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With 500+ papers and 20+ books spanning many scientific disciplines, Mark Burgin has left an indelible mark and legacy for future explorers of human thought and information technology professionals. In this paper, I discuss his contribution to the evolution of machine intelligence using his general theory of information (GTI) based on my discussions with him and various papers I co-authored during the past eight years. His construction of a new class of digital automata to overcome the barrier posed by the Church–Turing Thesis, and his contribution to super-symbolic computing with knowledge structures, cognizing oracles, and structural machines are leading to practical applications changing the future landscape of information systems. GTI provides a model for the operational knowledge of biological systems to build, operate, and manage life processes using 30+ trillion cells capable of replication and metabolism. The schema and associated operations derived from GTI are also used to model a digital genome specifying the operational knowledge of algorithms executing the software life processes with specific purposes using replication and metabolism. The result is a digital software system with a super-symbolic computing structure exhibiting autopoietic and cognitive behaviors that biological systems also exhibit. We discuss here one of these applications. [ABSTRACT FROM AUTHOR]

Simple Summary: Simple Summary: This article studies runs of homozygosity (ROHs) across the genome using high-density single-nucleotide polymorphism (SNP) arrays for the structural and functional annotation of genes localized inside or in close proximity to selected sections of the genome of Aberdeen Angus cattle. The obtained results could serve as a foundation for future studies aimed at identifying the genes and markers required to determine the most significant productive traits of cattle. The data confirm the effect of targeted selection on increasing the height, body size, and live weight in the population of Aberdeen Angus cattle. A large number of cattle breeds have marked phenotypic differences. They are valuable models for studying genome evolution. ROH analysis can facilitate the discovery of genomic regions that may explain phenotypic differences between breeds affecting traits of economic importance. This paper investigates genome-wide ROH of 189 Aberdeen Angus bulls using the Illumina Bovine GGP HD Beadchip150K to structurally and functionally annotate genes located within or in close ROH of the Aberdeen Angus cattle genome. The method of sequential SNP detection was used to determine the ROH. Based on this parameter, two ROH classes were allocated. The total length of all ROH islands was 11,493 Mb. As a result of studying the genomic architecture of the experimental population of Aberdeen Angus bulls, nine ROH islands and 255 SNPs were identified. Thirteen of these overlapped with regions bearing 'selection imprints' previously identified in other breeds of cattle, and five of these regions were identified in other Aberdeen Angus populations. The total length of the ROH islands was 11,493 Mb. The size of individual islands ranged from 0.038 to 1.812 Mb. Structural annotation showed the presence of 87 genes within the identified ROH islets. [ABSTRACT FROM AUTHOR]

In recent years, an increasing number of viruses have triggered outbreaks that pose a severe threat to both human and animal life, as well as caused substantial economic losses. It is crucial to understand the genomic structure and epidemiology of these viruses to guide effective clinical prevention and treatment strategies. Nanopore sequencing, a third-generation sequencing technology, has been widely used in genomic research since 2014. This technology offers several advantages over traditional methods and next-generation sequencing (NGS), such as the ability to generate ultra-long reads, high efficiency, real-time monitoring and analysis, portability, and the ability to directly sequence RNA or DNA molecules. As a result, it exhibits excellent applicability and flexibility in virus research, including viral detection and surveillance, genome assembly, the discovery of new variants and novel viruses, and the identification of chemical modifications. In this paper, we provide a comprehensive review of the development, principles, advantages, and applications of nanopore sequencing technology in animal and human virus research, aiming to offer fresh perspectives for future studies in this field. [ABSTRACT FROM AUTHOR]

The exact identification of promoter sequences remains a serious problem in computational biology, as the promoter prediction algorithms under development continue to produce false-positive results. Therefore, to fully assess the validity of predicted sequences, it is necessary to perform a comprehensive test of their properties, such as the presence of downstream transcribed DNA regions behind them, or chromatin accessibility for transcription factor binding. In this paper, we examined the promoter sequences of chromosome 1 of the rice Oryza sativa genome from the Database of Potential Promoter Sequences predicted using a mathematical algorithm based on the derivation and calculation of statistically significant promoter classes. In this paper TATA motifs and cis-regulatory elements were identified in the predicted promoter sequences. We also verified the presence of potential transcription start sites near the predicted promoters by analyzing CAGE-seq data. We searched for unannotated transcripts behind the predicted sequences by de novo assembling transcripts from RNA-seq data. We also examined chromatin accessibility in the region of the predicted promoters by analyzing ATAC-seq data. As a result of this work, we identified the predicted sequences that are most likely to be promoters for further experimental validation in an in vivo or in vitro system. [ABSTRACT FROM AUTHOR]

China leads the world in freshwater pearl production, an industry in which the triangle sail mussel (Sinohyriopsis cumingii) plays a pivotal role. In this paper, we report a high-quality chromosome-level genome assembly of S. cumingii with a size of 2.90 Gb—the largest yet reported among bivalves—and 89.92% anchorage onto 19 linkage groups. The assembled genome has 37,696 protein-coding genes and 50.86% repeat elements. A comparative genomic analysis revealed expansions of 752 gene families, mostly associated with biomineralization, and 237 genes under strong positive selection. Notably, the fibrillin gene family exhibited gene family expansion and positive selection simultaneously, and it also exhibited multiple high expressions after mantle implantation by transcriptome analysis. Furthermore, RNA silencing and an in vitro calcium carbonate crystallization assay highlighted the pivotal role played by one fibrillin gene in calcium carbonate deposition and aragonite transformation. This study provides a valuable genomic resource and offers new insights into the mechanism of pearl biomineralization. [ABSTRACT FROM AUTHOR]

Simple Summary: As an endemic and vulnerable fish from the upper Yangtze River in China, Schizothorax kozlovi holds significant scientific and ecological importance, yet it has received little attention so far. In this paper, we reported the characterization of the mitochondrial genome of S. kozlovi, and further investigated the phylogenetic relationships of Schizothorax. The results showed that the mitochondrial genome of S. kozlovi had a total size of 16,585 bp, a circular arrangement, and contained 13 PCGs, 22 tRNAs, two rRNAs, and two non-coding regions. Moreover, the phylogenetic analyses demonstrated that Schizothorax could be classified into four clades, and S. kozlovi was closely related to Schizothorax chongi. The present study enriched the basic biological data for S. kozlovi and provided fundamental references for the conservation of S. kozlovi and Schizothorax. Schizothorax kozlovi is an endemic and vulnerable fish species found in the upper Yangtze River in China. Over the past few years, the population resources of S. kozlovi have been nearly completely depleted owing to multiple contributing threats. While the complete mitochondrial genomes serve as important molecular markers for phylogenetic and genetic studies, the mitochondrial genome of S. kozlovi has still received little attention. In this study, we analyzed the characterization of the mitochondrial genome of S. kozlovi and investigated the phylogenetic relationships of Schizothorax. The complete mitochondrial genome of S. kozlovi was 16,585 bp in length, which contained thirty-seven genes (thirteen protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), twenty-two transfer RNA genes (tRNAs)) and two non-coding regions for the origin of light strand (OL) and the control region (CR). There were nine overlapping regions and seventeen intergenic spacers regions in the mitochondrial genome. The genome also showed a bias towards A + T content (55.01%) and had a positive AT-skew (0.08) and a negative GC-skew (−0.20). All the PCGs employed the ATG or GTG as the start codon and TAA, TAG, or single T as the stop codon. Additionally, all of the tRNAs displayed a typical cloverleaf secondary structure, except trnS1 which lacked the D arm. The phylogenetic analysis, based on the maximum likelihood (ML) and Bayesian inference (BI) methods, revealed that the topologies of the phylogenetic tree divided the Schizothorax into four clades and did not support the classification of Schizothorax based on morphology. The phylogenetic status of S. kozlovi was closely related to that of S. chongi. The present study provides valuable genomic information for S. kozlovi and new insights in phylogenetic relationships of Schizothorax. These data could also offer fundamental references and guidelines for the management and conservation of S. kozlovi and other species of Schizothorax. [ABSTRACT FROM AUTHOR]

