Chromosomal Sequences Research Articles

Chromosome-scale haplotype-phased genome assemblies of the male and female lines of wild asparagus (Asparagus kiusianus), a dioecious plant species.

Asparagus kiusianus is a disease-resistant dioecious plant species and a wild relative of garden asparagus (Asparagus officinalis). To enhance A. kiusianus genomic resources, advance plant science, and facilitate asparagus breeding, we determined the genome sequences of the male and female lines of A. kiusianus. Genome sequence reads obtained with a linked-read technology were assembled into four haplotype-phased contig sequences (∼1.6 Gb each) for the male and female lines. The contig sequences were aligned onto the chromosome sequences of garden asparagus to construct pseudomolecule sequences. Approximately 55,000 potential protein-encoding genes were predicted in each genome assembly, and ∼70% of the genome sequence was annotated as repetitive. Comparative analysis of the genomes of the two species revealed structural and sequence variants between the two species as well as between the male and female lines of each species. Genes with high sequence similarity with the male-specific sex determinant gene in A. officinalis, MSE1/AoMYB35/AspTDF1, were presented in the genomes of the male line but absent from the female genome assemblies. Overall, the genome sequence assemblies, gene sequences, and structural and sequence variants determined in this study will reveal the genetic mechanisms underlying sexual differentiation in plants, and will accelerate disease-resistance breeding in garden asparagus.

Whole-Genome Sequencing and Potassium-Solubilizing Mechanism of Bacillus aryabhattai SK1-7.

To analyze the whole genome of Bacillus aryabhattai strain SK1-7 and explore its potassium solubilization characteristics and mechanism, thus providing a theoretical basis for analyzing the utilization and improvement of insoluble potassium resources in soil. Genome information for Bacillus aryabhattai SK1-7 was obtained by using Illumina NovaSeq second-generation sequencing and GridION Nanopore ONT third-generation sequencing technology. The contents of organic acids and polysaccharides in fermentation broth of Bacillus aryabhattai SK1-7 were determined by high-performance liquid chromatography and the anthrone sulfuric acid method, and the expression levels of the potassium solubilization-related genes ackA, epsB, gltA, mdh and ppc were compared by real-time fluorescence quantitative PCR under different potassium source culture conditions. The whole genome of the strain consisted of a complete chromosome sequence and four plasmid sequences. The sequence sizes of the chromosomes and plasmids P1, P2, P3 and P4 were 5,188,391 bp, 136,204 bp, 124,862 bp, 67,200 bp and 12,374 bp, respectively. The GC contents were 38.2, 34.4, 33.6, 32.8, and 33.7%. Strain SK1-7 mainly secreted malic, formic, acetic and citric acids under culture with an insoluble potassium source. The polysaccharide content produced with an insoluble potassium source was higher than that with a soluble potassium source. The expression levels of five potassium solubilization-related genes with the insoluble potassium source were higher than those with the soluble potassium source.

Super-resolution Chromatin Visualization Using a CombinedMethod of Fluorescence In Situ Hybridization and Structured Illumination Microscopy in Solanum lycopersicum.

Chromatin organization influences gene and transposon expression, and regulates various cellular processes. Higher order chromatin structure has been widely studied using genomic approaches and microscopy imageanalyses. Chromosome conformation capture and sequencing the junction of DNA fragments enables the study of both chromatin interaction and chromosome folding. However, certain cell types are embedded in other cell types which complicate the process of studying them using high-throughput genomic approaches. To overcome this limitation, high-resolution microscopy techniques are now available to investigate chromatin organization in single cells. In this chapter, we provide a detailed protocol to prepare chromosome spreading from tomato nuclei, to label genomic loci by fluorescence in situ hybridization, and to visualize these locations at high resolution with Structured Illumination microscopy.

Huntington's Disease Gene Hunters: An Expanding Tale.

Huntington's Disease Gene Hunters: An Expanding Tale.

Constitutional chromothripsis of the APC locus as a cause of genetic predisposition to colon cancer

PurposeApproximately 20% of patients with clinical familial adenomatous polyposis (FAP) remain unsolved after molecular genetic analysis of the APC and other polyposis genes, suggesting additional pathomechanisms.MethodsWe applied multidimensional genomic analysis...

