Why repetitive DNA is essential to genome function

A chromosome-scale genome of Rhus chinensis Mill. provides new insights into plant-insect interaction and gallotannins biosynthesis

Rhus chinensis Mill., an economically valuable Anacardiaceae species, is parasitized by the galling aphid Schlechtendalia chinensis, resulting in the formation of the Chinese gallnut (CG). Here, we report a chromosomal-level genome assembly of R. chinensis, with a total size of 389.40 Mb and scaffold N50 of 23.02 Mb. Comparative genomic and transcriptome analysis revealed that the enhanced structure of CG and nutritional metabolism contribute to improving the adaptability of R. chinensis to S. chinensis by supporting CG and galling aphid growth. CG was observed to be abundant in hydrolysable tannins (HT), particularly gallotannin and its isomers. Tandem repeat clusters of dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH) and serine carboxypeptidase-like (SCPL) and their homologs involved in HT production were determined as specific to HT-rich species. The functional differentiation of DQD/SDH tandem duplicate genes and the significant contraction in the phenylalanine ammonia-lyase (PAL) gene family contributed to the accumulation of gallic acid and HT while minimizing the production of shikimic acid, flavonoids, and condensed tannins in CG. Furthermore, we identified one UDP glucosyltransferase (UGT84A), three carboxylesterase (CXE), and six SCPL genes from conserved tandem repeat clusters that are involved in gallotannin biosynthesis and hydrolysis in CG. We then constructed a regulatory network of these genes based on co-expression and transcription factor motif analysis. Our findings provide a genomic resource for the exploration of the underlying mechanisms of plant-galling insect interaction and highlight the importance of the functional divergence of tandem duplicate genes in the accumulation of secondary metabolites.

From tradition to innovation: conventional and deep learning frameworks in genome annotation

Following the milestone success of the Human Genome Project, the 'Encyclopedia of DNA Elements (ENCODE)' initiative was launched in 2003 to unearth information about the numerous functional elements within the genome. This endeavor coincided with the emergence of numerous novel technologies, accompanied by the provision of vast amounts of whole-genome sequences, high-throughput data such as ChIP-Seq and RNA-Seq. Extracting biologically meaningful information from this massive dataset has become a critical aspect of many recent studies, particularly in annotating and predicting the functions of unknown genes. The core idea behind genome annotation is to identify genes and various functional elements within the genome sequence and infer their biological functions. Traditional wet-lab experimental methods still rely on extensive efforts for functional verification. However, early bioinformatics algorithms and software primarily employed shallow learning techniques; thus, the ability to characterize data and features learning was limited. With the widespread adoption of RNA-Seq technology, scientists from the biological community began to harness the potential of machine learning and deep learning approaches for gene structure prediction and functional annotation. In this context, we reviewed both conventional methods and contemporary deep learning frameworks, and highlighted novel perspectives on the challenges arising during annotation underscoring the dynamic nature of this evolving scientific landscape.

Detection of Parasites in the Field: The Ever-Innovating CRISPR/Cas12a

The rapid and accurate identification of parasites is crucial for prompt therapeutic intervention in parasitosis and effective epidemiological surveillance. For accurate and effective clinical diagnosis, it is imperative to develop a nucleic-acid-based diagnostic tool that combines the sensitivity and specificity of nucleic acid amplification tests (NAATs) with the speed, cost-effectiveness, and convenience of isothermal amplification methods. A new nucleic acid detection method, utilizing the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) nuclease, holds promise in point-of-care testing (POCT). CRISPR/Cas12a is presently employed for the detection of Plasmodium falciparum, Toxoplasma gondii, Schistosoma haematobium, and other parasites in blood, urine, or feces. Compared to traditional assays, the CRISPR assay has demonstrated notable advantages, including comparable sensitivity and specificity, simple observation of reaction results, easy and stable transportation conditions, and low equipment dependence. However, a common issue arises as both amplification and cis-cleavage compete in one-pot assays, leading to an extended reaction time. The use of suboptimal crRNA, light-activated crRNA, and spatial separation can potentially weaken or entirely eliminate the competition between amplification and cis-cleavage. This could lead to enhanced sensitivity and reduced reaction times in one-pot assays. Nevertheless, higher costs and complex pre-test genome extraction have hindered the popularization of CRISPR/Cas12a in POCT.

The Killer's Web: Interconnection between Inflammation, Epigenetics and Nutrition in Cancer

Inflammation is a key contributor to both the initiation and progression of tumors, and it can be triggered by genetic instability within tumors, as well as by lifestyle and dietary factors. The inflammatory response plays a critical role in the genetic and epigenetic reprogramming of tumor cells, as well as in the cells that comprise the tumor microenvironment. Cells in the microenvironment acquire a phenotype that promotes immune evasion, progression, and metastasis. We will review the mechanisms and pathways involved in the interaction between tumors, inflammation, and nutrition, the limitations of current therapies, and discuss potential future therapeutic approaches.

Rex1BD and the 14-3-3 protein control heterochromatin organization at tandem repeats by linking RNAi and HDAC

Tandem DNA repeats are often organized into heterochromatin that is crucial for genome organization and stability. Recent studies revealed that individual repeats within tandem DNA repeats can behave very differently. How DNA repeats are assembled into distinct heterochromatin structures remains poorly understood. Here, we developed a genome-wide genetic screen using a reporter gene at different units in a repeat array. This screen led to identification of a conserved protein Rex1BD required for heterochromatin silencing. Our structural analysis revealed that Rex1BD forms a four-helix bundle structure with a distinct charged electrostatic surface. Mechanistically, Rex1BD facilitates the recruitment of Clr6 histone deacetylase (HDAC) by interacting with histones. Interestingly, Rex1BD also interacts with the 14-3-3 protein Rad25, which is responsible for recruiting the RITS (RNA-induced transcriptional silencing) complex to DNA repeats. Our results suggest that coordinated action of Rex1BD and Rad25 mediates formation of distinct heterochromatin structure at DNA repeats via linking RNAi and HDAC pathways.

Characteristics of HPV integration in cervical adenocarcinoma and squamous carcinoma

PURPOSE

HPV integration usually occurs in HPV-related cancer, and is the main cause of cancer. But the carcinogenic mechanism of HPV integration is unclear. The study aims to provide a theoretical basis for understanding the pathogenesis of cervical adenocarcinoma (AC) and cervical squamous carcinoma (SCC).

METHODS

We used HPV capture sequencing to obtain HPV integration sites in AC and SCC, and analyzed cytobands, distribution of genetic and genomic elements, identified integration hotspot genes, clinicopathological parameters, breakpoints of HPV16 and performed pathway analysis. Then we conducted immunohistochemical (IHC) assay to preliminarily verify the expression of most frequently integrated genes in AC, STARD3 and ERBB2.

RESULTS

The results revealed that the most frequently observed integrated cytoband was 17q12 in AC and 21p11.2 in SCC, respectively. The breakpoints in both AC and SCC were more tended to occur within gene regions, compared to intergenetic regions. Compared to SCC samples, AC samples had a higher prevalence of genomic elements. In AC, HPV integration has no significantly difference with clinicopathological parameters, but in SCC integration correlated with differentiation (P < 0.05). Breakpoints of HPV in SCC located in LCR more frequently compared to AC, which destroyed the activation of promoter p97. Hotspot genes of HPV integration were STARD3 and ERBB2 in AC, and RNA45S rDNA and MIR3648-1 in SCC, respectively. Meanwhile, we preliminarily proved that the expression of STARD3 and ERBB2, the most frequently integrated genes, would increase after integration.

CONCLUSION

These results suggested that HPV may utilize the powerful hosts' promoters to express viral oncogenes and overexpression of viral oncogenes plays a significant role in the carcinogenesis of SCC. In AC, HPV integration may affect hosts' oncogenes, and the dysregulation of oncogenes may primarily contribute to progression of AC.

A STRP-ed definition of Structured Tandem Repeats in Proteins

Tandem Repeat Proteins (TRPs) are a class of proteins with repetitive amino acid sequences that have been studied extensively for over two decades. Different features at the level of sequence, structure, function and evolution have been attributed to them by various authors. And yet many of its salient features appear only when looking at specific subclasses of protein tandem repeats. Here, we attempt to rationalize the existing knowledge on Tandem Repeat Proteins (TRPs) by pointing out several dichotomies. The emerging picture is more nuanced than generally assumed and allows us to draw some boundaries of what is not a "proper" TRP. We conclude with an operational definition of a specific subset, which we have denominated STRPs (Structural Tandem Repeat Proteins), which separates a subclass of tandem repeats with distinctive features from several other less well-defined types of repeats. We believe that this definition will help researchers in the field to better characterize the biological meaning of this large yet largely understudied group of proteins.