Simple Summary: The phylogenetic status of the family Nitidulidae and its sister group relationship remain controversial. Also, the phylogenetic status of the subfamily Meligethinae and its phylogenetic relationships with other subfamilies of Nitidulidae are not fully understood. Mitochondrial genome sequences can be used to study species identification, phylogeny, and population genetic structure, and to provide valuable molecular markers for further genetic studies. In this paper, two complete mitochondrial genomes of Meligethinae were provided for the first time, and the phylogenetic status of the family Nitidulidae and subfamily Meligethinae were explored based on the complete mitochondrial genomes. A comparative analysis of the general characteristics and non-coding region patterns of the complete mitochondrial genomes of Meligethinus tschungseni and Brassicogethes affinis revealed that the base composition and mitochondrial genome structure of these two species are markedly different. Given the results of the phylogenetic analysis based on 20 mitochondrial genomes, the status of Nitidulidae and its sister group relationship is discussed. We also attempted to analyze the taxonomic status of Meligethinae and its sister group relationship. This study will provide a basis for further studies on the higher phylogeny of Nitidulidae. The phylogenetic status of the family Nitidulidae and its sister group relationship remain controversial. Also, the status of the subfamily Meligethinae is not fully understood, and previous studies have been mainly based on morphology, molecular fragments, and biological habits, rather than the analysis of the complete mitochondrial genome. Up to now, there has been no complete mitochondrial genome report of Meligethinae. In this study, the complete mitochondrial genomes of Meligethinus tschungseni and Brassicogethes affinis (both from China) were provided, and they were compared with the existing complete mitochondrial genomes of Nitidulidae. The phylogenetic analysis among 20 species of Coleoptera was reconstructed via PhyloBayes analysis and Maximum likelihood (ML) analysis, respectively. The results showed that the full lengths of Meligethinus tschungseni and Brassicogethes affinis were 15,783 bp and 16,622 bp, and the AT contents were 77% and 76.7%, respectively. Each complete mitochondrial genome contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a control region (A + T-rich region). All the PCGs begin with the standard start codon ATN (ATA, ATT, ATG, ATC). All the PCGs terminate with a complete terminal codon, TAA or TAG, except cox1, cox2, nad4, and nad5, which terminate with a single T. Furthermore, all the tRNAs have a typical clover-leaf secondary structure except trnS1, whose DHU arm is missing in both species. The two newly sequenced species have different numbers and lengths of tandem repeat regions in their control regions. Based on the genetic distance and Ka/Ks analysis, nad6 showed a higher variability and faster evolutionary rate. Based on the available complete mitochondrial genomes, the results showed that the four subfamilies (Nitidulinae, Meligethinae, Carpophilinae, Epuraeinae) of Nitidulidae formed a monophyletic group and further supported the sister group relationship of Nitidulidae + Kateretidae. In addition, the taxonomic status of Meligethinae and the sister group relationship between Meligethinae and Nitidulinae (the latter as currently circumscribed) were also preliminarily explored. [ABSTRACT FROM AUTHOR]

For a long time, the construction of complete reference genomes for complex eukaryotic genomes has been hindered by the limitations of sequencing technologies. Recently, the Pacific Biosciences (PacBio) HiFi data and Oxford Nanopore Technologies (ONT) Ultra-Long data, leveraging their respective advantages in accuracy and length, have provided an opportunity for generating complete chromosome sequences. Nevertheless, for the majority of genomes, the chromosome-level assemblies generated using existing methods still miss a high proportion of sequences due to losing small contigs in the step of assembly and scaffolding. To address this shortcoming, in this paper, we propose a novel method that is able to identify and fill the gaps in the chromosome-level assembly by recalling the sequences in the lost small contigs. Experimental results on both real and simulated datasets demonstrate that this method is able to improve the completeness of the chromosome-level assembly. [ABSTRACT FROM AUTHOR]

Simple Summary: The eumenine wasps of the genus Rhynchium Spinola, 1806; Allorhynchium van der Vecht, 1963; Anterhynchium de Saussure, 1863; and Pararrhynchium de Saussure, 1855 are related and sometimes hard to tell apart from each other. In this study, we first reconstructed the phylogenetic relationships of these genera based on universal single-copy orthologs and ultraconserved elements extracted from 10 newly sequenced low-coverage whole genomes. The results showed that Allorhynchium and Lissodynerus are distinct from the other four taxa. The genus Rhynchium was recovered as monophyletic, whereas Anterhynchium was recovered as paraphyletic, with Anterhynchium (Dirhynchium) as a sister to Rhynchium and hence deserving a separate genus Dirhynchium; and within the genus Pararrhynchium, P. septemfasciatus feanus and P. venkataramani were separated, not clustered on a branch. It is suggested that the genus Lissodynerus should be restituted as a valid genus, not a synonym of the Pararrhynchium. The results are consistent with previous eumenine mitochondrial genome phylogenetic analyses. This paper confirms the feasibility of low-coverage whole genome eumenine wasp phylogenetics and provides a reference for subsequent research in Eumeninae. The subfamily Eumeninae is a large group of fierce predatory insects that prey mainly on the larvae of Lepidoptera pests. Because of the highly similar morphologies of the genus Rhynchium and its related genera in the subfamily, including Rhynchium Spinola, Allorhynchium van der Vecht, Anterhynchium de Saussure, Pararrhynchium de Saussure, it is essential to delineate their relationships. A previous phylogenetic analysis based on mitochondrial genomes suggested the inconsistent relationships of these genera under traditional classification based on morphological characters. In this study, we first used single-copy orthologs [USCO] and ultraconserved elements [UCE] extracted from 10 newly sequenced low-coverage whole genomes to resolve the phylogenetic relationships of the above genera. The newly sequenced genomes are 152.99 Mb to 211.49 Mb in size with high completeness (BUSCO complete: 91.5–95.6%) and G + C content (36.31–38.76%). Based on extracted 5811 USCOs and 2312 UCEs, the phylogenetic relationships of Rhynchium and its related genera were: ((Allorhynchium + Lissodynerus) + (Pararrhynchium + (Anterhynchium + (Dirhynchium + Rhynchium)))), which was consistent with the mitochondrial genome results. The results supported the genus Rhynchium as monophyletic, whereas Anterhynchium was recovered as paraphyletic, with Anterhynchium (Dirhynchium) as a sister to Rhynchium and hence deserving generic status; In addition, in the genus Pararrhynchium, P. septemfasciatus feanus and P. venkataramani were separated, not clustered on a branch, just as P. septemfasciatus feanus was not together with P. striatum based on mitochondrial genomes. Since Lissodynerus septemfasciatus, the type species of the genus Lissodynerus, was transferred to Pararrhynchium, it is considered that the genus Lissodynerus should be restituted as a valid genus, not a synonym of Pararrhynchium. [ABSTRACT FROM AUTHOR]

The existence of current species can be attributed to a dynamic interplay between evolutionary forces and the maintenance of genetic information. Heterochromatin is a major structural feature of the eukaryotic genome stability, a specialized type of chromatin that contains a complex and still poorly understood genomic compartment, extremely enriched in repeats and transposable elements [[15]] in which expressed genes are rare but not completely absent [[16]]. While mutations are the primary drivers of evolution, there are cellular mechanisms that counterbalance excessive variation and contribute to the stability of genes and genomes and preserve the faithful pass down of the genetic material from generation to generation. This form of symbiosis results in the destabilization of the mitochondrial genome (mtDNA) when mutations hit a subset of nuclear genes. [Extracted from the article]

Currently, one of the fastest-growing DNA sequencing technologies is nanopore sequencing. One of the key stages involved in processing sequencer data is the basecalling process, where the input sequence of currents measured on the nanopores of the sequencer reproduces the DNA sequences, called DNA reads. Many of the applications dedicated to basecalling, together with the DNA sequence, provide the estimated quality of the reconstruction of a given nucleotide (quality symbols are contained on every fourth line of the FASTQ file; each nucleotide in the FASTQ file corresponds to exactly one estimated nucleotide reconstruction quality symbol). Herein, we compare the estimated nucleotide reconstruction quality symbols (signs from every fourth line of the FASTQ file) reported by other basecallers. The conducted experiments consisted of basecalling the same raw datasets from the nanopore device by other basecallers and comparing the provided quality symbols, denoting the estimated quality of the nucleotide reconstruction. The results show that the estimated quality reported by different basecallers may vary, depending on the tool used, particularly in terms of range and distribution. Moreover, we mapped basecalled DNA reads to reference genomes and calculated matched and mismatched rates for groups of nucleotides with the same quality symbol. Finally, the presented paper shows that the estimated nucleotide reconstruction quality reported in the basecalling process is not used in any investigated tool for processing nanopore DNA reads. [ABSTRACT FROM AUTHOR]