Gain of Chromosome 6p Correlates with Severe Anaplasia, Cellular Hyperchromasia, and Extraocular Spread of Retinoblastoma.

PurposeGain of chromosome 6p has been associated with poor ocular survival in retinoblastoma and histopathologic grading of anaplasia with increased risk of metastatic spread and death. This study examined the correlation between these factors and other chromosomal abnormalities as well as results of whole genome sequencing, digital morphometry, and progression-free survival.DesignRetrospective cohort study from 2 United States tertiary referral centers.ParticipantsForty-two children who had undergone enucleation for retinoblastoma from January 2000 through December 2017.MethodsStatus of chromosomes 6p, 1q, 9q, and 16q was evaluated with fluorescence in situ hybridization, the degree of anaplasia and presence of histologic high-risk features were assessed by ocular pathologists, digital morphometry was performed on scanned tumor slides, and whole genome sequencing was performed on a subset of tumors. Progression-free survival was defined as absence of distant or local metastases or tumor growth beyond the cut end of the optic nerve.Main Outcome MeasuresCorrelation between each of chromosomal abnormalities, anaplasia, morphometry and sequencing results, and survival.ResultsForty-one of 42 included patients underwent primary enucleation and 1 was treated first with intra-arterial chemotherapy. Seven tumors showed mild anaplasia, 19 showed moderate anaplasia, and 16 showed severe anaplasia. All tumors had gain of 1q, 18 tumors had gain of 6p, 6 tumors had gain of 9q, and 36 tumors had loss of 16q. Tumors with severe anaplasia were significantly more likely to harbor 6p gains than tumors with nonsevere anaplasia (P < 0.001). Further, the hematoxylin staining intensity was significantly greater and that of eosin staining significantly lower in tumors with severe anaplasia (P < 0.05). Neither severe anaplasia (P = 0.10) nor gain of 6p (P = 0.21) correlated with histologic high-risk features, and severe anaplasia did not correlate to RB1, CREBBP, NSD1, or BCOR mutations in a subset of 14 tumors (P > 0.5). Patients with gain of 6p showed significantly shorter progression-free survival (P = 0.03, Wilcoxon test).ConclusionsGain of chromosome 6p emerges as a strong prognostic biomarker in retinoblastoma because it correlates with severe anaplasia, quantifiable changes in tumor cell staining characteristics, and extraocular spread.

A high-throughput multiplexing and selection strategy to complete bacterial genomes.

BackgroundBacterial whole-genome sequencing based on short-read technologies often results in a draft assembly formed by contiguous sequences. The introduction of long-read sequencing technologies permits those contiguous sequences to be unambiguously bridged into complete genomes. However, the elevated costs associated with long-read sequencing frequently limit the number of bacterial isolates that can be long-read sequenced. Here we evaluated the recently released 96 barcoding kit from Oxford Nanopore Technologies (ONT) to generate complete genomes on a high-throughput basis. In addition, we propose an isolate selection strategy that optimizes a representative selection of isolates for long-read sequencing considering as input large-scale bacterial collections.ResultsDespite an uneven distribution of long reads per barcode, near-complete chromosomal sequences (assembly contiguity = 0.89) were generated for 96 Escherichia coli isolates with associated short-read sequencing data. The assembly contiguity of the plasmid replicons was even higher (0.98), which indicated the suitability of the multiplexing strategy for studies focused on resolving plasmid sequences. We benchmarked hybrid and ONT-only assemblies and showed that the combination of ONT sequencing data with short-read sequencing data is still highly desirable (i) to perform an unbiased selection of isolates for long-read sequencing, (ii) to achieve an optimal genome accuracy and completeness, and (iii) to include small plasmids underrepresented in the ONT library.ConclusionsThe proposed long-read isolate selection ensures the completion of bacterial genomes that span the genome diversity inherent in large collections of bacterial isolates. We show the potential of using this multiplexing approach to close bacterial genomes on a high-throughput basis.

Y Chromosome Material in Turner Syndrome.