Genome-wide analysis of transposable elements and satellite DNA in Humulus scandens, a dioecious plant with XX/XY1Y2 chromosomes

Transposable elements (TEs) and satellite DNAs, two major categories of repetitive sequences, are expected to accumulate in non-recombining genome regions, including sex-linked regions, and contribute to sex chromosome evolution. The dioecious plant, Humulus scandens, can be used for studying the evolution of the XX/XY1Y2 sex chromosomes. In this study, we thoroughly examined the repetitive components of male and female H. scandens using next-generation sequencing data followed by bioinformatics analysis and florescence in situ hybridization (FISH). The H. scandens genome has a high overall repetitive sequence composition, 68.30% in the female and 66.78% in the male genome, with abundant long terminal repeat (LTR) retrotransposons (RTs), including more Ty3/Gypsy than Ty1/Copia elements, particularly two Ty3/Gypsy lineages, Tekay and Retand. Most LTR-RT lineages were found dispersed across the chromosomes, though CRM and Athila elements were predominately found within the centromeres and the pericentromeric regions. The Athila elements also showed clearly higher FISH signal intensities in the Y1 and Y2 chromosomes than in the X or autosomes. Three novel satellite DNAs were specifically distributed in the centromeric and/or telomeric regions, with markedly different distributions on the X, Y1, and Y2 chromosomes. Combined with FISH using satellite DNAs to stain chromosomes during meiotic diakinesis, we determined the synapsis pattern and distinguish pseudoautosomal regions (PARs). The results indicate that the XY1Y2 sex chromosomes of H. scandens might have originated from a centric fission event. This study improves our understanding of the repetitive sequence organization of H. scandens genome and provides a basis for further analysis of their chromosome evolution process.

C-value paradox: Genesis in misconception that natural selection follows anthropocentric parameters of 'economy' and 'optimum'

C-value paradox refers to the lack of correlation between biological complexity and the intuitively expected protein-coding genomic information or DNA content. Here I discuss five questions about this paradox: i) Do biologically complex organisms carry more protein-coding genes? ii) Does variable accumulation of selfish/ junk/ parasitic DNA underlie the c-value paradox? iii) Can nucleoskeletal or nucleotypic function of DNA explain the enigma of orders of magnitude high levels of DNA in some 'lower' taxa or in taxonomically related species? iv) Can the newly understood noncoding but functional DNA explain the c-value paradox? and, v) Does natural selection uniformly apply the anthropocentric parameters for 'optimum' and 'economy'? Answers to Q.1-5 are largely negative. Biology presents numerous 'anomalous' examples where the same end function/ phenotype is attained in different organisms through astoundingly diverse ways that appear 'illogical' in our perceptions. Such evolutionary oddities exist because natural selection, unlike a designer, exploits random and stochastic events to modulate the existing system. Consequently, persistence of the new-found 'solution/s' often appear bizarre, uneconomic, and therefore, paradoxical to human logic. The unexpectedly high c-values in diverse organisms are irreversible evolutionary accidents that persisted, and the additional DNA often got repurposed over the evolutionary time scale. Therefore, the c-value paradox is a redundant issue. Future integrative biological studies should address evolutionary mechanisms and processes underlying sporadic DNA expansions/ contractions, and how the newly acquired DNA content has been repurposed in diverse groups.

Abundance and Diversification of Repetitive Elements in Decapoda Genomes

Repetitive elements are a major component of DNA sequences due to their ability to propagate through the genome. Characterization of Metazoan repetitive profiles is improving; however, current pipelines fail to identify a significant proportion of divergent repeats in non-model organisms. The Decapoda order, for which repeat content analyses are largely lacking, is characterized by extremely variable genome sizes that suggest an important presence of repetitive elements. Here, we developed a new standardized pipeline to annotate repetitive elements in non-model organisms, which we applied to twenty Decapoda and six other Crustacea genomes. Using this new tool, we identified 10% more repetitive elements than standard pipelines. Repetitive elements were more abundant in Decapoda species than in other Crustacea, with a very large number of highly repeated satellite DNA families. Moreover, we demonstrated a high correlation between assembly size and transposable elements and different repeat dynamics between Dendrobranchiata and Reptantia. The patterns of repetitive elements largely reflect the phylogenetic relationships of Decapoda and the distinct evolutionary trajectories within Crustacea. In summary, our results highlight the impact of repetitive elements on genome evolution in Decapoda and the value of our novel annotation pipeline, which will provide a baseline for future comparative analyses.

Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts

The gut microbiota is a reservoir for antimicrobial resistance genes (ARGs). With current sequencing methods, it is difficult to assign ARGs to their microbial hosts, particularly if these ARGs are located on plasmids. Metagenomic chromosome conformation capture approaches (meta3C and Hi-C) have recently been developed to link bacterial genes to phylogenetic markers, thus potentially allowing the assignment of ARGs to their hosts on a microbiome-wide scale. Here, we generated a meta3C dataset of a human stool sample and used previously published meta3C and Hi-C datasets to investigate bacterial hosts of ARGs in the human gut microbiome. Sequence reads mapping to repetitive elements were found to cause problematic noise in, and may importantly skew interpretation of, meta3C and Hi-C data. We provide a strategy to improve the signal-to-noise ratio by discarding reads that map to insertion sequence elements and to the end of contigs. We also show the importance of using spike-in controls to quantify whether the cross-linking step in meta3C and Hi-C protocols has been successful. After filtering to remove artefactual links, 87 ARGs were assigned to their bacterial hosts across all datasets, including 27 ARGs in the meta3C dataset we generated. We show that commensal gut bacteria are an important reservoir for ARGs, with genes coding for aminoglycoside and tetracycline resistance being widespread in anaerobic commensals of the human gut.

Assessment of DNA mutagenicity induced by He-Ne laser using Salmonella typhimurium strains

Helium-neon (He-Ne) laser mutagenesis is widely used in microbiology and plant breeding. In this study, two frameshift mutant representative strains of Salmonella typhimurium TA97a and TA98 and two base pair substitution types TA100 and TA102 were employed as model microorganisms to assess DNA mutagenicity induced by He-Ne laser (3 J·cm^-2·s^-1, 632.8 nm) for 10, 20, and 30 min. The results revealed that the optimal laser application was 6 h in the mid-logarithmic growth stage. Low-power He-Ne laser for short treatment inhibited cell growth, and continued treatment stimulated the metabolism. The effects of the laser on TA98 and TA100 were the most prominent. Sequencing results from 1500 TA98 revertants showed that there were 88 insertion and deletion (InDel) types in the hisD3052 gene, of which the InDels unique to laser were 21 more than that of the control. Sequencing results from 760 TA100 revertants indicated that laser treatment created Pro (CCC) in the product of the hisG46 gene more likely to be replaced by His (CAC) or Ser (TCC) than by Leu (CTC). Two unique non-classical base substitutions, CCC → TAC and CCC → CAA, also appeared in the laser group. These findings will provide a theoretical basis for further exploration of laser mutagenesis breeding. KEY POINTS: • Salmonella typhimurium served as model organism for laser mutagenesis study. • Laser promoted the occurrence of InDels in the hisD3052 gene of TA98. • Laser promoted the occurrence of base substitution in the hisG46 gene of TA100.

Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae)

The Zygophyllum and Tetraena genera are intriguingly important ecologically and medicinally. Based on morphological characteristics, T. hamiensis var. qatarensis, and T. simplex were transferred from Zygophyllum to Tetraena with the least genomic datasets available. Hence, we sequenced the T. hamiensis and T. simplex and performed in-depth comparative genomics, phylogenetic analysis, and estimated time divergences. The complete plastomes ranged between 106,720 and 106,446 bp-typically smaller than angiosperms plastomes. The plastome circular genomes are divided into large single-copy regions (~ 80,964 bp), small single-copy regions (~ 17,416 bp), and two inverted repeats regions (~ 4170 bp) in both Tetraena species. An unusual shrinkage of IR regions 16-24 kb was identified. This resulted in the loss of 16 genes, including 11 ndh genes which encode the NADH dehydrogenase subunits, and a significant size reduction of Tetraena plastomes compared to other angiosperms. The inter-species variations and similarities were identified using genome-wide comparisons. Phylogenetic trees generated by analyzing the whole plastomes, protein-coding genes, matK, rbcL, and cssA genes exhibited identical topologies, indicating that both species are sisters to the genus Tetraena and may not belong to Zygophyllum. Similarly, based on the entire plastome and proteins coding genes datasets, the time divergence of Zygophyllum and Tetraena was 36.6 Ma and 34.4 Ma, respectively. Tetraena stem ages were 31.7 and 18.2 Ma based on full plastome and protein-coding genes. The current study presents the plastome as a distinguishing and identification feature among the closely related Tetraena and Zygophyllum species. It can be potentially used as a universal super-barcode for identifying plants.