Ehretiaceae is a family in the order Boraginales. It contains more than 150 species. The Ehretiaceae classification has remained elusive and changed over time from subfamily to family, or vice versa. In this paper, we sequenced, characterized, and analyzed the complete chloroplast (cp) genomes of Ehretia cymosa and Ehretia obtusifolia, and their cp genomes were compared to those of related species. The length of the chloroplast genomes of E. cymosa was 156,328 bp, whereas that of E. obtusifolia was 155,961 bp. Each genome contained 114 genes, including 80 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Repeat analysis revealed that complement, forward, palindromic, and reverse repeats were present in the chloroplast genomes of both species. Simple sequence repeat analysis showed that the chloroplast genomes of E. cymosa and E. obtusifolia comprise 141 and 139 microsatellites, respectively. Phylogenetic analysis based on Bayesian and maximum likelihood analyses divided the order Boraginales into two well-supported clades. The first clade includes a single family (Boraginaceae), and the second clade includes three families (Ehretiaceae, Cordiaceae, and Heliotropiaceae). This study provides valuable genomic resources and insights into the evolutionary relationships within Boraginales. [ABSTRACT FROM AUTHOR]

Identifying the mutational processes that shape the nucleotide composition of the mitochondrial genome (mtDNA) is fundamental to better understand how these genomes evolve. Several methods have been proposed to analyze DNA sequence nucleotide composition and skewness, but most of them lack any measurement of statistical support or were not developed taking into account the specificities of mitochondrial genomes. A new methodology is presented, which is specifically developed for mtDNA to detect compositional changes or asymmetries (AT and CG skews) based on nonparametric regression models and their derivatives. The proposed method also includes the construction of confidence intervals, which are built using bootstrap techniques. This paper introduces an R package, known as seq2R, that implements the proposed methodology. Moreover, an illustration of the use of seq2R is provided using real data, specifically two publicly available complete mtDNAs: the human (Homo sapiens) sequence and a nematode (Radopholus similis) mitogenome sequence. [ABSTRACT FROM AUTHOR]

Sporotrichosis is known as a subacute or chronic infection, which is caused by thermodimorphic fungi of the genus Sporothrix. It is a cosmopolitan infection, which is more prevalent in tropical and subtropical regions and can affect both humans and other mammals. The main etiological agents causing this disease are Sporothrix schenckii, Sporothrix brasiliensis, and Sporothrix globosa, which have been recognized as members of the Sporothrix pathogenic clade. Within this clade, S. brasiliensis is considered the most virulent species and represents an important pathogen due to its distribution and prevalence in different regions of South America, such as Brazil, Argentina, Chile, and Paraguay, and Central American countries, such as Panama. In Brazil, S. brasiliensis has been of great concern due to the number of zoonotic cases that have been reported over the years. In this paper, a detailed review of the current literature on this pathogen and its different aspects will be carried out, including its genome, pathogen-host interaction, resistance mechanisms to antifungal drugs, and the caused zoonosis. Furthermore, we provide the prediction of some putative virulence factors encoded by the genome of this fungal species. [ABSTRACT FROM AUTHOR]

Orphan genes (OGs) may evolve from noncoding sequences or be derived from older coding material. Some shares of OGs are present in all sequenced genomes, participating in the biochemical and physiological pathways of many species, while many of them may be associated with the response to environmental stresses and species-specific traits or regulatory patterns. However, identifying OGs is a laborious and time-consuming task. This paper presents an automated predictor, XGBoost-A2OGs (identification of OGs for angiosperm based on XGBoost), used to identify OGs for seven angiosperm species based on hybrid features and XGBoost. The precision and accuracy of the proposed model based on fivefold cross-validation and independent testing reached 0.90 and 0.91, respectively, outperforming other classifiers in cross-species validation via other models, namely, Random Forest, AdaBoost, GBDT, and SVM. Furthermore, by analyzing and subdividing the hybrid features into five sets, it was proven that different hybrid feature sets influenced the prediction performance of OGs involving eudicot and monocot groups. Finally, testing of small-scale empirical datasets of each species separately based on optimal hybrid features revealed that the proposed model performed better for eudicot groups than for monocot groups. [ABSTRACT FROM AUTHOR]

Simple Summary: The paper describes a study to assess the stability of the genomes of bovine embryo transfer recipients following in vitro fertilization using cytogenetic tests and to analyze the effects of selected vitamins and micro- and macroelements on genome integrity. Genome stability was analyzed using the sister chromatid exchange, fragile site, and comet assays. The effects of selected micro- and macroelements and vitamins on the levels of chromosomal instabilities generated in the cows were analyzed. Genome instability can lead to a wide variety of diseases. Many endogenous and exogenous factors influence the level of damage to genetic material. Genome integrity depends on factors such as the fidelity of DNA replication, normal DNA organization in the chromosomes, and repair mechanisms. Genome stability influences fertility, embryonic development, and the maintenance of pregnancy. In the case of in vitro fertilization, it can be an important factor determining the success of the procedure. The aim of the study was to assess the stability of the genomes of recipient cows following in vitro fertilization using cytogenetic tests and to analyze the effects of selected vitamins and micro- and macroelements on genome integrity. Genome stability was analyzed using the sister chromatid exchange, fragile site, and comet assays. The material for analysis was peripheral blood from 20 Holstein-Friesian heifers that were embryo transfer recipients. The effect of selected micro- and macroelements and vitamins on the genome stability of the cows was analyzed. Folic acid was shown to significantly influence the level of damage identified using the SCE, FS, and SCGE assays, while iron affected SCE and SCGE results, and zinc affected FS. [ABSTRACT FROM AUTHOR]

In this paper, we report the complete mitochondrial genome of the northern smooth-tailed treeshrew Dendrogale murina, which was sequenced for the first time using the Illumina next-generation sequencing (NGS) technology. The total length of the mitochondrial genome is 16,844–16,850 bp and encodes 37 genes, including two ribosomal RNAs (rRNAs) 12S and 16S, 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and a D-loop in the characteristic arrangement of family Tupaiidae (Mammalia: Scandentia). The overall base composition of the complete mitochondrial DNA is A (33.5%), C (25.5%), G (13.9%), and T (27.1%). Phylogenetic analysis of Scandentia mitochondrial genomes showed a classic pattern, which was revealed previously while using individual phylogenetic markers. The result of the current study is consistent with one based on the latest morphological studies, with the basal position of Ptilocercus and Dendrogale sister to the rest of the Tupaiidae genera. The divergence time of the Dendrogale genus is estimated as Eocene–Oligocene, with the mean value of 35.8 MYA, and the Ptilocercus genus probably separated at about 46.3 MYA. We observe an increase in the age of all nodes within the Scandentia, except for a decrease in the age of separation of Ptilocercus. This result can be explained both by the addition of new mitochondrial genome data in the analysis and the usage of new calibration points from recently published data. [ABSTRACT FROM AUTHOR]