BackgroundTurner Syndrome (TS) is a frequently identified chromosomal disease in humans characterized by short stature, sexual infantilism, streak gonads, primary amenorrhea, and a number of somatic anomalies. Approximately 55% of TS individuals have a nonmosaic 45,X karyotype. In addition, a cell line with a Y chromosome is present in 5% of patients, which is undetectable by the standard cytogenetic analysis. The identification of Y chromatin in some TS individuals has been associated with the development of gonadoblastoma. Therefore, it is important to exclude the presence of Y chromatin in TS individuals. In this study, it was planned to detect cases with mosaicism in terms of Y chromatin with the help of Y whole chromosome probes (WCP) from individuals with TS by fluorescence in situ hybridization (FISH) analysis.MethodologyForty-four patients with Turner syndrome, who were being followed up in the Genetics Unit, were contacted and invited for the study. Of the 44 invited patients, 28 responded to the invitation. In this study, it was planned to detect TS patients with mosaicism in terms of Y chromatin with the help of the Y whole chromosome probe.ResultsThe majority of the cases (71.42%) included in the study carried pure X monosomy, which is the classical Turner syndrome karyotype. Other structural X chromosome aberrations, in isolated or mosaic forms, were less frequently represented. Y chromosome sequences were searched in 28 cases with Turner syndrome by the FISH method using Y whole chromosome probe. Y chromosome sequence was detected in one (3.5%) case of 28 cases.ConclusionsIt is recommended that individuals with Turner syndrome be screened for Y chromatin. Detection of this will provide information and guidance to individuals with Turner syndrome, especially in terms of the risk of developing gonadoblastoma, with advanced clinical consultation. This study was conducted to emphasize the importance of this.

Fanconi-like anemia related to a FANCM mutation

Fanconi anemia is primarily inherited as an autosomal recessive genetic disorder with common delays in diagnosis and challenging treatments. Fanconi anemia patients have a high risk of developing solid tumors, particularly in the head and neck or anogenital regions.The diagnosis of Fanconi anemia is primarily based on the chromosomal breakage but FA gene sequencing is recommended in all patients with a positive chromosome fragility test.Here, we present a 32-year-old man with advanced tonsil squamous cell carcinoma and fatal toxicity after the first cycle of chemotherapy. No anemia was present. A recent variant mutation if the FANCM gene was detected (c1511_1515delGAGTA (pArg504AsnfsTer29)).Homozygous or double heterozygous pathogenic variants have been reported in FANCM and linked to azoospermia and primary ovarian failure without anemia. Alterations in this gene have also been associated with a genetic predisposition for solid tumors (breast and ovarian cancer) and hematological malignancies (B-cell acute lymphoblastic leukemia).Due to the hypersensitivity of these patients to DNA-damaging agents such as chemotherapy and radiotherapy, surgery is the best treatment option for malignant solid tumors. Dose reductions or alternative regimens of chemotherapy and/or radiotherapy are recommended in FA patients who develop a malignant tumor.

In silico analysis and expression profiling of S-domain receptor-like kinases (SD-RLKs) under different abiotic stresses in Arabidopsis thaliana

