species, providing insights into the molecular basis for metabolic rear-rangement in stressing conditions such as high light and/or nitrogen starvation, where astaxanthin biosynthesis is triggered. These data constitute a rich genetic resource for biotechnological manipulation of Haematococcus lacustris highlighting potential targets to improve astaxanthin and carotenoid productivity.

Mutual annotation-based prediction of protein domain functions with Domain2GO

Identifying unknown functional properties of proteins is essential for understanding their roles in both health and disease states. The domain composition of a protein can reveal critical information in this context, as domains are structural and functional units that dictate how the protein should act at the molecular level. The expensive and time-consuming nature of wet-lab experimental approaches prompted researchers to develop computational strategies for predicting the functions of proteins. In this study, we proposed a new method called Domain2GO that infers associations between protein domains and function-defining gene ontology (GO) terms, thus redefining the problem as domain function prediction. Domain2GO uses documented protein-level GO annotations together with proteins' domain annotations. Co-annotation patterns of domains and GO terms in the same proteins are examined using statistical resampling to obtain reliable associations. As a use-case study, we evaluated the biological relevance of examples selected from the Domain2GO-generated domain-GO term mappings via literature review. Then, we applied Domain2GO to predict unknown protein functions by propagating domain-associated GO terms to proteins annotated with these domains. For function prediction performance evaluation and comparison against other methods, we employed Critical Assessment of Function Annotation 3 (CAFA3) challenge datasets. The results demonstrated the high potential of Domain2GO, particularly for predicting molecular function and biological process terms, along with advantages such as producing interpretable results and having an exceptionally low computational cost. The approach presented here can be extended to other ontologies and biological entities to investigate unknown relationships in complex and large-scale biological data. The source code, datasets, results, and user instructions for Domain2GO are available at https://github.com/HUBioDataLab/Domain2GO. Additionally, we offer a user-friendly online tool at https://huggingface.co/spaces/HUBioDataLab/Domain2GO, which simplifies the prediction of functions of previously unannotated proteins solely using amino acid sequences.

Exploring the gene expression network involved in the heat stress response of a thermotolerant tomato genotype

BACKGROUND

The increase in temperatures due to the current climate change dramatically affects crop cultivation, resulting in yield losses and altered fruit quality. Tomato is one of the most extensively grown and consumed horticultural products, and although it can withstand a wide range of climatic conditions, heat stress can affect plant growth and development specially on the reproductive stage, severely influencing the final yield. In the present work, the heat stress response mechanisms of one thermotolerant genotype (E42) were investigated by exploring its regulatory gene network. This was achieved through a promoter analysis based on the identification of the heat stress elements (HSEs) mapping in the promoters, combined with a gene co-expression network analysis aimed at identifying interactions among heat-related genes.

RESULTS

Results highlighted 82 genes presenting HSEs in the promoter and belonging to one of the 52 gene networks obtained by the GCN analysis; 61 of these also interact with heat shock factors (Hsfs). Finally, a list of 13 candidate genes including two Hsfs, nine heat shock proteins (Hsps) and two GDSL esterase/lipase (GELPs) were retrieved by focusing on those E42 genes exhibiting HSEs in the promoters, interacting with Hsfs and showing variants, compared to Heinz reference genome, with HIGH and/or MODERATE impact on the translated protein. Among these, the Gene Ontology annotation analysis evidenced that only LeHsp100 (Solyc02g088610) belongs to a network specifically involved in the response to heat stress.

CONCLUSIONS

As a whole, the combination of bioinformatic analyses carried out on genomic and trascriptomic data available for tomato, together with polymorphisms detected in HS-related genes of the thermotolerant E42 allowed to determine a subset of candidate genes involved in the HS response in tomato. This study provides a novel approach in the investigation of abiotic stress response mechanisms and further studies will be conducted to validate the role of the highlighted genes.

Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation

To preserve their varietal attributes, established grapevine cultivars (Vitis vinifera L. ssp. vinifera) must be clonally propagated, due to their highly heterozygous genomes. Malbec is a France-originated cultivar appreciated for producing high-quality wines and is the offspring of cultivars Prunelard and Magdeleine Noire des Charentes. Here, we have built a diploid genome assembly of Malbec, after trio binning of PacBio long reads into the two haploid complements inherited from either parent. After haplotype-aware deduplication and corrections, complete assemblies for the two haplophases were obtained with a very low haplotype switch-error rate (<0.025). The haplophase alignment identified > 25% of polymorphic regions. Gene annotation including RNA-seq transcriptome assembly and ab initio prediction evidence resulted in similar gene model numbers for both haplophases. The annotated diploid assembly was exploited in the transcriptomic comparison of four clonal accessions of Malbec that exhibited variation in berry composition traits. Analysis of the ripening pericarp transcriptome using either haplophases as a reference yielded similar results, although some differences were observed. Particularly, among the differentially expressed genes identified only with the Magdeleine-inherited haplotype as reference, we observed an over-representation of hypothetically hemizygous genes. The higher berry anthocyanin content of clonal accession 595 was associated with increased abscisic acid responses, possibly leading to the observed overexpression of phenylpropanoid metabolism genes and deregulation of genes associated with abiotic stress response. Overall, the results highlight the importance of producing diploid assemblies to fully represent the genomic diversity of highly heterozygous woody crop cultivars and unveil the molecular bases of clonal phenotypic variation.