Simple Summary: The search for new, effective and low-toxicity anticancer drugs is one of the most important tasks of modern medicinal chemistry. Pentacyclic triterpenoids constitute an important class of biologically active compounds with a wide range of biological and pharmacological activities. These compounds are of particular interest due to their antitumor and antiviral properties. Triterpenoids exhibit low toxicity to animals even at high concentrations, but their relatively low potential for biological action, low water solubility and unfavorable absorption and metabolism parameters are a serious obstacle to the use of these substances in clinical practice. In the framework of the presented work, we synthesize a series of ionic compounds based on betulinic, ursolic and oleanolic acids, which could, in our view, improve the solubility of these compounds and their permeability through biological membranes. The present research paper details the synthesis of novel ionic compounds based on triterpene acids (betulinic, oleanolic and ursolic), with these acids acting both as anions and connected through a spacer with various nitrogen-containing compounds (pyridine, piperidine, morpholine, pyrrolidine, triethylamine and dimethylethanolamine) and acting as a cation. Based on the latter, a large number of ionic compounds with various counterions (BF4-, SbF6-, PF6-, CH3COO-, C6H5SO3-, m-C6H4(OH)COO- and CH3CH(OH)COO-) have been synthesized. We studied the cytotoxicity of the synthesized compounds on the example of various tumor (Jurkat, K562, U937, HL60, A2780) and conditionally normal (HEK293) cell lines. IC50 was determined, and the influence of the structure and nature of the anion and cation on the antitumor activity was specified. Intracellular signaling, apoptosis induction and effects of the most active ionic compounds on the cell cycle and mitochondria have been discussed by applying modern methods of multiparametric enzyme immunoassay and flow cytometry. [ABSTRACT FROM AUTHOR]

Simple Summary: Papillary thyroid carcinoma is still the most common endocrine tumor, most of which can be diagnosed by pathological results. However, there is still a small number of cases that are difficult to judge malignancy. In this study, we performed an integrative analysis of DNA methylation and RNA array from our cohort for potential papillary thyroid cancer-specific indicators. SERINC2, one of the differentially methylated and expressed genes, was first identified as a potential tumor-driven indicator in papillary thyroid carcinoma. We confirmed the influence of SERINC2 on proliferation and apoptosis in vitro after intervention or overexpression. Furthermore, we found tryptophan metabolism as a potential pathway targeted by SERINC2 through the investigation of data from the Cancer Dependency Map. In conclusion, our results demonstrate the whole-genome DNA methylation and gene expression profiles of papillary thyroid carcinoma, identify a new tumor-driven indicator, and provide a novel insight into the etiology of papillary thyroid cancer. Most papillary thyroid carcinomas (PTCs) can be diagnosed preoperatively by routine evaluation, such as thyroid ultrasonography and fine-needle aspiration biopsy. Nevertheless, understanding how to differentiate indolent thyroid tumors from aggressive thyroid cancers remains a challenge, which may cause overtreatment. This study aimed to identify papillary thyroid cancer-specific indicators with whole-genome DNA methylation and gene expression profiles utilizing Infinium Methylation EPIC BeadChip (850k) and RNA arrays. In this paper, we report SERINC2 as a potential tumor-driven indicator in PTC. The up-regulated expression levels of SERINC2 were verified in PTC cell lines via qPCR. Then, cell counting kit 8 (CCK-8), wound healing, and flow cytometric assays were performed to confirm the influence of SERINC2 on proliferation and apoptosis in PTC cell lines after intervention or overexpression. Moreover, the investigation of data from the Cancer Dependency Map (DepMap) provided a potential pathway targeted by SERINC2. The activation of the tryptophan metabolic pathway may reduce the dependency of SERINC2 in thyroid cancers. In conclusion, our results demonstrate the whole-genome DNA methylation and gene expression profiles of papillary thyroid carcinoma, identify SERINC2 as a potential tumor-driven biomarker, and preliminarily verify its function in PTC. [ABSTRACT FROM AUTHOR]

Camellia gigantocarpa is one of the oil-tea trees whose seeds can be used to extract high-quality vegetable oil. To date, there are no data on the mitochondrial genome of the oil-tea tree, in contrast to the tea-tree C. sinensis, which belongs to the same genus. In this paper, we present the first complete mitochondrial genomes of C. gigantocarpa obtained using PacBio Hi-Fi (high-fidelity) and Hi-C sequencing technologies to anchor the 970,410 bp genome assembly into a single sequence. A set of 44 protein-coding genes, 22 non-coding genes, 746 simple sequence repeats (SSRs), and more than 201 kb of repetitive sequences were annotated in the genome assembly. The high percentage of repetitive sequences in the mitochondrial genome of C. gigantocarpa (20.81%) and C.sinensis (22.15%, tea tree) compared to Arabidopsis thaliana (4.96%) significantly increased the mitogenome size in the genus Camellia. The comparison of the mitochondrial genomes between C. gigantocarpa and C. sinensis revealed genes exhibit high variance in gene order and low substitution rate within the genus Camellia. Information on the mitochondrial genome provides a better understanding of the structure and evolution of the genome in Camellia and may contribute to further study of the after-ripening process of oil-tea trees. [ABSTRACT FROM AUTHOR]

This paper explores the manners in which Indigenous and allied non-Indigenous researchers, medical directors, and knowledge-keepers (among others) extend the ethical precepts and social justice commitments that are inherent in community-based participatory research (CBPR) approaches to genomics. By means of a genealogical analysis of bioethical discourses, I examine the problem in which genomic science claims to offer potentially beneficial genetic screening tools to Indigenous and racialized peoples who have and continue to struggle with historical health inequity, exploitation, and exclusion by the very biomedical institutions which would be charged with the task of ethically introducing these biomedical tools. This investigation focuses on Indigenous data sovereignty (IDS) as an approach established by Indigenous communities and scientists to gain access to the benefits of genomic health which, if the field's promises are true, aims to counter the historical neglect or exploitation by biomedical researchers and institutions. I chart the role of CBPR principals as it pertains to collective efforts by both Indigenous communities and non-Indigenous allies to create the social, biomedical, and institutional conditions to improve Indigenous health equity in the context of genomic science in two specific studies: the Silent Genome initiative (British Columbia) and the Aotearoa Variome (Aotearoa/New Zealand). This investigation contributes insights to social science literatures in health equity for racialized communities, biomedical ethics, Indigenous Science and Technology Studies, and decolonial biomedical and technoscience histories. [ABSTRACT FROM AUTHOR]

The capsalid monogeneans are important pathogens that generally infect marine fishes and have a substantial impact on fish welfare in aquaculture systems worldwide. However, the current mitogenome information on capsalids has received little attention, limiting the understanding of their evolution and phylogenetic relationships with other monogeneans. This paper reports the complete mitochondrial genomes of Capsala katsuwoni and Capsala martinieri for the first time, which we obtained using a next-generation sequencing method. The mitogenomes of C. katsuwoni and C. martinieri are 13,265 and 13,984 bp in length, respectively. Both species contain the typical 12 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. The genome compositions show a moderate A+T bias (66.5% and 63.9% for C. katsuwoni and C. martinieri, respectively) and exhibit a negative AT skew but a positive GC skew in both species. One gene block rearrangement was found in C. katsuwoni in comparison with other capsalid species. Instead of being basal to the Gyrodactylidea and Dactylogyridea or being clustered with Dactylogyridea, all species of Capsalidea are grouped into a monophyletic clade. Our results clarify the gene rearrangement process and evolutionary status of Capsalidae and lay a foundation for further phylogenetic studies of monogeneans. [ABSTRACT FROM AUTHOR]

Synonymous codon bias in the viral genome affects protein translation and gene expression, suggesting that the synonymous codon mutant plays an essential role in influencing virulence and evolution. However, how the recessive mutant form contributes to virus evolvability remains elusive. In this paper, we characterize how the Senecavirus A (SVA), a picornavirus, utilizes synonymous codon mutations to influence its evolution, resulting in the adaptive evolution of the virus to adverse environments. The phylogenetic tree and Median-joining (MJ)-Network of these SVA lineages worldwide were constructed to reveal SVA three-stage genetic development clusters. Furthermore, we analyzed the codon bias of the SVA genome of selected strains and found that SVA could increase the GC content of the third base of some amino acid synonymous codons to enhance the viral RNA adaptive evolution. Our results highlight the impact of recessive mutation of virus codon bias on the evolution of the SVA and uncover a previously underappreciated evolutionary strategy for SVA. They also underline the importance of understanding the genetic evolution of SVA and how SVA adapts to the adverse effects of external stress. [ABSTRACT FROM AUTHOR]