BackgroundS-domain receptor-like kinases (SD-RLKs) are an important and multi-gene subfamily of plant receptor-like/pelle kinases (RLKs), which are known to play a significant role in the development and immune responses of Arabidopsis thaliana. The conserved cysteine residues in the extracellular domain of SD-RLKs make them interesting candidates for sensing reactive oxygen species (ROS), assisting oxidative stress mitigation and associated signaling pathways during abiotic stresses. However, how closely SD-RLKs are interrelated to abiotic stress mitigation and signaling remains unknown in A. thaliana.ResultsThis study was initiated by examining the chromosomal localization, phylogeny, sequence and differential expression analyses of 37 SD-RLK genes using publicly accessible microarray datasets under cold, osmotic stress, genotoxic stress, drought, salt, UV-B, heat and wounding. Out of 37 SD-RLKs, 12 genes displayed differential expression patterns in both the root and the shoot tissues. Promoter structure analysis suggested that these 12 SD-RLK genes harbour several potential cis-regulatory elements (CREs), which are involved in regulating multiple abiotic stress responses. Based on these observations, we investigated the expression patterns of 12 selected SD-RLKs under ozone, wounding, oxidative (methyl viologen), UV-B, cold, and light stress at different time points using semi-qRT-PCR. Of these 12 SD-SRKs, the genes At1g61360, At1g61460, At1g61380, and At4g27300 emerged as potential candidates that maintain their expression in most of the stress treatments till exposure for 12 h. Expression patterns of these four genes were further verified under similar stress treatments using qRT-PCR. The expression analysis indicated that the gene At1g61360, At1g61380, and At1g61460 were mostly up-regulated, whereas the expression of At4g27300 either up- or down-regulated in these conditions.ConclusionsTo summarize, the computational analysis and differential transcript accumulation of SD-RLKs under various abiotic stresses suggested their association with abiotic stress tolerance and related signaling in A. thaliana. We believe that a further detailed study will decipher the specific role of these representative SD-RLKs in abiotic stress mitigation vis-a-vis signaling pathways in A. thaliana.

Higher Prevalence of Multi-Drug Resistant Gonococcal Infections Among Patients with Prior Gonococcal and Chlamydia Infections

Abstract Introduction/Objective Neisseria gonorrhoeae (NG) is the 2nd most common cause of sexually transmitted infection worldwide. WHO data from 2009-14 showed widespread resistance to ciprofloxacin (97%), azithromycin (81%), and oral cefixime and injectable ceftriaxone (66%). We have investigated local epidemiology of antimicrobial resistance in PCR-confirmed NG by chromosomal multi-locus sequence typing and analysis. Methods/Case Report Clinical specimens of 85 patients who tested positive for NG using automated PCR (COBAS 4800; Roche Diagnostics) were used in this study. The samples were amplified by PCR using 10 primers (Integrated DNA Technologies, USA) targeting seven antibiotic resistance-associated loci in the bacterial chromosome (penA, mtrR, ponA, porB, gyr, parC and 23s rRNA) and sequenced on a 48-channel ABI 3730 Sanger sequencer (Thermo Fisher). The resulting sequences were analyzed using the NG Sequence Typing for Antibiotic Resistance (NG-STAR) database for matching alleles, correlating to clinical resistance. Results were analyzed by Chi-square or Fisher’s exact tests. Results (if a Case Study enter NA) Most patients positive for NG were non-Hispanic Black males (60%), with mean age of 25 years (range: 14-53 years). 23.5% had Chlamydia trachomatis (CT) co-infection, and 29.4% had other sexually transmitted infections, such as syphilis, HIV and HPV. 15.0% had previous NG infection, and 12% had previous CT infection. Sixty-five samples (76.5%) yielded at least one gene locus with a DNA sequence with &amp;gt;95% similarity in the NG-STAR database. About half (50.6%) of these sample had confirmed resistance mutations, 5 of which indicated resistance to multiple antibiotics. All specimens with porB and gyr mutations were resistant to penicillins, ceftriaxone, cefixime, erythromycin, tetracycline and ciprofloxacin. Most of those with mtrR mutations were resistant to ciprofloxacin. Most of those with mutations (with or without resistance) had previous NG infection. Significant correlation was observed between those with at least 1 mutated gene locus and CT co-infection (p=0.0001). Conclusion A significant proportion of our patients tested positive for resistance mutations, a majority of whom had previous NG infection. There was significant correlation between the presence of mutations and CT co-infection. These findings warrant utilization of culture and sensitivity testing in patients with previous NG and CT co-infection.

Differential DNA methylation between long-winged and short-winged adults of Nilaparvata lugens.