Constrained disorder principle-based variability is fundamental for biological processes: Beyond biological relativity and physiological regulatory networks

The constrained disorder principle (CDP) defines systems based on their degree of disorder bounded by dynamic boundaries. The principle explains stochasticity in living and non-living systems. Denis Noble described the importance of stochasticity in biology, emphasizing stochastic processes at molecular, cellular, and higher levels in organisms as having a role beyond simple noise. The CDP and Noble's theories (NT) claim that biological systems use stochasticity. This paper presents the CDP and NT, discussing common notions and differences between the two theories. The paper presents the CDP-based concept of taking the disorder beyond its role in nature to correct malfunctions of systems and improve the efficiency of biological systems. The use of CDP-based algorithms embedded in second-generation artificial intelligence platforms is described. In summary, noise is inherent to complex systems and has a functional role. The CDP provides the option of using noise to improve functionality.

Omics in the Red Palm Weevil Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae): A Bridge to the Pest

The red palm weevil (RPW), Rhynchophorus ferrugineus (Coleoptera: Curculionidae), is the most devastating pest of palm trees worldwide. Mitigation of the economic and biodiversity impact it causes is an international priority that could be greatly aided by a better understanding of its biology and genetics. Despite its relevance, the biology of the RPW remains poorly understood, and research on management strategies often focuses on outdated empirical methods that produce sub-optimal results. With the development of omics approaches in genetic research, new avenues for pest control are becoming increasingly feasible. For example, genetic engineering approaches become available once a species's target genes are well characterized in terms of their sequence, but also population variability, epistatic interactions, and more. In the last few years alone, there have been major advances in omics studies of the RPW. Multiple draft genomes are currently available, along with short and long-read transcriptomes, and metagenomes, which have facilitated the identification of genes of interest to the RPW scientific community. This review describes omics approaches previously applied to RPW research, highlights findings that could be impactful for pest management, and emphasizes future opportunities and challenges in this area of research.

Self-empowerment of life through RNA networks, cells and viruses

Our understanding of the key players in evolution and of the development of all organisms in all domains of life has been aided by current knowledge about RNA stem-loop groups, their proposed interaction motifs in an early RNA world and their regulative roles in all steps and substeps of nearly all cellular processes, such as replication, transcription, translation, repair, immunity and epigenetic marking. Cooperative evolution was enabled by promiscuous interactions between single-stranded regions in the loops of naturally forming stem-loop structures in RNAs. It was also shown that cooperative RNA stem-loops outcompete selfish ones and provide foundational self-constructive groups (ribosome, editosome, spliceosome, etc.). Self-empowerment from abiotic matter to biological behavior does not just occur at the beginning of biological evolution; it is also essential for all levels of socially interacting RNAs, cells and viruses.

Self-empowerment of life through RNA networks, cells and viruses

Our understanding of the key players in evolution and of the development of all organisms in all domains of life has been aided by current knowledge about RNA stem-loop groups, their proposed interaction motifs in an early RNA world and their regulative roles in all steps and substeps of nearly all cellular processes, such as replication, transcription, translation, repair, immunity and epigenetic marking. Cooperative evolution was enabled by promiscuous interactions between single-stranded regions in the loops of naturally forming stem-loop structures in RNAs. It was also shown that cooperative RNA stem-loops outcompete selfish ones and provide foundational self-constructive groups (ribosome, editosome, spliceosome, etc.). Self-empowerment from abiotic matter to biological behavior does not just occur at the beginning of biological evolution; it is also essential for all levels of socially interacting RNAs, cells and viruses.

Chromosome-level genome assembly of a high-altitude-adapted frog (Rana kukunoris) from the Tibetan plateau provides insight into amphibian genome evolution and adaptation

BACKGROUND

The high-altitude-adapted frog Rana kukunoris, occurring on the Tibetan plateau, is an excellent model to study life history evolution and adaptation to harsh high-altitude environments. However, genomic resources for this species are still underdeveloped constraining attempts to investigate the underpinnings of adaptation.

RESULTS

The R. kukunoris genome was assembled to a size of 4.83 Gb and the contig N50 was 1.80 Mb. The 6555 contigs were clustered and ordered into 12 pseudo-chromosomes covering ~ 93.07% of the assembled genome. In total, 32,304 genes were functionally annotated. Synteny analysis between the genomes of R. kukunoris and a low latitude species Rana temporaria showed a high degree of chromosome level synteny with one fusion event between chr11 and chr13 forming pseudo-chromosome 11 in R. kukunoris. Characterization of features of the R. kukunoris genome identified that 61.5% consisted of transposable elements and expansions of gene families related to cell nucleus structure and taste sense were identified. Ninety-five single-copy orthologous genes were identified as being under positive selection and had functions associated with the positive regulation of proteins in the catabolic process and negative regulation of developmental growth. These gene family expansions and positively selected genes indicate regions for further interrogation to understand adaptation to high altitude.

CONCLUSIONS

Here, we reported a high-quality chromosome-level genome assembly of a high-altitude amphibian species using a combination of Illumina, PacBio and Hi-C sequencing technologies. This genome assembly provides a valuable resource for subsequent research on R. kukunoris genomics and amphibian genome evolution in general.

Studies on ultrasound-mediated insertion-deletion polymorphisms of DNA and underlying mechanisms based on Ames tester strains

Low-lethality ultrasound technology has received more and more attention in regulating microorganisms of fermentation industry. Herein, two representative Ames tester strains TA97a and TA98 as model organisms were used to explore the effects of ultrasound on insertion-deletion (InDel) polymorphisms of microbial DNA and its underlying mechanisms. Results revealed that a promotion was observed in the reversion mutation of TA98 upon sonication. Sequencing results from 1752 TA98 revertants showed that there was a total of 127 InDels, of which the InDels unique to ultrasound were 36 more than that of the control. Compared with the control, ultrasound-mediated InDels of DNA displayed additional -29 bp deletion and +7 ∼ +43 bp insertions of direct repeat sequences. Combined with the analysis of transcriptomics and prediction of secondary structure of single-stranded DNA from InDels core region (No. 832 ∼ 915 bp) in hisD3052 gene of TA98 strain, ultrasound-mediated "thermal breathing" mechanism was proposed based on the formation of DNA hairpin structure with micro-homologous sequence. This finding implied that low-intensity ultrasound is expected to be developed a new low-lethal mutagenic technology for continuous mutagenesis.

Recent advances in metagenomic analysis of different ecological niches for enhanced biodegradation of recalcitrant lignocellulosic biomass

Lignocellulose wastes stemming from agricultural residues can offer an excellent opportunity as alternative energy solutions in addition to fossil fuels. Besides, the unrestrained burning of agricultural residues can lead to the destruction of the soil microflora and associated soil sterilization. However, the difficulties associated with the biodegradation of lignocellulose biomasses remain as a formidable challenge for their sustainable management. In this respect, metagenomics can be used as an effective option to resolve such dilemma because of its potential as the next generation sequencing technology and bioinformatics tools to harness novel microbial consortia from diverse environments (e.g., soil, alpine forests, and hypersaline/acidic/hot sulfur springs). In light of the challenges associated with the bulk-scale biodegradation of lignocellulose-rich agricultural residues, this review is organized to help delineate the fundamental aspects of metagenomics towards the assessment of the microbial consortia and novel molecules (such as biocatalysts) which are otherwise unidentifiable by conventional laboratory culturing techniques. The discussion is extended further to highlight the recent advancements (e.g., from 2011 to 2022) in metagenomic approaches for the isolation and purification of lignocellulolytic microbes from different ecosystems along with the technical challenges and prospects associated with their wide implementation and scale-up. This review should thus be one of the first comprehensive reports on the metagenomics-based analysis of different environmental samples for the isolation and purification of lignocellulose degrading enzymes.