This paper presents a deep analysis of the accessory genome of an economically promising strain of Ensifer (Sinorhizobium) meliloti, L6-AK89, obtained as a result of next-generation high-throughput sequencing (MiSeq, MinIon). Strain L6-AK89 is a StrR mutant of the native strain CIAM1775, a symbiont of Medicago lupulina that adapted to a saline and arid habitat in NW Kazakhstan. CIAM1775 is an effective inoculant of M. lupulina cv. Mira (fodder type standard), cultivated on moderately acid soils in the NW agricultural region of Russia. Strain L6-AK89 makes it possible to obtain the expected high (>150%) increases in dry mass of the same plant variety in plant tests. The L6-AK89 genome has an increased proportion of sequences related to the accessory elements relative to reference strain Rm1021, 7.4% versus 4.8%. A set of 53 nod/noe/nol/nif/fdx/fix genes and 32 genes involved in stress tolerance together with 16S rRNA and recA–atpD–glnII–gyrB–dnaJ were evaluated. The high symbiotic efficiency of L6-АК89 with hop clover is most likely due to unique features of its genome, in combination with structural differences in its nod and stress-related genes, as well as unique clusters of quorum-sensing genes and osmoprotector synthesis. [ABSTRACT FROM AUTHOR]

Identification of genomic variability in population plays an important role in the clinical diagnostics of human genetic diseases. Thanks to rapid technological development in the field of massive parallel sequencing technologies, also known as next-generation sequencing (NGS), complex genomic analyses are now easier and cheaper than ever before, which consequently leads to more effective utilization of these techniques in clinical practice. However, interpretation of data from NGS is still challenging due to several issues caused by natural variability of DNA sequences in human populations. Therefore, development and realization of projects focused on description of genetic variability of local population (often called "national or digital genome") with a NGS technique is one of the best approaches to address this problem. The next step of the process is to share such data via publicly available databases. Such databases are important for the interpretation of variants with unknown significance or (likely) pathogenic variants in rare diseases or cancer or generally for identification of pathological variants in a patient's genome. In this paper, we have compiled an overview of published results of local genome sequencing projects from United Kingdom and Europe together with future plans and perspectives for newly announced ones. [ABSTRACT FROM AUTHOR]

In this paper, we explore a generative music method that can compose atonal and tonal music in different styles. One of the main differences between regular engineering problems and artistic expressions is that goals and constraints are usually ill-defined in the latter case; in fact the rules here could or should be transgressed more regularly. For this reason, our approach does not use a pre-existing dataset to imitate or extract rules from. Instead, it uses formal grammars as a representation method than can retain just the basic features, common to any form of music (e.g., the appearance of rhythmic patterns, the evolution of tone or dynamics during the composition, etc.). Exploring different musical spaces is the responsibility of a program interface that translates musical specifications into the fitness function of a genetic algorithm. This function guides the evolution of those basic features enabling the emergence of novel content. In this study, we then assess the outcome of a particular music specification (guitar ballad) in a controlled real-world setup. As a result, the generated music can be considered similar to human-composed music from a perceptual perspective. This endorses our approach to tackle arts algorithmically, as it is able to produce novel content that complies with human expectations. [ABSTRACT FROM AUTHOR]

The fungal genus Fonsecaea contains etiological agents of human chromoblastomycosis, a (sub)tropical, (sub)cutaneous implantation disease caused by plant contact. The invasive potential differs significantly between species. Infections by Fonsecaea monophora are believed to originate from the environment and the species has been reported as one of the main causative agents of the disease, but also of cases of primary brain infection. The epidemiology of the disease has not been fully elucidated and questions related to its infection route and virulence are still to be clarified. The environmental species Fonsecaea erecta was isolated from organic material and living plants in endemic areas for chromoblastomycosis in Brazil. The present paper describes Agrobacterium tumefaciens-mediated transformation (AMT) of the environmental species F. erecta and the pathogenic species F. monophora. We propose the use of Agrobacterium transformation for future gene function studies related to Fonsecaea virulence and pathogenicity. We evaluated the co-cultivation ratios 1:1, 10:1 and 100:1 (Agrobacterium:conidia) at 28 °C during 72 h. pAD1625 and pCAMDsRed plasmids were inserted into both species. Confirmation of transformation was realized by hph gene amplification and Southern blot determined the amount of foreign DNA integrated into the genome. In order to evaluate a potential link between environmental and clinical strains, we obtained red fluorescent transformants after pCAMDsRed insertion. We observed by confocal fluorescence microscopy that both F. monophora and F. erecta were able to colonize the palm Bactris gasipaes, penetrating the epidermis. These results contribute to understanding the ability of Fonsecaea species to adapt to different environmental and host conditions. [ABSTRACT FROM AUTHOR]

Protein complexes play significant roles in cellular processes. Identifying protein complexes from protein-protein interaction (PPI) networks is an effective strategy to understand biological processes and cellular functions. A number of methods have recently been proposed to detect protein complexes. However, most of methods predict protein complexes from static PPI networks, and usually overlook the inherent dynamics and topological properties of protein complexes. In this paper, we proposed a novel method, called NABCAM (Neighbor Affinity-Based Core-Attachment Method), to identify protein complexes from dynamic PPI networks. Firstly, the centrality score of every protein is calculated. The proteins with the highest centrality scores are regarded as the seed proteins. Secondly, the seed proteins are expanded to complex cores by calculating the similarity values between the seed proteins and their neighboring proteins. Thirdly, the attachments are appended to their corresponding protein complex cores by comparing the affinity among neighbors inside the core, against that outside the core. Finally, filtering processes are carried out to obtain the final clustering result. The result in the DIP database shows that the NABCAM algorithm can predict protein complexes effectively in comparison with other state-of-the-art methods. Moreover, many protein complexes predicted by our method are biologically significant. [ABSTRACT FROM AUTHOR]

Chlorellacean members are common in aquatic or subaerial habitats, and many of them have significant economic value. Taxonomic reports and organelle genome data for the Nannochloris clade, an important subgroup within this family, are limited, hindering the understanding and exploitation of this clade. In this study, a fusiform-celled strain, FACHB-3607, was isolated from a pond in China. Through examination of morphological characteristics and phylogenetic analyses of rbcL, 18S rDNA, and ITS, it was identified as a new species within the Nannochloris clade, named Koliella bifissiva sp. nov. In addition, this study provided a first insight into the organellar genomes of the genus Koliella. The K. bifissiva chloroplast had a 99.8 kb genome, and the mitochondrion had a 40.8 kb genome, which are moderate sizes within the Nannochloris clade. Phylogenomic analysis showed that K. bifissiva is most closely related to Nannochloris sp. "desiccata", followed by Marvania. In contrast, Picochlorum was the most distantly related species. The organelle genomes of the Nannochloris clade display dynamic evolution, reflected in variations in genome size, gene content and order, and selection pressure. This research enhances our knowledge of species diversity and evolutionary history in the Nannochloris clade. [ABSTRACT FROM AUTHOR]

Human adenovirus (HAdV) F40/41 is an important pathogen in pediatric acute gastroenteritis cases. However, the diversity of study designs and diagnostic methods often leads to misinterpretations of their impact. Our study explored the genetic diversity of HAdV-F40/41 in Brazil using a specific qPCR assay for HAdV species F, combined with a phylogenetic analysis of the partial hexon and fiber genes. Our results demonstrated that HAdV-F41 strains predominated and exhibited higher diversity than HAdV-F40 strains. Based on the hexon gene, Brazilian HAdV-F41 strains were grouped into two genome type clusters (GTC), further divided into subclusters, with most strains clusteringto GTC2. The partial shaft region of the fiber gene exhibited higher conservation among HAdV-F41. The specific qPCR assay for HAdV species F identified HAdV-F in an additional 31.5% (34/108) of previously uncharacterized HAdV-positive samples detected using a non-specific HAdV qPCR assay. Both assays strongly correlated in detecting HAdV-F, and the specific qPCR assay for enteric types can enhance HAdV surveillance, especially when sequencing is not possible. Our study provides novel insights regarding the genetic diversity of HAdV-F species in Brazil. [ABSTRACT FROM AUTHOR]