Trophic Position of the White Worm (Enchytraeus albidus) in the Context of Digestive Enzyme Genes Revealed by Transcriptomics Analysis

To assess the impact of Enchytraeidae (potworms) on the functioning of the decomposer system, knowledge of the feeding preferences of enchytraeid species is required. Different food preferences can be explained by variations in enzymatic activities among different enchytraeid species, as there are no significant differences in the morphology or anatomy of their alimentary tracts. However, it is crucial to distinguish between the contribution of microbial enzymes and the animal's digestive capacity. Here, we computationally analyzed the endogenous digestive enzyme genes in Enchytraeus albidus. The analysis was based on RNA-Seq of COI-monohaplotype culture (PL-A strain) specimens, utilizing transcriptome profiling to determine the trophic position of the species. We also corroborated the results obtained using transcriptomics data from genetically heterogeneous freeze-tolerant strains. Our results revealed that E. albidus expresses a wide range of glycosidases, including GH9 cellulases and a specific digestive SH3b-domain-containing i-type lysozyme, previously described in the earthworm Eisenia andrei. Therefore, E. albidus combines traits of both primary decomposers (primary saprophytophages) and secondary decomposers (sapro-microphytophages/microbivores) and can be defined as an intermediate decomposer. Based on assemblies of publicly available RNA-Seq reads, we found close homologs for these cellulases and i-type lysozymes in various clitellate taxa, including Crassiclitellata and Enchytraeidae.

Intestinal cell diversity and treatment responses in a parasitic nematode at single cell resolution

BACKGROUND

Parasitic nematodes, significant pathogens for humans, animals, and plants, depend on diverse organ systems for intra-host survival. Understanding the cellular diversity and molecular variations underlying these functions holds promise for developing novel therapeutics, with specific emphasis on the neuromuscular system's functional diversity. The nematode intestine, crucial for anthelmintic therapies, exhibits diverse cellular phenotypes, and unraveling this diversity at the single-cell level is essential for advancing knowledge in anthelmintic research across various organ systems.

RESULTS

Here, using novel single-cell transcriptomics datasets, we delineate cellular diversity within the intestine of adult female Ascaris suum, a parasitic nematode species that infects animals and people. Gene transcripts expressed in individual nuclei of untreated intestinal cells resolved three phenotypic clusters, while lower stringency resolved additional subclusters and more potential diversity. Clusters 1 and 3 phenotypes displayed variable congruence with scRNA phenotypes of C. elegans intestinal cells, whereas the A. suum cluster 2 phenotype was markedly unique. Distinct functional pathway enrichment characterized each A. suum intestinal cell cluster. Cluster 2 was distinctly enriched for Clade III-associated genes, suggesting it evolved within clade III nematodes. Clusters also demonstrated differential transcriptional responsiveness to nematode intestinal toxic treatments, with Cluster 2 displaying the least responses to short-term intra-pseudocoelomic nematode intestinal toxin treatments.

CONCLUSIONS

This investigation presents advances in knowledge related to biological differences among major cell populations of adult A. suum intestinal cells. For the first time, diverse nematode intestinal cell populations were characterized, and associated biological markers of these cells were identified to support tracking of constituent cells under experimental conditions. These advances will promote better understanding of this and other parasitic nematodes of global importance, and will help to guide future anthelmintic treatments.

The updated genome of the Hungarian population of Aedes koreicus

Vector-borne diseases pose a potential risk to human and animal welfare, and understanding their spread requires genomic resources. The mosquito Aedes koreicus is an emerging vector that has been introduced into Europe more than 15 years ago but only a low quality, fragmented genome was available. In this study, we carried out additional sequencing and assembled and characterized the genome of the species to provide a background for understanding its evolution and biology. The updated genome was 1.1 Gbp long and consisted of 6099 contigs with an N50 value of 329,610 bp and a BUSCO score of 84%. We identified 22,580 genes that could be functionally annotated and paid particular attention to the identification of potential insecticide resistance genes. The assessment of the orthology of the genes indicates a high turnover at the terminal branches of the species tree of mosquitoes with complete genomes, which could contribute to the adaptation and evolutionary success of the species. These results could form the basis for numerous downstream analyzes to develop targets for the control of mosquito populations.