Nilaparvata lugens, a catastrophic rice pest in South East Asia, has adults with wing dimorphism. DNA methylation has been proved to play an important role in regulation of phenotype differentiation in insects. In this study, methylation sensitive amplification polymorphism (MSAP) was used to investigate the cytosine methylation state at CCGG sites in macropterous male adults (MMA) and brachypterous male adults (BMA) of brown planthopper. In MMA, the fully methylated ratio was 2.96%, hemi-methylated ratio 3.83% and total methylated ratio 6.79%. In BMA, they were 5.53%, 4.19% and 9.72%, respectively. There were significant differences in the methylation of the target sites (CCGG) between MMA and BMA (ØST = 0.2614, P = 0.0354). Based the PCoA results, a much clear separation were also shown between MMA and BMA along the first coordinate (38.8% of variance explained). We also cloned and got nine satisfactory sequences with different methylation states between MMA and BMA. Two of them have similarity with male-specific sequence in chromosome Y and lipophorin receptor gene in N. lugens, respectively. The result showed that the methylation patterns and levels were different between two wing phenotypes of N. lugens, and will facilitate research on the epigenetic mechanism of insect wing dimorphism.

Chromosome-specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing.

We developed a method to tag telomeres and measure telomere length by nanopore sequencing in the yeast S. cerevisiae. Nanopore allows long-read sequencing through the telomere, through the subtelomere, and into unique chromosomal sequence, enabling assignment of telomere length to a specific chromosome end. We observed chromosome end–specific telomere lengths that were stable over 120 cell divisions. These stable chromosome-specific telomere lengths may be explained by slow clonal variation or may represent a new biological mechanism that maintains equilibrium unique to each chromosome end. We examined the role of RIF1 and TEL1 in telomere length regulation and found that TEL1 is epistatic to RIF1 at most telomeres, consistent with the literature. However, at telomeres that lack subtelomeric Y′ sequences, tel1Δ rif1Δ double mutants had a very small, but significant, increase in telomere length compared with the tel1Δ single mutant, suggesting an influence of Y′ elements on telomere length regulation. We sequenced telomeres in a telomerase-null mutant (est2Δ) and found the minimal telomere length to be ∼75 bp. In these est2Δ mutants, there were apparent telomere recombination events at individual telomeres before the generation of survivors, and these events were significantly reduced in est2Δ rad52Δ double mutants. The rate of telomere shortening in the absence of telomerase was similar across all chromosome ends at ∼5 bp per generation. This new method gives quantitative, high-resolution telomere length measurement at each individual chromosome end and suggests possible new biological mechanisms regulating telomere length.

Cestodes in the genomic era.

The first cestode genomes were obtained by an international consortium led by the Wellcome Sanger Institute that included representative institutions from countries where the sequenced parasites have been studied for decades, in part because they are etiological agents of endemic diseases (Argentina, Uruguay, Mexico, Canada, UK, Germany, Switzerland, Ireland, USA, Japan, and China). After this, several complete genomes were obtained reaching 16 species to date. Cestode genomes have smaller relative size compared to other animals including free-living flatworms. Moreover, the features genome size and repeat content seem to differ in the two analyzed orders. Cyclophyllidean species have smaller genomes and with fewer repetitive content than Diphyllobothriidean species. On average, cestode genomes have 13,753 genes with 6 exons per gene and 41% GC content. More than 5,000 shared cestode proteins were accurately annotated by the integration of gene predictions and transcriptome evidence being more than 40% of these proteins of unknown function. Several gene losses and reduction of gene families were found and could be related to the extreme parasitic lifestyle of these species. The application of cutting-edge sequencing technology allowed the characterization of the terminal sequences of chromosomes that possess unique characteristics. Here, we review the current status of knowledge of complete cestode genomes and place it within a comparative genomics perspective. Multidisciplinary work together with the implementation of new technologies will provide valuable information that can certainly improve our chances to finally eradicate or at least control diseases caused by cestodes.

Differential enrichment of yeast DNA in SARS-CoV-2 and related genomes supports synthetic origin hypothesis