Dendrocalamus brandisii (Munro) Kurz is a sympodial bamboo species with a wide distribution in tropical and subtropical regions. Due to its remarkable regenerative ability and exceptional flavor, this species plays a pivotal role in bolstering the economies of numerous nations across these regions. We recently published a high-quality genome of this species. To date, no study results have identified the optimal reference genes for quantitative real-time polymerase chain reaction (qRT-PCR) normalization in Dendrocalamus brandisii. qRT-PCR offers a highly accurate and effective approach to analyzing gene expression. However, the precision of the resulting quantitative data hinges on the correct choice of reference genes. Twenty-one potential reference genes were identified from the D. brandisii transcriptomes. Their expression in 23 samples, including 8 different tissue organs and 15 samples of D. brandisii under various treatment conditions, were evaluated through qRT-PCR. Subsequently, four software programs—Delta CT, geNorm, NormFinder, and RefFinder—were employed to compare their expression stability. The results revealed that the selection of optimal reference genes varied based on the particular organ and condition being examined. EF-1-α-2 consistently exhibits the most stable expression across diverse tissues, while ACTIN-1, TUBULIN-1, and EF-1-α-2 were the most consistent reference genes in roots, culms, and leaves under various treatments, respectively. In this study, we identified and characterized appropriate internal genes utilized for calibrating qRT-PCR analyses of D. brandisii across different tissue organs and under various treatments. This research will provide key insights for advancing the study of gene functionality and molecular biology in D. brandisii and related species [ABSTRACT FROM AUTHOR]

Suillus is one of the most important genera of ectomycorrhizal fungi. As a model for studying host specificity, its molecular fragments and nuclear genome have been analyzed. However, its mitochondrial genome has not yet been reported. In this study, we assembled five mitogenomes of Suillus and analyzed and compared their basic characteristics. Owing to the large number of introns as well as intergenic regions, the mitogenomic lengths of species of Suillus were greater than those of other species of Boletales. We identified two main patterns of gene order arrangement in the members of the order Boletales. The Ka/Ks values of 15 protein-coding genes were <1 for the mitochondrial genes of 39 Boletales species, indicating their conserved evolution. Phylogenetic trees, reconstructed using the mitogenomes, indicated that the genus Suillus was monophyletic. Phylogenetic results based on the internal transcribed spacer region and mitogenome were used to confirm the distribution of Suillus placidus in China. The results showed that the mitogenome was superior in distinguishing species compared with a single molecular fragment. This is the first study to investigate the mitogenome of Suillus, enriching the mitogenome information and providing basic data for the phylogeny, resource conservation, and genetic diversity of this genus. [ABSTRACT FROM AUTHOR]

Simple Summary: Oral lichen planus (OLP) is a chronic inflammatory disease of autoimmune nature and unknown etiology which affects approximately 1% of the world's population. The most important feature of OLP is its behavior as an oral potentially malignant disorder (OPMD). The current study is the first systematic review and meta-analysis designed to evaluate the degree of existing scientific evidence on the cancer hallmarks proposed in 2011 by Hanahan and Weinberg, defined as the characteristics that cells must fulfill in order to be considered neoplastic cells in all types of tumors that affect humans. This systematic review and meta-analysis includes 110 studies which recruited 7064 cases of OLP, in which the expression of 104 molecular biomarkers were analyzed through an immunohistochemical technique. The earliest oncogenic molecular mechanisms that could justify the malignant transformation of this disease are analyzed in depth and critically discussed on the basis of evidence. We aimed to qualitatively and quantitatively analyze, through a systematic review and meta-analysis, the current evidence on the differential expression of the hallmarks of cancer in oral lichen planus (OLP) samples, in order to know the earliest molecular mechanisms that could be involved in the malignant transformation of this oral potentially malignant disorder. We searched MEDLINE/PubMed, Embase, Web of Science, and Scopus for studies published before November 2023. We evaluated the methodological quality of studies and carried out meta-analyses to fulfill our objectives. Inclusion criteria were met by 110 primary-level studies, with 7065 OLP samples, in which the expression of 104 biomarkers were analyzed through immunohistochemistry. Most OLP samples showed sustained cell proliferation signaling (65.48%, 95%CI = 51.87–78.02), anti-apoptotic pathways (55.93%, 95%CI = 35.99–75.0), genome instability (48.44%, 95%CI = 13.54–84.19), and tumor-promoting inflammation events (83.10%, 95%CI = 73.93–90.74). Concurrently, OLP samples also harbored tumor growth suppressor mechanisms (64.00%, 95%CI = 53.27–74.12). In conclusion, current evidence indicates that molecular mechanisms promoting hyperproliferative signaling, an antiapoptotic state with genomic instability, and an escape of epithelial cells from immune destruction, are developed in LP-affected oral mucosa. It is plausible that these events are due to the actions exerted by the chronic inflammatory infiltrate. Malignant transformation appears to be prevented by tumor suppressor genes, which showed consistent upregulation in OLP samples. [ABSTRACT FROM AUTHOR]

The utility of the mitochondrial genomes (mitogenomes) in analyzing the evolutionary history of animals has been proven. Five deep-sea corals (Bathypathes sp.1, Bathypathes sp.2, Schizopathidae 1, Trissopathes sp., and Leiopathes sp.) were collected in the South China Sea (SCS). Initially, the structures and collinearity of the five deep-sea coral mitogenomes were analyzed. The gene arrangements in the five deep-sea coral mitogenomes were similar to those in the order Antipatharia, which evidenced their conservation throughout evolutionary history. Additionally, to elucidate the slow evolutionary rates in Hexacorallia mitogenomes, we conducted comprehensive analyses, including examining phylogenetic relationships, performing average nucleotide identity (ANI) analysis, and assessing GC-skew dissimilarity combining five deep-sea coral mitogenomes and 522 reference Hexacorallia mitogenomes. Phylogenetic analysis using 13 conserved proteins revealed that species clustered together at the order level, and they exhibited interspersed distributions at the family level. The ANI results revealed that species had significant similarities (identity > 85%) within the same order, while species from different orders showed notable differences (identity < 80%). The investigation of the Hexacorallia mitogenomes also highlighted that the GC-skew dissimilarity was highly significant at the order level, but not as pronounced at the family level. These results might be attributed to the slow evolution rate of Hexacorallia mitogenomes and provide evidence of mitogenomic diversity. Furthermore, divergence time analysis revealed older divergence times assessed via mitogenomes compared with nuclear data, shedding light on significant evolutionary events shaping distinct orders within Hexacorallia corals. Those findings provide new insights into understanding the slow evolutionary rates of deep-sea corals in all lineages of Hexacorallia using their mitogenomes. [ABSTRACT FROM AUTHOR]

Background/Objectives: Rapid genome-wide sequencing (rGWS) continues to transform the care provided to infants with genetic conditions in neonatal intensive care units (NICUs). Previous research has demonstrated that rGWS has immense benefits on patient care; however, little is known about non-genetic healthcare providers' (HCPs) experiences and perspectives of working with rGWS and supporting families through the rGWS testing process in Canadian NICU facilities. To address this gap, we surveyed and conducted semi-structured interviews with non-genetic HCPs of diverse professions from NICUs in British Columbia. Methods: An interpretive description approach was used to analyze interview transcripts to identify patterns and variations in non-genetic HCPs' experiences and perceptions with rGWS. Results: Participants had varying degrees of exposure to rGWS and levels of comfort with the testing process. Numerous barriers affecting the implementation of rGWS were identified, including low levels of comprehension of rGWS, longer turn-around times than expected, and having to apply for provincial government approval to access testing. Participants desired more education on rGWS, clear guidelines on the use of rGWS in NICUs, and resources for non-genetic HCPs and parents to support implementation. Conclusions: The results from this study can inform the development of workflows and educational resources on the use of rGWS in NICUs, helping to ensure that the NICU team is supported to optimize rGWS implementation. [ABSTRACT FROM AUTHOR]

The efficient preparation of single-stranded DNA (ssDNA) rings, as a macromolecular construction approach with topological features, has aroused much interest due to the ssDNA rings' numerous applications in biotechnology and DNA nanotechnology. However, an extra splint is essential for enzymatic circularization, and by-products of multimers are usually present at high concentrations. Here, we proposed a simple and robust strategy using permuted precursor (linear ssDNA) for circularization by forming an intramolecular dynamic nick using a part of the linear ssDNA substrate itself as the template. After the simulation of the secondary structure for desired circular ssDNA, the linear ssDNA substrate is designed to have its ends on the duplex part (≥5 bp). By using this permuted substrate with 5′-phosphate, the splint-free circularization is simply carried out by T4 DNA ligase. Very interestingly, formation of only several base pairs (2–4) flanking the nick is enough for ligation, although they form only instantaneously under ligation conditions. More significantly, the 5-bp intramolecular duplex part commonly exists in genomes or functional DNA, demonstrating the high generality of our approach. Our findings are also helpful for understanding the mechanism of enzymatic DNA ligation from the viewpoint of substrate binding. [ABSTRACT FROM AUTHOR]