Sympatric Speciation in Mole Rats and Wild Barley and Their Genome Repeatome Evolution: A Commentary

The theories of sympatric speciation (SS) and coding and noncoding (cd and ncd =repeatome)  genome function are still contentious. Studies on SS in our two new models, "Evolution Canyon" and "Evolution Plateau", in Israel, divergent microclimatically and geologically-edaphically, respectively, indicated that in ecologically divergent microsites SS is a common speciation model across life from bacteria to mammals. Genomically, the intergenic ncd repeatome was and is still regarded by many biologists as "selfish," "junk," and non-functional. In contrast, it is considered by the encyclopedia of DNA elements discovery as biochemically functional and regulatory, and the transposable elements were considered earlier by Barbara McClintock as "controlling elements" of genes. Remarkably, it is found that repeated elements can statistically identify significantly, the five species of subterranean mole rats of Spalax ehrenbergi superspecies adapted to increasingly arid climatic trend southward in Israel. Moreover, it is first discovered in the SS studies in two distant taxa, subterranean mole rats and wild barley, and later also in spiny mice in Israel and subterranean zokors in China, that the noncoding repeatome is genomically mirroring the image of the protein-coding genome in divergent ecologies. It is shown that this mirroring image is statistically significant both within and between the ecologically divergent taxa supporting the hypothesis that much of the repeatome might be regulatory and selected as the protein-coding genome by the same ecological stresses.

The Nuclear-to-Cytoplasmic Ratio: Coupling DNA Content to Cell Size, Cell Cycle, and Biosynthetic Capacity

Though cell size varies between different cells and across species, the nuclear-to-cytoplasmic (N/C) ratio is largely maintained across species and within cell types. A cell maintains a relatively constant N/C ratio by coupling DNA content, nuclear size, and cell size. We explore how cells couple cell division and growth to DNA content. In some cases, cells use DNA as a molecular yardstick to control the availability of cell cycle regulators. In other cases, DNA sets a limit for biosynthetic capacity. Developmentally programmed variations in the N/C ratio for a given cell type suggest that a specific N/C ratio is required to respond to given physiological demands. Recent observations connecting decreased N/C ratios with cellular senescence indicate that maintaining the proper N/C ratio is essential for proper cellular functioning. Together, these findings suggest a causative, not simply correlative, role for the N/C ratio in regulating cell growth and cell cycle progression.

Gene body methylation in cancer: molecular mechanisms and clinical applications

DNA methylation is an important epigenetic mechanism that regulates gene expression. To date, most DNA methylation studies have focussed on CpG islands in the gene promoter region, and the mechanism of methylation and the regulation of gene expression after methylation have been clearly elucidated. However, genome-wide methylation studies have shown that DNA methylation is widespread not only in promoters but also in gene bodies. Gene body methylation is widely involved in the expression regulation of many genes and is closely related to the occurrence and progression of malignant tumours. This review focusses on the formation of gene body methylation patterns, its regulation of transcription, and its relationship with tumours, providing clues to explore the mechanism of gene body methylation in regulating gene transcription and its significance and application in the field of oncology.

Drug-food Interactions in the Era of Molecular Big Data, Machine Intelligence, and Personalized Health

The drug-food interaction brings forth changes in the clinical effects of drugs. While favourable interactions bring positive clinical outcomes, unfavourable interactions may lead to toxicity. This article reviews the impact of food intake on drug-food interactions, the clinical effects of drugs, and the effect of drug-food in correlation with diet and precision medicine. Emerging areas in drug-food interactions are the food-genome interface (nutrigenomics) and nutrigenetics. Understanding the molecular basis of food ingredients, including genomic sequencing and pharmacological implications of food molecules, helps to reduce the impact of drug-food interactions. Various strategies are being leveraged to alleviate drug-food interactions; measures including patient engagement, digital health, approaches involving machine intelligence, and big data are a few of them. Furthermore, delineating the molecular communications across dietmicrobiome- drug-food-drug interactions in a pharmacomicrobiome framework may also play a vital role in personalized nutrition. Determining nutrient-gene interactions aids in making nutrition deeply personalized and helps mitigate unwanted drug-food interactions, chronic diseases, and adverse events from their onset. Translational bioinformatics approaches could play an essential role in the next generation of drug-food interaction research. In this landscape review, we discuss important tools, databases, and approaches along with key challenges and opportunities in drug-food interaction and its immediate impact on precision medicine.

Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the Triticeae

Aegilops crassa Boiss. is polyploid grass species that grows in the eastern part of the Fertile Crescent, Afghanistan, and Middle Asia. It consists of tetraploid (4x) and hexaploid (6x) cytotypes (2n = 4x = 28, D¹D (Abdolmalaki et al., 2019) X^crX^cr and 2n = 6x = 42, D¹D (Abdolmalaki et al., 2019) X^crX^crD²D (Adams and Wendel, 2005), respectively) that are similar morphologically. Although many Aegilops species were used in wheat breeding, the genetic potential of Ae. crassa has not yet been exploited due to its uncertain origin and significant genome modifications. Tetraploid Ae. crassa is thought to be the oldest polyploid Aegilops species, the subgenomes of which still retain some features of its ancient diploid progenitors. The D¹ and D² subgenomes of Ae. crassa were contributed by Aegilops tauschii (2n = 2x = 14, DD), while the X^cr subgenome donor is still unknown. Owing to its ancient origin, Ae. crassa can serve as model for studying genome evolution. Despite this, Ae. crassa is poorly studied genetically and no genome sequences were available for this species. We performed low-coverage genome sequencing of 4x and 6x cytotypes of Ae. crassa, and four Ae. tauschii accessions belonging to different subspecies; diploid wheatgrass Thinopyrum bessarabicum (J^b genome), which is phylogenetically close to D (sub)genome species, was taken as an outgroup. Subsequent data analysis using the pipeline RepeatExplorer2 allowed us to characterize the repeatomes of these species and identify several satellite sequences. Some of these sequences are novel, while others are found to be homologous to already known satellite sequences of Triticeae species. The copy number of satellite repeats in genomes of different species and their subgenome (D¹ or X^cr) affinity in Ae. crassa were assessed by means of comparative bioinformatic analysis combined with quantitative PCR (qPCR). Fluorescence in situ hybridization (FISH) was performed to map newly identified satellite repeats on chromosomes of common wheat, Triticum aestivum, 4x and 6x Ae. crassa, Ae. tauschii, and Th. bessarabicum. The new FISH markers can be used in phylogenetic analyses of the Triticeae for chromosome identification and the assessment of their subgenome affinities and for evaluation of genome/chromosome constitution of wide hybrids or polyploid species.

Genomic virulence genes profile analysis of Salmonella enterica isolates from animal and human in China from 2004 to 2019

Salmonella is a momentously zoonotic and food-borne pathogen that seriously threats human and animal health around the world. Salmonella pathogenicity is closely related to its virulence genes profile. However, conventional virulence gene analysis methods cannot truly reveal whole virulence genes carried by Salmonella. In this study, whole genome sequencing in combination with Virulence Factor Database were applied to investigate whole virulence gene profiles of 243 Salmonella isolates from animals and humans in China from 2004 to 2019. The results showed that a total of 670 virulence genes were identified in Salmonella, among them, 319 virulence genes were found in all the Salmonella tested isolates, and 9 virulence genes were unique to Salmonella. The 670 virulence genes were classified into 14 categories according to their functions, and the genes related to adherence, effector delivery system, immune modulation, motility and nutritional/metabolic factors accounted for 84.63%. Relationships between virulence genes and serovars, sequence types indicated that strains belonged to the same serovar or sequence type had similar virulence genes profiles, however, isolates from different sources, years and locations of isolation had variable virulence gene profiles. In addition, copy number of virulence genes and homologous virulence genes shared with other pathogens were also analyzed in this study. In summary, we investigated pan-genomic virulence gene profiles and molecular epidemiology of Salmonella isolates from humans and animals in China from 2004 to 2019. These findings are beneficial for pathogenic monitoring, investigation of virulence evolution as well as prevention and control of Salmonella.