Background: Knowledge about the origin of SARS-CoV-2 is necessary for both a biological and epidemiological understanding of the COVID-19 pandemic. Evidence suggests that a proximal evolutionary ancestor of SARS-CoV-2 belongs to the bat coronavirus family. However, as further evidence for a direct zoonosis remains limited, alternative modes of SARS-CoV-2 biogenesis should be also considered. Results: Here we show that the genomes from SARS-CoV-2 and from SARS-CoV-1 are differentially enriched with short chromosomal sequences from the yeast S. cerevisiae at focal positions that are known to be critical for virus replication, host cell invasion, and host immune response. Specifically, for SARS-CoV-2, we identify two sites: one at the start of the viral replicase domain, and the other at the end of the spike gene past its critical domain junction; for SARS-CoV-1, one at the start of the RNA dependent RNA polymerase gene, and the other at the start of the spike protein’s receptor binding domain. As yeast is not a natural host for this virus family, we propose a directed passage model for viral constructs, including virus replicase, in yeast cells based on co-transformation of virus DNA plasmids carrying yeast selectable genetic markers followed by intra-chromosomal homologous recombination through gene conversion. Highly differential sequence homology data across yeast chromosomes congruent with chromosomes harboring specific auxotrophic markers further support this passage model. Model and data together allow us to infer a hypothetical tripartite genome assembly scheme for the synthetic biogenesis of SARS-CoV-2 and SARS-CoV-1. Conclusions: These results provide evidence that the genome sequences of SARS-CoV-1, SARS-CoV-2, but not that of RaTG13, BANAL-20-52 and all other closest SARS coronavirus family members identified, are carriers of distinct homology signals that might point to large-scale genomic editing during a passage of directed replication and chromosomal integration inside genetically modified yeast cells.

Co-Occurrence of blaOXA-23 in the Chromosome and Plasmid: Increased Fitness in Carbapenem-Resistant Acinetobacter baumannii.

This study aims to explore the co-occurrence of chromosomal and plasmid blaOXA-23 in carbapenem-resistant A. baumannii (CRAB) and its influence on phenotypes. A total of 11 CRAB isolates containing copies of blaOXA-23 on the chromosome and plasmid (CO), as well as 18 closely related isolates with blaOXA-23, located on either the chromosome or plasmid (SI), were selected for the determination of antibiotic susceptibility, virulence phenotype, and characteristic genomic differences. The co-occurrence of blaOXA-23 on the CRAB chromosome and plasmids did not enhance carbapenem resistance, but trimethoprim/sulfamethoxazole exhibited significantly reduced minimum inhibitory concentrations in CO. CO demonstrated a higher degree of fitness compared to SI. An increased biofilm formation ability and serum tolerance were also identified in CO, which may be associated with virulence genes, which include csuD, entE, pgaA, and plc. blaOXA-23-carrying transposons were found at different insertion sites on the chromosome. The most common site was AbaR-type genomic islands (50%). Two types of plasmids were found in CO. The co-occurrence of blaOXA-23 on the chromosome and a plasmid in CRAB had little effect on carbapenem susceptibility but was accompanied by increased fitness and virulence. Different origins and independent insertions of blaOXA-23-carrying transposons were identified in both the chromosomal and plasmid sequences.

Differential enrichment of yeast DNA in SARS-CoV-2 and related genomes supports synthetic origin hypothesis

Background: Knowledge about the origin of SARS-CoV-2 is necessary for both a biological and epidemiological understanding of the COVID-19 pandemic. Evidence suggests that a proximal evolutionary ancestor of SARS-CoV-2 belongs to the bat coronavirus family. However, as further evidence for a direct zoonosis remains limited, alternative modes of SARS-CoV-2 biogenesis should be also considered. Results: Here we show that genomes from SARS-CoV-2 and from closely related coronaviruses are differentially enriched with short chromosomal sequences from the yeast S. cerevisiae at focal positions that are known to be critical for virus replication, host cell invasion, and host immune response. Specifically, for SARS-CoV-2, we identify two sites: one at the start of the viral replicase domain, and the other at the end of the spike gene past its critical domain junction; for SARS-CoV-1, one at the start of the RNA dependent RNA polymerase gene, and the other at the start of the spike protein’s receptor binding domain. As yeast is not a natural host for this virus family, we propose a directed passage model for viral constructs, including virus replicase, in yeast cells based on co-transformation of virus DNA plasmids carrying yeast selectable genetic markers followed by intra-chromosomal homologous recombination through gene conversion. Highly differential sequence homology data across yeast chromosomes congruent with chromosomes harboring specific auxotrophic markers further support this passage model. Model and data together allow us to infer a hypothetical tripartite genome assembly scheme for the synthetic biogenesis of SARS-CoV-2 and SARS-CoV-1. Conclusions: These results provide evidence that the genome sequences of SARS-CoV-1, SARS-CoV-2, but not that of RaTG13 and all other closest SARS coronavirus family members identified, are carriers of distinct homology signals that might point to large-scale genomic editing during a passage of directed replication and chromosomal integration inside genetically modified yeast cells.