Simple Summary: The present study aimed to characterize the complete mitochondrial genome of Streptopelia decaocto (Frivaldszky, 1838) and investigated the evolutionary relationships among species within the Columbidae family. The mtDNA full sequence length of S. decaocto was 17,160 bp. The mitogenome of S. decaocto comprised 13 PCGs, 22 tRNA genes, 2 rRNA genes, non-coding regions, and a control region. Analysis of the entire mtDNA of S. decaocto revealed consistently positive AT-skew values, except for nad3, nad6, and the D-loop. Conversely the GC-skew values were consistently negative, except for nad6. These findings suggest that S. decaocto belongs to the Columbinae subfamily. In this research, the mitochondrial genome of the Streptopelia decaocto was sequenced and examined for the first time to enhance the comprehension of the phylogenetic relationships within the Columbidae. The complete mitochondrial genome of Streptopelia decaocto (17,160 bp) was structurally similar to the recognized members of the Columbidae family, but with minor differences in gene size and arrangement. The structural AT content was 54.12%. Additionally, 150 mitochondrial datasets, representing valid species, were amassed in this investigation. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees and evolutionary time relationships of species were reconstructed based on cytb gene sequences. The findings from the phylogenetic evaluations suggest that the S. decaocto was classified under the Columbinae subfamily, diverging from the Miocene approximately 8.1 million years ago, indicating intricate evolutionary connections with its close relatives, implying a history of species divergence and geographic isolation. The diversification of the Columbidae commenced during the Late Oligocene and extended into the Miocene. This exploration offers crucial molecular data for the S. decaocto, facilitating the systematic taxonomic examination of the Columbidae and Columbiformes, and establishing a scientific foundation for species preservation and genetic resource management. [ABSTRACT FROM AUTHOR]

Polyploid wheats include a group of tetraploids known as Timopheevii (AuAuGG), which are represented by two subspecies: Triticum timopheevii ssp. timopheevii (cultivated) and Triticum timopheevii ssp. araraticum (wild). The combined use of electrophoretic (SDS-PAGE) and chromatographic (RP-HPLC) techniques carried out on high-molecular-weight glutenin subunits (HMW-GSs) permitted the association of different x- and y-type subunits to the A and G genomes and the assessment of allelic variation present at corresponding loci. The results also revealed that in both subspecies, accessions are present that possess expressed y-type subunits at the Glu-A1 locus. Genes corresponding to these subunits were amplified and amplicons corresponding to x- and y-type genes associated with the A genome were detected in all accessions, including those without expressed x- and y-type subunits. The comparison with genes of polyploid wheats confirmed the structural characteristics of typical y-type genes, with the presence of seven cysteine residues and with hexapeptide and nonapeptide repeat motifs. The identification of wild and cultivated T. timopheevii with both x- and y-type glutenin subunits at the Glu-A1 and Glu-G1 loci represents a useful source for the modification of the allelic composition of HMW-GSs in cultivated wheats with the ultimate objective of improving technological properties. [ABSTRACT FROM AUTHOR]

The barbel chub (Squaliobarbus curriculus), the only species in the genus, is widely distributed in freshwater lakes and rivers at different latitudes in East Asia, with fishery and biodiversity importance, and is an emerging commercially important fish in China. However, the resource of this species has dramatically declined due to anthropogenic activities such as over-exploitation, as well as water pollution. Genomic resources for S. curriculus are useful for the management and sustainable utilization of this important fish species, and also for a better understanding of its genetic variation in the region. Here, we report the chromosome-level assembly of the S. curriculus genome obtained from the integration of PacBio long sequencing and Hi-C technology. A total of 155.34 Gb high-quality PacBio sequences were generated, and the preliminary genome assembly was 894.95 Mb in size with a contig N50 being 20.34 Mb. By using Hi-C data, 99.42% of the assembled sequences were anchored to 24 pseudochromosomes, with chromosome lengths ranging from 27.22 to 58.75 Mb. A total of 25,779 protein-coding genes were predicted, 94.70% of which were functionally annotated. Moreover, S. curriculus shows resistance to grass carp haemorrhagic disease (GCHD) caused by grass carp reovirus (GCRV), which seriously hinders the status and future perspectives of commercial grass carp production. Phylogenetic analysis indicated that S. curriculus diverged with grass carp (Ctenopharyngodon idellus) approximately 20.80 million years ago. Annotations of the expanded gene families were found to be largely enriched in immune-related KEGG pathway categories. Moreover, a total of 18 Toll-like receptor (TLR) genes were identified from the whole genome of S. curriculus. The high-quality genome assembled in this study will provide a valuable resource for accelerating ecological, evolutionary, and genetic research on S. curriculus. [ABSTRACT FROM AUTHOR]

Genomic medicine is moving from research to the clinic. There is a lack of evidence about the impact of genomic medicine interventions on health outcomes. This is due in part to a lack of standardized outcome measures that can be used across different programs to evaluate the impact of interventions targeted to specific genetic conditions. The eMERGE Outcomes working group (OWG) developed measures to collect information on outcomes following the return of genomic results to participants for several genetic disorders. These outcomes were compared to outcome intervention pairs for genetic disorders developed independently by the ClinGen Actionability working group (AWG). In general, there was concordance between the defined outcomes between the two groups. The ClinGen outcomes tended to be from a higher level and the AWG scored outcomes represented a subset of outcomes referenced in the accompanying AWG evidence review. eMERGE OWG outcomes were more detailed and discrete, facilitating a collection of relevant information from the health records. This paper demonstrates that common outcomes for genomic medicine interventions can be identified. Further work is needed to standardize outcomes across genomic medicine implementation projects and to make these publicly available to enhance dissemination and assist in making precision public health a reality. [ABSTRACT FROM AUTHOR]

Comparison of metabolic pathways provides a systematic way for understanding the evolutionary and phylogenetic relationships in systems biology. Although a number of phylogenetic methods have been developed, few efforts have been made to provide a unified phylogenetic framework that sufficiently reflects the metabolic features of organisms. In this paper, we propose a phylogenetic framework that characterizes the metabolic features of organisms by aligning multiple metabolic pathways using functional module mapping. Our method transforms the alignment of multiple metabolic pathways into constructing the union graph of pathways, builds mappings between functional modules of pathways in the union graph, and infers phylogenetic relationships among organisms based on module mappings. Experimental results show that the use of functional module mapping enables us to correctly categorize organisms into main categories with specific metabolic characteristics. Traditional genome-based phylogenetic methods can reconstruct phylogenetic relationships, whereas our method can offer in-depth metabolic analysis for phylogenetic reconstruction, which can add insights into traditional phyletic reconstruction. The results also demonstrate that our phylogenetic trees are closer to the classic classifications in comparison to existing classification methods using metabolic pathway data. [ABSTRACT FROM AUTHOR]

Formetagenomics datasets, datasets of complex polyploid genomes, and other high-variation genomics datasets, there are difficulties with the analysis, error detection and variant calling, stemming from the challenges of discerning sequencing errors from biological variation. Confirming base candidates with high frequency of occurrence is no longer a reliable measure because of the natural variation and the presence of rare bases. The paper discusses an approach to the application of machine learning models to classify bases into erroneous and rare variations after preselecting potential error candidates with a weighted frequency measure, which aims to focus on unexpected variations by using the inter-sequence pairwise similarity. Different similarity measures are used to account for different types of datasets. Four machine learning models are implemented and tested. [ABSTRACT FROM AUTHOR]