Taxonomy, comparative genomics of Mullein (Verbascum, Scrophulariaceae), with implications for the evolution of Verbascum and Lamiales

BACKGROUND

The genus Verbascum L. (Scrophulariaceae) is distributed in Africa, Europe, and parts of Asia, with the Mediterranean having the most species variety. Several researchers have already worked on the phylogenetic and taxonomic analysis of Verbascum by using ITS data and chloroplast genome fragments and have produced different conclusions. The taxonomy and phylogenetic relationships of this genus are unclear.

RESULTS

The complete plastomes (cp) lengths for V. chaixii, V. songaricum, V. phoeniceum, V. blattaria, V. sinaiticum, V. thapsus, and V. brevipedicellatum ranged from 153,014 to 153,481 bp. The cp coded 114 unique genes comprising of 80 protein-coding genes, four ribosomal RNA (rRNA), and 30 tRNA genes. We detected variations in the repeat structures, gene expansion on the inverted repeat, and single copy (IR/SC) boundary regions. The substitution rate analysis indicated that some genes were under purifying selection pressure. Phylogenetic analysis supported the sister relationship of (Lentibulariaceae + Acanthaceae + Bignoniaceae + Verbenaceae + Pedaliaceae) and (Lamiaceae + Phyrymaceae + Orobanchaceae + Paulowniaceae + Mazaceae) in Lamiales. Within Scrophulariaceae, Verbascum was sister to Scrophularia, while Buddleja formed a monophyletic clade from (Scrophularia + Verbascum) with high bootstrap support values. The relationship of the nine species within Verbascum was highly supported.

CONCLUSION

Based on the phylogenetic results, we proposed to reinstate the species status of V. brevipedicellatum (Engl.) Hub.-Mor. Additionally, three genera (Mazus, Lancea, and Dodartia) placed in the Phyrymaceae family formed a separate clade within Lamiaceae. The classification of the three genera was supported by previous studies. Thus, the current study also suggests the circumscription of these genera as documented previously to be reinstated. The divergence time of Lamiales was approximated to be 86.28 million years ago (Ma) (95% highest posterior density (HPD), 85.12-89.91 Ma). The complete plastomes sequence data of the Verbascum species will be important for understanding the Verbascum phylogenetic relationships and evolution in order Lamiales.

Nuclear organization by satellite DNA, SAF-A/hnRNPU and matrix attachment regions

The need of large-scale chromatin organization in the nucleus has become more and more appreciated. The higher order nuclear organization ultimately regulate a plethora of biological processes including transcription, DNA replication, and DNA repair. In this context, it is of critical importance to understand the mechanisms that allow higher order nuclear organization. Scaffold Attachment Factor A (SAF-A/hnRNPU), which was originally identified as the component of nuclear matrix, has emerged as an important regulator of higher order nuclear organization. It is shown that SAF-A/hnRNPU binds to tandem repeats (TRs) and scaffold/matrix attachment regions (S/MAR) in a sequence-non-specific, but structure-specific manner (e.g. DNA curvature). Recent studies showed that SAF-A interacts with chromatin-associated RNAs (caRNAs) to regulate interphase chromatin structures in a transcription-dependent manner. It is proposed that SAF-A/hnRNPU and caRNAs form a dynamic, transcriptionally responsive chromatin mesh that organizes chromatin in a large scale. The common structural features of S/MAR and pericentromeric (periCEN) TR promotes SAF-A-mediated association with each other. Collectively a model is presented wherein SAF-A/hnRNPU and periCEN TR are the key players in large-scale nuclear organization that supports general transcription.

Whole-genome survey and phylogenetic analysis of Gadus macrocephalus

Gadus macrocephalus (Pacific cod) is an economically important species on the northern coast of the Pacific. Although numerous studies on G. macrocephalus exist, there are few reports on its genomic data. Here, we used whole-genome sequencing data to elucidate the genomic characteristics and phylogenetic relationship of G. macrocephalus. From the 19-mer frequency distribution, the genome size was estimated to be 658.22 Mb. The heterozygosity, repetitive sequence content and GC content were approximately 0.62%, 27.50% and 44.73%, respectively. The draft genome sequences were initially assembled, yielding a total of 500,760 scaffolds (N50 = 3565 bp). A total of 789,860 microsatellite motifs were identified from the genomic data, and dinucleotide repeat was the most dominant simple sequence repeat motif. As a byproduct of whole-genome sequencing, the mitochondrial genome was assembled to investigate the evolutionary relationships between G. macrocephalus and its relatives. On the basis of 13 protein-coding gene sequences of the mitochondrial genome of Gadidae species, the maximum likelihood phylogenetic tree showed that complicated relationships and divergence times among Gadidae species. Demographic history analysis revealed changes in the G. macrocephalus population during the Pleistocene by using the pairwise sequentially Markovian coalescent model. These findings supplement the genomic data of G. macrocephalus, and make a valuable contribution to the whole-genome studies on G. macrocephalus.

Repeat expression is linked to patient survival and exhibits single nucleotide variation in pancreatic cancer revealing LTR70:r.879A>G

Despite an overwhelming number of cancer literature reporting the links between patient survival and the expression levels of genes or mutations/single nucleotide variations (SNVs) on them, there is only limited information on repeat elements, which make at least half the human genome. Here, we analysed RNA-seq data obtained from primary pancreatic cancer tissues of 51 patients and revealed that two transposons, HERVI-int and X6A_LINE, showed an upregulation trend in the patients who lived shorter, along with 56 other potential repeats which were linked to survival. We also detected expressed single nucleotide variations (SNVs) on repeats, among which LTR70:r.879A>G stands out with the effect of its presence on this particular repeat's expression levels and a significant link to overall patient survival. Interestingly, the expression of LTR70:r.879A>G correlated with different cancer genes in comparison to its reference version highlighting the involvement of BRAF and Fumerate Hydratase with this expressed SNV. This is one of the first studies revealing possible links between repeat expression and survival in cancer and it warrants further research in this avenue.

Multiple heterochromatin diversification events in the genome of fungus-farming ants: insights from repetitive sequences

A substantial portion of the eukaryotic genome includes repetitive DNA, which is important for its stability, regulation, and architecture. Fungus-farming ant genomes show remarkable structural rearrangement rates that were necessary for the establishment of their agriculture-based lifestyle, highlighting the relevance of this peculiar group in understanding the repetitive portion of ant genome. Chromosomal banding studies are in accordance with genomic data because they show that repetitive heterochromatic sequences of basal and derivative Attina species are GC-rich, an uncommon trait in Formicidae. To understand the evolutionary dynamics of heterochromatin in Attina, we compared GC-rich heterochromatin patterns between the Paleoattina and Neoattina clades of this subtribe. To this end, we hybridized the Mrel-C₀t probe (highly and moderately repetitive DNA) obtained from Mycetomoellerius relictus, Neoattina with GC-rich heterochromatin, in karyotypes of Paleoattina and Neoattina species. Additionally, we mapped the repetitive sequences (GA)₁₅ and (TTAGG)₆ in species of the two clades to investigate their organization and evolutionary patterns in the genome of Attina. The Mrel-C₀t probe marked the heterochromatin in M. relictus, in other Mycetomoellerius spp., and in species of Mycetarotes, Cyphomyrmex, and Sericomyrmex (Neoattina). In Mycetomoellerius urichii, only pericentromeric heterochromatin was marked with Mrel-C₀t. No marking was observed in Paleoattina species or in Atta and Acromyrmex (Neoattina). These results indicated that different evolutionary events led to heterochromatin differentiation in Attina. The most likely hypothesis is that GC-rich heterochromatin arose in the common ancestor of the two clades and accumulated various changes throughout evolution. The sequences (GA)₁₅ and (TTAGG)₆ located in euchromatin and telomeres, respectively, showed more homogeneous results among the species.

msRepDB: a comprehensive repetitive sequence database of over 80 000 species

Repeats are prevalent in the genomes of all bacteria, plants and animals, and they cover nearly half of the Human genome, which play indispensable roles in the evolution, inheritance, variation and genomic instability, and serve as substrates for chromosomal rearrangements that include disease-causing deletions, inversions, and translocations. Comprehensive identification, classification and annotation of repeats in genomes can provide accurate and targeted solutions towards understanding and diagnosis of complex diseases, optimization of plant properties and development of new drugs. RepBase and Dfam are two most frequently used repeat databases, but they are not sufficiently complete. Due to the lack of a comprehensive repeat database of multiple species, the current research in this field is far from being satisfactory. LongRepMarker is a new framework developed recently by our group for comprehensive identification of genomic repeats. We here propose msRepDB based on LongRepMarker, which is currently the most comprehensive multi-species repeat database, covering >80 000 species. Comprehensive evaluations show that msRepDB contains more species, and more complete repeats and families than RepBase and Dfam databases. (https://msrepdb.cbrc.kaust.edu.sa/pages/msRepDB/index.html).