The draft genome of Spiraea crenata L. (Rosaceae) - the first complete genome in tribe Spiraeeae

Spiraea crenata L. is a deciduous shrub distributed across the Eurasian steppe zone. The species is of cultural and horticultural importance and occurs in scattered populations throughout its westernmost range. Currently, there is no genomic information on the tribe of Spiraeeae. Therefore we sequenced and assembled the whole genome of S. crenata using second- and third-generation sequencing and a hybrid assembly approach to expand genomic resources for conservation and support research on this horticulturally important lineage. In addition to the organellar genomes (the plastome and the mitochondrion), we present the first draft genome of the species with an estimated size of 220 Mbp, an N50 value of 7.7 Mbp, and a BUSCO score of 96.0%. Being the first complete genome in tribe Spiraeeae, this may not only be the first step in the genomic study of a rare plant but also a contribution to genomic resources supporting the study of biodiversity and evolutionary history of Rosaceae.

In silico characterization of five novel disease-resistance proteins in Oryza sativa sp. japonica against bacterial leaf blight and rice blast diseases

In the current study, gene network analysis revealed five novel disease-resistance proteins against bacterial leaf blight (BB) and rice blast (RB) diseases caused by Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae (M. oryzae), respectively. In silico modeling, refinement, and model quality assessment were performed to predict the best structures of these five proteins and submitted to ModelArchive for future use. An in-silico annotation indicated that the five proteins functioned in signal transduction pathways as kinases, phospholipases, transcription factors, and DNA-modifying enzymes. The proteins were localized in the nucleus and plasma membrane. Phylogenetic analysis showed the evolutionary relation of the five proteins with disease-resistance proteins (XA21, OsTRX1, PLD, and HKD-motif-containing proteins). This indicates similar disease-resistant properties between five unknown proteins and their evolutionary-related proteins. Furthermore, gene expression profiling of these proteins using public microarray data showed their differential expression under Xoo and M. oryzae infection. This study provides an insight into developing disease-resistant rice varieties by predicting novel candidate resistance proteins, which will assist rice breeders in improving crop yield to address future food security through molecular breeding and biotechnology.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03893-5.

CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair

Elucidating gene function is a major goal in biology, especially among non-model organisms. However, doing so is complicated by the fact that molecular conservation does not always mirror functional conservation, and that complex relationships among genes are responsible for encoding pathways and higher-order biological processes. Co-expression, a promising approach for predicting gene function, relies on the general principal that genes with similar expression patterns across multiple conditions will likely be involved in the same biological process. For Cryptococcus neoformans, a prevalent human fungal pathogen greatly diverged from model yeasts, approximately 60% of the predicted genes in the genome lack functional annotations. Here, we leveraged a large amount of publicly available transcriptomic data to generate a C. neoformans Co-Expression Network (CryptoCEN), successfully recapitulating known protein networks, predicting gene function, and enabling insights into the principles influencing co-expression. With 100% predictive accuracy, we used CryptoCEN to identify 13 new DNA damage response genes, underscoring the utility of guilt-by-association for determining gene function. Overall, co-expression is a powerful tool for uncovering gene function, and decreases the experimental tests needed to identify functions for currently under-annotated genes.

Prioritization of Trypanosoma brucei editosome protein interactions interfaces at residue resolution through proteome-scale network analysis

BACKGROUND

Trypanosoma brucei is the causative agent for trypanosomiasis in humans and livestock, which presents a growing challenge due to drug resistance. While identifying novel drug targets is vital, the process is delayed due to a lack of functional information on many of the pathogen's proteins. Accordingly, this paper presents a computational framework for prioritizing drug targets within the editosome, a vital molecular machinery responsible for mitochondrial RNA processing in T. brucei. Importantly, this framework may eliminate the need for prior gene or protein characterization, potentially accelerating drug discovery efforts.

RESULTS

By integrating protein-protein interaction (PPI) network analysis, PPI structural modeling, and residue interaction network (RIN) analysis, we quantitatively ranked and identified top hub editosome proteins, their key interaction interfaces, and hotspot residues. Our findings were cross-validated and further prioritized by incorporating them into gene set analysis and differential expression analysis of existing quantitative proteomics data across various life stages of T. brucei. In doing so, we highlighted PPIs such as KREL2-KREPA1, RESC2-RESC1, RESC12A-RESC13, and RESC10-RESC6 as top candidates for further investigation. This includes examining their interfaces and hotspot residues, which could guide drug candidate selection and functional studies.

CONCLUSION

RNA editing offers promise for target-based drug discovery, particularly with proteins and interfaces that play central roles in the pathogen's life cycle. This study introduces an integrative drug target identification workflow combining information from the PPI network, PPI 3D structure, and reside-level information of their interface which can be applicable to diverse pathogens. In the case of T. brucei, via this pipeline, the present study suggested potential drug targets with residue-resolution from RNA editing machinery. However, experimental validation is needed to fully realize its potential in advancing urgently needed antiparasitic drug development.