The ability to clone large DNA fragments from genomes is valuable for both basic and applied research, such as the construction of synthetic genomes, and the expression of biosynthetic gene clusters (BGCs) for natural product discovery. Here, we report a fast and efficient platform for the direct capture of genome DNAs, by combining CRISPR and Gibson assembly. We demonstrate this method with the ability of cloning large DNA fragments ranging from 30 to 77 kb from various host genomes, achieving a near 100% cloning fidelity for DNA fragments below 50 kb. We next demonstrate this method by the cloning of a 40 kb fragment from Streptomyces ceruleus A3(2), which is rich in BGCs for natural products; and used this method cloning the 40 kb fengycin synthetic gene cluster from B. subtilis 168, encoding for a class of peptides with bioactivity. This method provides efficient and simple opportunities for assembling large DNA constructs from distant sources. [ABSTRACT FROM AUTHOR]

Simple Summary: An urgent demand exists to identify inherited genetic risk variants for prostate cancer (PrCa), particularly in DNA damage repair genes targetable with precision medicine-based strategies. Though the most heritable common cancer, discovery of rare germline PrCa risk variants is hampered by their low frequency, even in sizeable population datasets. Through utilising two large, independent, familial PrCa resources and their likely enrichment of rare causative variants, we provide robust evidence for several novel risk variants in DNA damage repair genes. Rare, inherited variants in DNA damage repair (DDR) genes have a recognised role in prostate cancer (PrCa) susceptibility. In addition, these genes are therapeutically targetable. While rare variants are informing clinical management in other common cancers, defining the rare disease-associated variants in PrCa has been challenging. Here, whole-genome and -exome sequencing data from two independent, high-risk Australian and North American familial PrCa datasets were interrogated for novel DDR risk variants. Rare DDR gene variants (predicted to be damaging and present in two or more family members) were identified and subsequently genotyped in 1963 individuals (700 familial and 459 sporadic PrCa cases, 482 unaffected relatives, and 322 screened controls), and association analyses accounting for relatedness (MQLS) undertaken. In the combined datasets, rare ERCC3 (rs145201970, p = 2.57 × 10−4) and BRIP1 (rs4988345, p = 0.025) variants were significantly associated with PrCa risk. A PARP2 (rs200603922, p = 0.028) variant in the Australian dataset and a MUTYH (rs36053993, p = 0.031) variant in the North American dataset were also associated with risk. Evaluation of clinicopathological characteristics provided no evidence for a younger age or higher-grade disease at diagnosis in variant carriers, which should be taken into consideration when determining genetic screening eligibility criteria for targeted, gene-based treatments in the future. This study adds valuable knowledge to our understanding of PrCa-associated DDR genes, which will underpin effective clinical screening and treatment strategies. [ABSTRACT FROM AUTHOR]

Biological invasions have been identified as the fifth cause of biodiversity loss, and their subsequent dispersal represents a major ecological challenge. The aquatic invasive species Ludwigia grandiflora subsp. hexapetala (Lgh) and Ludwigia peploides subsp. montevidensis (Lpm) are largely distributed in aquatic environments in North America and in Europe. However, they also present worrying terrestrial forms that are able to colonize wet meadows. To comprehend the mechanisms of the terrestrial adaptation of Lgh and Lpm, it is necessary to develop their genomic resources, which are currently poorly documented. We performed de novo assembly of the mitogenomes of Lgh and Lpm through hybrid assemblies, combining short reads (SR) and/or long reads (LR) before annotating both mitogenomes. We successfully assembled the mitogenomes of Lgh and Lpm into two circular molecules each, resulting in a combined total length of 711,578 bp and 722,518 bp, respectively. Notably, both the Lgh and Lpm molecules contained plastome-origin sequences, comprising 7.8% of the mitochondrial genome length. Additionally, we identified recombinations that were mediated by large repeats, suggesting the presence of multiple alternative conformations. In conclusion, our study presents the first high-quality mitogenomes of Lpm and Lgh, which are the only ones in the Myrtales order found as two circular molecules. [ABSTRACT FROM AUTHOR]

This study is the first report to characterize the Rhodus uyekii genome and study the development of microsatellite markers and their markers applied to the genetic structure of the wild population. Genome assembly was based on PacBio HiFi and Illumina HiSeq paired-end sequencing, resulting in a draft genome assembly of R. uyekii. The draft genome was assembled into 2652 contigs. The integrity assessment of the assemblies indicates that the quality of the draft assemblies is high, with 3259 complete BUSCOs (97.2%) in the database of Verbrata. A total of 31,166 predicted protein-coding genes were annotated in the protein database. The phylogenetic tree showed that R. uyekii is a close but distinct relative of Onychostoma macrolepis. Among the 10 fish genomes, there were significant gene family expansions (8–2387) and contractions (16–2886). The average number of alleles amplified by the 21 polymorphic markers ranged from 6 to 23, and the average PIC value was 0.753, which will be useful for evolutionary and genetic analysis. Using population genetic analysis, we analyzed genetic diversity and the genetic structures of 120 individuals from 6 populations. The average number of alleles per population ranged from 7.6 to 9.9, observed heterozygosity ranged from 0.496 to 0.642, and expected heterozygosity ranged from 0.587 to 0.783. Discriminant analysis of principal components According to the analysis method, the population was divided into three populations (BS vs. DC vs. GG, GC, MS, DC). In conclusion, our study provides a useful resource for comparative genomics, phylogeny, and future population studies of R. uyekii. [ABSTRACT FROM AUTHOR]

Wastewater-based epidemiology (WBE) is useful for detecting pathogen prevalence and may serve to effectively monitor diseases across broad scales. WBE has been used throughout the COVID-19 pandemic to track disease burden through quantifying SARS-CoV-2 RNA present in wastewater. Aside from case load estimation, WBE is being used to assay viral genomic diversity and emerging potential SARS-CoV-2 variants. Here, we present a study in which we sequenced RNA extracted from sewage influent obtained from eight wastewater treatment plants representing 16 million people in Southern California from April 2020 to August 2021. We sequenced SARS-CoV-2 with two methods: Illumina Respiratory Virus-Enriched metatranscriptomic sequencing (N = 269), and QIAseq SARS-CoV-2-tiled amplicon sequencing (N = 95). We classified SARS-CoV-2 reads into lineages and sublineages that approximated named variants and identified single nucleotide variants (SNVs), of which many are putatively novel SNVs and SNVs of unknown potential function and prevalence. Through our retrospective study, we also show that several SARS-CoV-2 sublineages were detected in wastewater before clinical detection, which may assist in the prediction of future variants of concern. Lastly, we show that sublineage diversity was similar across Southern California and that diversity changed over time, indicating that WBE is effective across megaregions. As the COVID-19 pandemic moves to new phases, and SARS-CoV-2 variants emerge, monitoring wastewater is important to understand local- and population-level dynamics of the virus. These results will aid in our ability to monitor the evolutionary potential of SARS-CoV-2 and help understand circulating SNVs to further combat COVID-19. [ABSTRACT FROM AUTHOR]

Plant ploidy manipulation is often required for breeding purposes. However, there is no comprehensive review covering genome doubling in vegetable crops despite the abundance of data for a large number of vegetable species. Similar to other species, genome doubling is required in vegetable crops to obtain doubled haploids (DHs). It is also utilized for the production of polyploids to overcome interspecific hybrid sterility and improve agricultural traits. Spontaneous haploid genome duplication (SHGD) occurs in many Apiaceae, Brassicaceae, Cucurbitaceae, and Solanaceae crops, allowing for the laborious treatment with antimitotic agents to be bypassed. SHGD mechanisms are not fully understood, but existing data suggest that SHGD can occur via nuclear fusion, endoreduplication, or other mechanisms during microspore or ovule early embryogenic development. Other studies show that SHGD can occur at later developmental stages during extended plant growth in vitro or ex vitro, possibly due to the presence of phytohormones in the medium and/or diploid cell competitive advantage. For unresponsive accessions and species with rare SHGD, such as onion (Allium cepa L.) and beet cultivars (Beta vulgaris subsp. vulgaris L.), antimitotic agent treatment has to be applied. Antimitotic agent application efficiency depends on the treatment conditions, especially the agent concentration and exposure time. Also, plant developmental stage is critical for agent accessibility and plant survival. The existing methods can be used to further improve genome doubling methodology for major vegetable crops and other species. [ABSTRACT FROM AUTHOR]