Identification of differentially expressed genomic repeats in primary hepatocellular carcinoma and their potential links to biological processes and survival

Hepatocellular carcinoma (HCC) is one of the deadliest cancers. Research on HCC so far primarily focused on genes and provided limited information on genomic repeats, which constitute more than half of the human genome and contribute to genomic stability. In line with this, repeat dysregulation was significantly shown to be pathological in various cancers and other diseases. In this study, we aimed to determine the full repeat expression profile of HCC for the first time. We utilised two independent RNA-seq datasets obtained from primary HCC tumours with matched normal tissues of 20 and 17 HCC patients, respectively. We quantified repeat expressions and analysed their differential expression. We also identified repeats that are cooperatively expressed with genes by constructing a gene coexpression network. Our results indicated that HCC tumours in both datasets harbour 24 differentially expressed repeats and even more elements were coexpressed with genes involved in various metabolic pathways. We discovered that two L1 elements (L1M3b, L1M3de) were downregulated and a handful of HERV subfamily repeats (HERV-Fc1-int, HERV3-int, HERVE_a-int, HERVK11D-int, HERVK14C-int, HERVL18-int) were upregulated with the exception of HERV1_LTRc, which was downregulated. Various LTR elements (LTR32, LTR9, LTR4, LTR52-int, LTR70) and MER elements (MER11C, MER11D, MER57C1, MER9a1, MER74C) were implicated along with few other subtypes including Charlie12, MLT2A2, Tigger15a, Tigger 17b. The only satellite repeat differentially expressed in both datasets was GSATII, whose expression was upregulated in 33 (>90%) out of 37 patients. Notably, GSATII expression correlated with HCC survival genes. Elements discovered here promise future studies to be considered for biomarker and HCC therapy research. The coexpression pattern of the GSATII satellite with HCC survival genes and the fact that it has been upregulated in the vast majority of patients make this repeat particularly stand out for HCC.

Unitary structure of palindromes in DNA

We investigate the quantum behavior encountered in palindromes within DNA structure. In particular, we reveal the unitary structure of usual palindromic sequences found in genomic DNAs of all living organisms, using the Schwinger's approach. We clearly demonstrate the role played by palindromic configurations with special emphasis on physical symmetries, in particular subsymmetries of unitary structure. We unveil the prominence of unitary structure in palindromic sequences in the sense that vitally significant information endowed within DNA could be transformed unchangeably in the process of transcription. We introduce a new symmetry relation, namely purine-purine or pyrimidine-pyrimidine symmetries (p-symmetry) in addition to the already known symmetry relation of purine-pyrimidine symmetries (pp-symmetry) given by Chargaff's rule. Therefore, important vital functions of a living organisms are protected by means of these symmetric features. It is understood that higher order palindromic sequences could be generated in terms of the basis of the highest prime numbers that make up the palindrome sequence number. We propose that violation of this unitary structure of palindromic sequences by means of our proposed symmetries leads to a mutation in DNA, which could offer a new perspective in the scientific studies on the origin and cause of mutation.

The large bat Helitron DNA transposase forms a compact monomeric assembly that buries and protects its covalently bound 5'-transposon end

Helitrons are widespread eukaryotic DNA transposons that have significantly contributed to genome variability and evolution, in part because of their distinctive, replicative rolling-circle mechanism, which often mobilizes adjacent genes. Although most eukaryotic transposases form oligomers and use RNase H-like domains to break and rejoin double-stranded DNA (dsDNA), Helitron transposases contain a single-stranded DNA (ssDNA)-specific HUH endonuclease domain. Here, we report the cryo-electron microscopy structure of a Helitron transposase bound to the 5'-transposon end, providing insight into its multidomain architecture and function. The monomeric transposase forms a tightly packed assembly that buries the covalently attached cleaved end, protecting it until the second end becomes available. The structure reveals unexpected architectural similarity to TraI, a bacterial relaxase that also catalyzes ssDNA movement. The HUH active site suggests how two juxtaposed tyrosines, a feature of many replication initiators that use HUH nucleases, couple the conformational shift of an α-helix to control strand cleavage and ligation reactions.

A sensitive repeat identification framework based on short and long reads

Numerous studies have shown that repetitive regions in genomes play indispensable roles in the evolution, inheritance and variation of living organisms. However, most existing methods cannot achieve satisfactory performance on identifying repeats in terms of both accuracy and size, since NGS reads are too short to identify long repeats whereas SMS (Single Molecule Sequencing) long reads are with high error rates. In this study, we present a novel identification framework, LongRepMarker, based on the global de novo assembly and k-mer based multiple sequence alignment for precisely marking long repeats in genomes. The major characteristics of LongRepMarker are as follows: (i) by introducing barcode linked reads and SMS long reads to assist the assembly of all short paired-end reads, it can identify the repeats to a greater extent; (ii) by finding the overlap sequences between assemblies or chomosomes, it locates the repeats faster and more accurately; (iii) by using the multi-alignment unique k-mers rather than the high frequency k-mers to identify repeats in overlap sequences, it can obtain the repeats more comprehensively and stably; (iv) by applying the parallel alignment model based on the multi-alignment unique k-mers, the efficiency of data processing can be greatly optimized and (v) by taking the corresponding identification strategies, structural variations that occur between repeats can be identified. Comprehensive experimental results show that LongRepMarker can achieve more satisfactory results than the existing de novo detection methods (https://github.com/BioinformaticsCSU/LongRepMarker).

Toward the massive genome of Proteus anguinus-illuminating longevity, regeneration, convergent evolution, and metabolic disorders

Deciphering the genetic code of organisms with unusual phenotypes can help answer fundamental biological questions and provide insight into mechanisms relevant to human biomedical research. The cave salamander Proteus anguinus (Urodela: Proteidae), also known as the olm, is an example of a species with unique morphological and physiological adaptations to its subterranean environment, including regenerative abilities, resistance to prolonged starvation, and a life span of more than 100 years. However, the structure and sequence of the olm genome is still largely unknown owing to its enormous size, estimated at nearly 50 gigabases. An international Proteus Genome Research Consortium has been formed to decipher the olm genome. This perspective provides the scientific and biomedical rationale for exploring the olm genome and outlines potential outcomes, challenges, and methodological approaches required to analyze and annotate the genome of this unique amphibian.

Comparative Genomic and Transcriptomic Analysis of Naegleria fowleri Clinical and Environmental Isolates

Out of over 40 species of Naegleria, which are free-living thermophilic amebae found in freshwater and soil worldwide, only Naegleria fowleri infects humans, causing primary amebic meningoencephalitis (PAM), a typically fatal brain disease. To understand the population structure of Naegleria species and the genetic relationships between N. fowleri isolates and to detect pathogenic factors, we characterized 52 novel clinical and environmental N. fowleri genomes and a single Naegleria lovaniensis strain, along with transcriptomic data for a subset of 37 N. fowleri isolates. Whole-genome analysis of 56 isolates from three Naegleria species (N. fowleri, N. lovaniensis, and Naegleria gruberi) identified several genes unique to N. fowleri that have previously been linked to the pathogenicity of N. fowleri, while other unique genes could be associated with novel pathogenicity factors in this highly fatal pathogen. Population structure analysis estimated the presence of 10 populations within the three Naegleria species, of which 7 populations were within N. fowleri. The whole-nuclear-genome (WNG) phylogenetic analysis showed an overall geographical clustering of N. fowleri isolates, with few exceptions, and provided higher resolution in identifying potential clusters of isolates beyond that of the traditional locus typing. There were only 34 genes that showed significant differences in gene expression between the clinical and environmental isolates. Genomic data generated in this study can be used for developing rapid molecular assays and to conduct future population-based global genomic analysis and will also be a valuable addition to genomic reference databases, where shotgun metagenomics data from routine water samples could be searched for the presence of N. fowleri strains. IMPORTANCE N. fowleri, the only known Naegleria species to infect humans, causes fatal brain disease. PAM cases from 1965 to 2016 showed <20 cases per year globally. Out of approximately 150 cases in North America since 1962, only four PAM survivors are known, yielding a >97% case fatality rate, which is critically high. Although the pathogenesis of N. fowleri has been studied for the last 50 years, pathogenetic factors that lead to human infection and breaching the blood-brain barrier remain unknown. In addition, little is known regarding the genomic diversity both within N. fowleri isolates and among Naegleria species. In this study, we generated novel genome sequences and performed comparative genomic and transcriptomic analysis of a set of 52 N. fowleri draft genome sequences from clinical and environmental isolates derived from all over the world in the last 53 years, which will help shape future genome-wide studies and develop sensitive assays for routine surveillance.