Opportunity to improve livestock traits using 3D genomics.

The advent of high-throughput chromosome conformation capture and sequencing (Hi-C) has enabled researchers to probe the 3D architecture of the mammalian genome in a genome-wide manner. Simultaneously, advances in epigenomic assays, such as chromatin immunoprecipitation and sequencing (ChIP-seq) and DNase-seq, have enabled researchers to study cis-regulatory interactions and chromatin accessibility across the same genome-wide scale. The use of these data has revealed many unique insights into gene regulation and disease pathomechanisms in several model organisms. With the advent of these high-throughput sequencing technologies, there has been an ever-increasing number of datasets available for study; however, this is often limited to model organisms. Livestock species play critical roles in the economies of developing and developed nations alike. Despite this, they are greatly underrepresented in the 3D genomics space; Hi-C and related technologies have the potential to revolutionise livestock breeding by enabling a more comprehensive understanding of how production traits are controlled. The growth in human and model organism Hi-C data has seen a surge in the availability of computational tools for use in 3D genomics, with some tools using machine learning techniques to predict features and improve dataset quality. In this review, we provide an overview of the 3D genome and discuss the status of 3D genomics in livestock before delving into advancing the field by drawing inspiration from research in human and mouse. We end by offering future directions for livestock research in the field of 3D genomics.

Transcriptomics and methylomics study on the effect of iodine-containing drug FS-1 on Escherichia coli ATCC BAA-196.

Aim: Promising results on application of iodine-containing nano-micelles, FS-1, against antibiotic-resistant Escherichia coli was demonstrated. Materials & methods: RNA sequencing for transcriptomics and the complete genome sequencing by SMRT PacBio were followed by genome assembly and methylomics. Results & conclusion: FS-1-treated E. coli showed an increased susceptibility to antibiotics ampicillin and gentamicin. Cultivation with FS-1 caused gene expression alterations toward anaerobic respiration, increased anabolism and inhibition of many nutrient uptake systems. Main targets of iodine-containing particles were cell membrane structures causing oxidative, osmotic and acidic stresses. Identification of methylated nucleotides showed an altered pattern in the FS-1-treated culture. Possible role of transcriptional and epigenetic modifications in the observed increase in susceptibility to gentamicin and ampicillin were discussed.

Multiple Genetic Rare Variants in Autism Spectrum Disorders: A Single-Center Targeted NGS Study

Many studies based on chromosomal microarray and next-generation sequencing (NGS) have identified hundreds of genes associated with autism spectrum disorder (ASD) risk, demonstrating that there are several complex genetic factors that contribute to ASD risk. We performed targeted NGS gene panels for 120 selected genes, in a clinical population of 40 children with well-characterized ASD. The variants identified were annotated and filtered, focusing on rare variants with a minimum allele frequency &lt;1% in GnomAD. We found 147 variants in 39 of the 40 patients. It was possible to perform family segregation analysis in 28 of the 40 patients. We found 4 de novo and 101 inherited variants. For the inherited variants, we observed that all the variants identified in the patients came equally from the paternal and maternal genetic makeup. We identified 9 genes that are more frequently mutated than the others, and upon comparing the mutational frequency of these 9 genes in our cohort and the mutational frequency in the GnomAD population, we found significantly increased frequencies of rare variants in our study population. This study supports the hypothesis that ASD is the result of a combination of rare deleterious variants (low contribution) and many low-risk alleles (genetic background), highlighting the importance of MET and SLIT3 and the potentially stronger involvement of FAT1 and VPS13B in ASD. Taken together, our findings reinforce the importance of using gene panels to understand the contribution of the different genes already associated with ASD in the pathogenesis of the disease.