First Description of a Satellite DNA in Manatees' Centromeric Regions

Trichechus manatus and Trichechus inunguis are the two Sirenia species that occur in the Americas. Despite their increasing extinction risk, many aspects of their biology remain understudied, including the repetitive DNA fraction of their genomes. Here we used the sequenced genome of T. manatus and TAREAN to identify satellite DNAs (satDNAs) in this species. We report the first description of TMAsat, a satDNA comprising ~0.87% of the genome, with ~684bp monomers and centromeric localization. In T. inunguis, TMAsat showed similar monomer length, chromosome localization and conserved CENP-B box-like motifs as in T. manatus. We also detected this satDNA in the Dugong dugon and in the now extinct Hydrodamalis gigas genomes. The neighbor-joining tree shows that TMAsat sequences from T. manatus, T. inunguis, D. dugon, and H. gigas lack species-specific clusters, which disagrees with the predictions of concerted evolution. We detected a divergent TMAsat-like homologous sequence in elephants and hyraxes, but not in other mammals, suggesting this sequence was already present in the common ancestor of Paenungulata, and later became a satDNA in the Sirenians. This is the first description of a centromeric satDNA in manatees and will facilitate the inclusion of Sirenia in future studies of centromeres and satDNA biology.

DeepGRP: engineering a software tool for predicting genomic repetitive elements using Recurrent Neural Networks with attention

BACKGROUND

Repetitive elements contribute a large part of eukaryotic genomes. For example, about 40 to 50% of human, mouse and rat genomes are repetitive. So identifying and classifying repeats is an important step in genome annotation. This annotation step is traditionally performed using alignment based methods, either in a de novo approach or by aligning the genome sequence to a species specific set of repetitive sequences. Recently, Li (Bioinformatics 35:4408-4410, 2019) developed a novel software tool dna-brnn to annotate repetitive sequences using a recurrent neural network trained on sample annotations of repetitive elements.

RESULTS

We have developed the methods of dna-brnn further and engineered a new software tool DeepGRP. This combines the basic concepts of Li (Bioinformatics 35:4408-4410, 2019) with current techniques developed for neural machine translation, the attention mechanism, for the task of nucleotide-level annotation of repetitive elements. An evaluation on the human genome shows a 20% improvement of the Matthews correlation coefficient for the predictions delivered by DeepGRP, when compared to dna-brnn. DeepGRP predicts two additional classes of repeats (compared to dna-brnn) and is able to transfer repeat annotations, using RepeatMasker-based training data to a different species (mouse). Additionally, we could show that DeepGRP predicts repeats annotated in the Dfam database, but not annotated by RepeatMasker. DeepGRP is highly scalable due to its implementation in the TensorFlow framework. For example, the GPU-accelerated version of DeepGRP is approx. 1.8 times faster than dna-brnn, approx. 8.6 times faster than RepeatMasker and over 100 times faster than HMMER searching for models of the Dfam database.

CONCLUSIONS

By incorporating methods from neural machine translation, DeepGRP achieves a consistent improvement of the quality of the predictions compared to dna-brnn. Improved running times are obtained by employing TensorFlow as implementation framework and the use of GPUs. By incorporating two additional classes of repeats, DeepGRP provides more complete annotations, which were evaluated against three state-of-the-art tools for repeat annotation.

Complete Chloroplast Genome Sequence of Fortunella venosa (Champ. ex Benth.) C.C.Huang (Rutaceae): Comparative Analysis, Phylogenetic Relationships, and Robust Support for Its Status as an Independent Species

Fortunella venosa (Rutaceae) is an endangered species endemic to China and its taxonomic status has been controversial. The genus Fortunella contains a variety of important economic plants with high value in food, medicine, and ornamental. However, the placement of Genus Fortunella into Genus Citrus has led to controversy on its taxonomy and Systematics. In this present research, the Chloroplast genome of F. venosa was sequenced using the second-generation sequencing, and its structure and phylogenetic relationship analyzed. The results showed that the Chloroplast genome size of F. venosa was 160,265 bp, with a typical angiosperm four-part ring structure containing a large single copy region (LSC) (87,597 bp), a small single copy region (SSC) (18,732 bp), and a pair of inverted repeat regions (IRa\IRb) (26,968 bp each). There are 134 predicted genes in Chloroplast genome, including 89 protein-coding genes, 8 rRNAs, and 37 tRNAs. The GC-content of the whole Chloroplast genome was 43%, with the IR regions having a higher GC content than the LSC and the SSC regions. There were no rearrangements present in the Chloroplast genome; however, the IR regions showed obvious contraction and expansion. A total of 108 simple sequence repeats (SSRs) were present in the entire chloroplast genome and the nucleotide polymorphism was high in LSC and SSC. In addition, there is a preference for codon usage with the non-coding regions being more conserved than the coding regions. Phylogenetic analysis showed that species of Fortunella are nested in the genus of Citrus and the independent species status of F. venosa is supported robustly, which is significantly different from F. japonica. These findings will help in the development of DNA barcodes that can be useful in the study of the systematics and evolution of the genus Fortunella and the family Rutaceae.

Losing DNA methylation at repetitive elements and breaking bad

Background

DNA methylation is an epigenetic chromatin mark that allows heterochromatin formation and gene silencing. It has a fundamental role in preserving genome stability (including chromosome stability) by controlling both gene expression and chromatin structure. Therefore, the onset of an incorrect pattern of DNA methylation is potentially dangerous for the cells. This is particularly important with respect to repetitive elements, which constitute the third of the human genome.

Main body

Repetitive sequences are involved in several cell processes, however, due to their intrinsic nature, they can be a source of genome instability. Thus, most repetitive elements are usually methylated to maintain a heterochromatic, repressed state. Notably, there is increasing evidence showing that repetitive elements (satellites, long interspersed nuclear elements (LINEs), Alus) are frequently hypomethylated in various of human pathologies, from cancer to psychiatric disorders. Repetitive sequences’ hypomethylation correlates with chromatin relaxation and unscheduled transcription. If these alterations are directly involved in human diseases aetiology and how, is still under investigation.

Conclusions

Hypomethylation of different families of repetitive sequences is recurrent in many different human diseases, suggesting that the methylation status of these elements can be involved in preservation of human health. This provides a promising point of view towards the research of therapeutic strategies focused on specifically tuning DNA methylation of DNA repeats.

What prevents mainstream evolutionists teaching the whole truth about how genomes evolve?

The common belief that the neo-Darwinian Modern Synthesis (MS) was buttressed by the discoveries of molecular biology is incorrect. On the contrary those discoveries have undermined the MS. This article discusses the many processes revealed by molecular studies and genome sequencing that contribute to evolution but nonetheless lie beyond the strict confines of the MS formulated in the 1940s. The core assumptions of the MS that molecular studies have discredited include the idea that DNA is intrinsically a faithful self-replicator, the one-way transfer of heritable information from nucleic acids to other cell molecules, the myth of "selfish DNA", and the existence of an impenetrable Weismann Barrier separating somatic and germ line cells. Processes fundamental to modern evolutionary theory include symbiogenesis, biosphere interactions between distant taxa (including viruses), horizontal DNA transfers, natural genetic engineering, organismal stress responses that activate intrinsic genome change operators, and macroevolution by genome restructuring (distinct from the gradual accumulation of local microevolutionary changes in the MS). These 21st Century concepts treat the evolving genome as a highly formatted and integrated Read-Write (RW) database rather than a Read-Only Memory (ROM) collection of independent gene units that change by random copying errors. Most of the discoverers of these macroevolutionary processes have been ignored in mainstream textbooks and popularizations of evolutionary biology, as we document in some detail. Ironically, we show that the active view of evolution that emerges from genomics and molecular biology is much closer to the 19th century ideas of both Darwin and Lamarck. The capacity of cells to activate evolutionary genome change under stress can account for some of the most negative clinical results in oncology, especially the sudden appearance of treatment-resistant and more aggressive tumors following therapies intended to eradicate all cancer cells. Knowing that extreme stress can be a trigger for punctuated macroevolutionary change suggests that less lethal therapies may result in longer survival times.

High Rates of Genome Rearrangements and Pathogenicity of Shigella spp

Shigella are pathogens originating within the Escherichia lineage but frequently classified as a separate genus. Shigella genomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella evolution. We found that Shigella experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic E. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different Shigella lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all Shigella strains that also showed a high level of sequence conservation in the promoter and further in the 5′-intergenic region. In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli, we found a rate of genome rearrangements comparable to those in other E. coli and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These data indicate that the accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands.

The transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content

Background

Extensive molecular differences exist between proliferative and differentiated cells. Here, we conduct a meta-analysis of publicly available transcriptomic datasets from preimplantation and differentiation stages examining the architectural properties and content of genes whose abundance changes significantly across developmental time points.

Results

Analysis of preimplantation embryos from human and mouse showed that short genes whose introns are enriched in Alu (human) and B (mouse) elements, respectively, have higher abundance in the blastocyst compared to the zygote. These highly expressed genes encode ribosomal proteins or metabolic enzymes. On the other hand, long genes whose introns are depleted in repetitive elements have lower abundance in the blastocyst and include genes from signaling pathways. Additionally, the sequences of the genes that are differentially expressed between the blastocyst and the zygote contain distinct collections of pyknon motifs that differ between up- and down-regulated genes. Further examination of the genes that participate in the stem cell-specific protein interaction network shows that their introns are short and enriched in Alu (human) and B (mouse) elements. As organogenesis progresses, in both human and mouse, we find that the primarily short and repeat-rich expressed genes make way for primarily longer, repeat-poor genes. With that in mind, we used a machine learning-based approach to identify gene signatures able to classify human adult tissues: we find that the most discriminatory genes comprising these signatures have long introns that are repeat-poor and include transcription factors and signaling-cascade genes. The introns of widely expressed genes across human tissues, on the other hand, are short and repeat-rich, and coincide with those with the highest expression at the blastocyst stage.

Conclusions

Protein-coding genes that are characteristic of each trajectory, i.e., proliferation/pluripotency or differentiation, exhibit antithetical biases in their intronic and exonic lengths and in their repetitive-element content. While the respective human and mouse gene signatures are functionally and evolutionarily conserved, their introns and exons are enriched or depleted in organism-specific repetitive elements. We posit that these organism-specific repetitive sequences found in exons and introns are used to effect the corresponding genes’ regulation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-020-00928-8.

Functional and characteristic analysis of an appressorium-specific promoter PMagas1 in Metarhizium acridum

Entomopathogenic fungi have been used as important biological control agents throughout the world. To improve the biocontrol efficacy of entomopathogenic fungi, many genes have been used to improve fungal virulence or tolerance to adverse conditions via modulating their expression with strong promoters. The Magas1 gene is specifically expressed during appressorium formation and contributes to the virulence in Metarhizium acridum. In this study, we analyzed the functional region of the promoter of Magas1 gene (PMagas1) in M. acridum using 5'-deletion technique with enhanced green fluoresces protein (EGFP) as a reporter. Results showed the full length of the PMagas1 was at least 897 bp. Two regions (-897 to -611 bp and -392 to -328 bp) were essential for the activity of PMagas1. An engineered M. acridum strain was constructed with PMagas1 driving the expression of a subtilisin-like proteinase gene Pr1A (PMagas1-PR1A). Bioassay showed that the virulence was significantly increased in PMagas1-PR1A strain compared to wild type strain. Pmagas1 promoter is suitable for the overexpression of some genes during the infection of entomopathogenic fungi, which avoids the waste of nutritional resources and the influence on other fungal characteristics during the saprophytic process of constitutive promoter.

Hypermethylation of WNT3A gene and non-syndromic cleft lip and/or palate in association with in utero exposure to lead: A mediation analysis

OBJECTIVES

We aim to investigate association between WNT3A methylation and risk of non-syndromic cleft lip and/or palate (NSCL/P), and examine mediating effect of WNT3A methylation on the association of NSCL/P and lead (Pb) exposure in fetuses.

METHODS

DNA methylation of WNT3A in umbilical cord blood was determined among 59 NSCL/P cases and 118 non-malformed controls. Mediation analysis was performed to evaluate the potential mediating effect of WNT3A methylation on association between concentrations of Pb in umbilical cord and risk for NSCL/P. Additionally, an animal experiment in which cleft palates were induced by lead acetate was conducted.

RESULTS

The overall average methylation level of WNT3A was significant higher in NSCL/P cases as compared to controls. The risk for NSCL/P was increased by 1.90-fold with hypermethylation of WNT3A. Significant correlation was observed between concentrations of Pb in umbilical cord and methylation level of WNT3A. The hypermethylation of WNT3A had a mediating effect by 9.32% of total effect of Pb on NSCL/P risk. Gender-specific association between WNT3A methylation and NSCL/P was observed in male fetuses, and the percentage of the mediating effect increased to 14.28%. Animal experiment of mice showed that maternal oral exposure to lead acetate may result in cleft palate in offspring.

CONCLUSION

Hypermethylation of WNT3A was associated with the risk for NSCL/P and may be partly explain the association between exposure to Pb and risk for NSCL/P. The teratogenic and fetotoxic effects of Pb were found in mice.

Novel type of coagulation equation and its application to DNA repeat expansion process

DNA molecules containing repetitive motifs are prone to expand in their lengths. Once there appear a head to tail tandem of two identical DNA sequences in the system, they can propagate indefinitely by the mechanism involving cycles of staggered annealing of complementary DNA strands of variable lengths and polymerase mediated filling-in of the generated overhangs. Microgene Polymerization Reaction (MPR) is an experimental model for expansion of short repetitive DNA to longer lengths. The testable kinetic model of (MPR) was formulated and solved numerically by Itsko et al. in Kinetics of Repeat Propagation in the Microgene Polymerization Reaction (2009). Here, the simple cases of MPR were solved analytically using modified Smoluchowski coagulation equation. It was found that the repeats propagate according to Gumbel probability density function when the distribution of lengths of obtained polymers follows inverted Gumbel probability density function.

The evolutionary genetics of personality

Genetic influences on personality differences are ubiquitous, but their nature is not well understood. A theoretical framework might help, and can be provided by evolutionary genetics. We assess three evolutionary genetic mechanisms that could explain genetic variance in personality differences: selective neutrality, mutation‐selection balance, and balancing selection. Based on evolutionary genetic theory and empirical results from behaviour genetics and personality psychology, we conclude that selective neutrality is largely irrelevant, that mutation‐selection balance seems best at explaining genetic variance in intelligence, and that balancing selection by environmental heterogeneity seems best at explaining genetic variance in personality traits. We propose a general model of heritable personality differences that conceptualises intelligence as fitness components and personality traits as individual reaction norms of genotypes across environments, with different fitness consequences in different environmental niches. We also discuss the place of mental health in the model. This evolutionary genetic framework highlights the role of gene‐environment interactions in the study of personality, yields new insight into the person‐situation‐debate and the structure of personality, and has practical implications for both quantitative and molecular genetic studies of personality. Copyright © 2007 John Wiley & Sons, Ltd.

Evolutionary dynamics of the SARS-CoV-2 ORF8 accessory gene

The new SARS-CoV-2 poses a significant threat to human health but many aspects of its basic biology remain unknown. Its genome encodes accessory genes that differ significantly within coronaviruses and contribute to the virus pathogenicity. Among accessory genes, open reading frame 8 (ORF8) stands out by being highly variable and showing structural changes suspected to be related with the virus ability to spread. However, the function of ORF8 remains to be elucidated, making it less studied than other SARS-CoV-2 genes. Here I show that ORF8 is poorly conserved among related coronaviruses. The ORF8 phylogeny built using 11,113 SARS-CoV-2 sequences revealed traces of a typical expanding population with a small number of highly frequent lineages. Interestingly, I detected several nonsense mutations and three main deletions in the ORF8 gene that either remove or significantly change the ORF8 protein. These findings suggest that SARS-CoV-2 can persist without a functional ORF8 protein. Deletion breakpoints were found located in predicted hairpins suggesting a possible involvement of these elements in the rearrangement process. Although the function of ORF8 remains to be elucidated, its structural plasticity and high diversity suggest an important role in SARS-CoV-2 pathogenicity.