Read-depth analysis
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The female flower of hop (Humulus lupulus var. lupulus) is an essential ingredient that gives characteristic aroma, bitterness and durability/stability to beer. However, the molecular genetic basis for identifying DNA markers in hop for breeding and to study its domestication has been poorly established. Here, we provide draft genomes for two hop cultivars [cv. Saazer (SZ) and cv. Shinshu Wase (SW)] and a Japanese wild hop [H. lupulus var. cordifolius; also known as Karahanasou (KR)]. Sequencing and de novo assembly of genomic DNA from heterozygous SW plants generated scaffolds with a total size of 2.05 Gb, corresponding to approximately 80% of the estimated genome size of hop (2.57 Gb). The scaffolds contained 41,228 putative protein-encoding genes. The genome sequences for SZ and KR were constructed by aligning their short sequence reads to the SW reference genome and then replacing the nucleotides at single nucleotide polymorphism (SNP) sites. De novo RNA sequencing (RNA-Seq) analysis of SW revealed the developmental regulation of genes involved in specialized metabolic processes that impact taste and flavor in beer. Application of a novel bioinformatics tool, phylogenetic comparative RNA-Seq (PCP-Seq), which is based on read depth of genomic DNAs and RNAs, enabled the identification of genes related to the biosynthesis of aromas and flavors that are enriched in SW compared to KR. Our results not only suggest the significance of historical human selection process for enhancing aroma and bitterness biosyntheses in hop cultivars, but also serve as crucial information for breeding varieties with high quality and yield.
- MeSH
- délka genomu MeSH
- dieta MeSH
- fylogeneze MeSH
- genom rostlinný * MeSH
- Humulus genetika metabolismus MeSH
- kvantitativní znak dědičný MeSH
- květy genetika MeSH
- organely genetika MeSH
- pivo * MeSH
- polymerázová řetězová reakce s reverzní transkripcí MeSH
- regulace genové exprese u rostlin MeSH
- repetitivní sekvence nukleových kyselin genetika MeSH
- rostlinné geny MeSH
- sekvenční analýza DNA MeSH
- sekvenční analýza RNA MeSH
- stanovení celkové genové exprese MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The recent human Monkeypox outbreak underlined the importance of studying basic biology of orthopoxviruses. However, the transcriptome of its causative agent has not been investigated before neither with short-, nor with long-read sequencing approaches. This Oxford Nanopore long-read RNA-Sequencing dataset fills this gap. It will enable the in-depth characterization of the transcriptomic architecture of the monkeypox virus, and may even make possible to annotate novel host transcripts. Moreover, our direct cDNA and native RNA sequencing reads will allow the estimation of gene expression changes of both the virus and the host cells during the infection. Overall, our study will lead to a deeper understanding of the alterations caused by the viral infection on a transcriptome level.
- MeSH
- komplementární DNA MeSH
- lidé MeSH
- nanopórové sekvenování * MeSH
- opičí neštovice * MeSH
- stanovení celkové genové exprese MeSH
- transkriptom MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- dataset MeSH
Approximately 13% of the human genome at certain motifs have the potential to form noncanonical (non-B) DNA structures (e.g., G-quadruplexes, cruciforms, and Z-DNA), which regulate many cellular processes but also affect the activity of polymerases and helicases. Because sequencing technologies use these enzymes, they might possess increased errors at non-B structures. To evaluate this, we analyzed error rates, read depth, and base quality of Illumina, Pacific Biosciences (PacBio) HiFi, and Oxford Nanopore Technologies (ONT) sequencing at non-B motifs. All technologies showed altered sequencing success for most non-B motif types, although this could be owing to several factors, including structure formation, biased GC content, and the presence of homopolymers. Single-nucleotide mismatch errors had low biases in HiFi and ONT for all non-B motif types but were increased for G-quadruplexes and Z-DNA in all three technologies. Deletion errors were increased for all non-B types but Z-DNA in Illumina and HiFi, as well as only for G-quadruplexes in ONT. Insertion errors for non-B motifs were highly, moderately, and slightly elevated in Illumina, HiFi, and ONT, respectively. Additionally, we developed a probabilistic approach to determine the number of false positives at non-B motifs depending on sample size and variant frequency, and applied it to publicly available data sets (1000 Genomes, Simons Genome Diversity Project, and gnomAD). We conclude that elevated sequencing errors at non-B DNA motifs should be considered in low-read-depth studies (single-cell, ancient DNA, and pooled-sample population sequencing) and in scoring rare variants. Combining technologies should maximize sequencing accuracy in future studies of non-B DNA.
MOTIVATION: Repetitive DNA makes up large portions of plant and animal nuclear genomes, yet it remains the least-characterized genome component in most species studied so far. Although the recent availability of high-throughput sequencing data provides necessary resources for in-depth investigation of genomic repeats, its utility is hampered by the lack of specialized bioinformatics tools and appropriate computational resources that would enable large-scale repeat analysis to be run by biologically oriented researchers. RESULTS: Here we present RepeatExplorer, a collection of software tools for characterization of repetitive elements, which is accessible via web interface. A key component of the server is the computational pipeline using a graph-based sequence clustering algorithm to facilitate de novo repeat identification without the need for reference databases of known elements. Because the algorithm uses short sequences randomly sampled from the genome as input, it is ideal for analyzing next-generation sequence reads. Additional tools are provided to aid in classification of identified repeats, investigate phylogenetic relationships of retroelements and perform comparative analysis of repeat composition between multiple species. The server allows to analyze several million sequence reads, which typically results in identification of most high and medium copy repeats in higher plant genomes.
- MeSH
- algoritmy MeSH
- DNA chemie MeSH
- Eukaryota genetika MeSH
- fylogeneze MeSH
- genom MeSH
- internet MeSH
- repetitivní sekvence nukleových kyselin * MeSH
- sekvenční analýza DNA * MeSH
- shluková analýza MeSH
- software * MeSH
- vysoce účinné nukleotidové sekvenování * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Heavy metal pollution is an increasing global concern. Among heavy metals, mercury (Hg) is especially dangerous because of its massive release into the environment and high toxicity, especially for aquatic organisms. The molecular response mechanisms of algae to Hg exposure are mostly unknown. Here, we combine physiological, biochemical, and transcriptomic analysis to provide, for the first time, a comprehensive view on the pathways activated in Chromera velia in response to toxic levels of Hg. Production of hydrogen peroxide and superoxide anion, two reactive oxygen species (ROS), showed opposite patterns in response to Hg2+ while reactive nitrogen species (RNS) levels did not change. A deep RNA sequencing analysis generated a total of 307,738,790 high-quality reads assembled in 122,874 transcripts, representing 89,853 unigenes successfully annotated in databases. Detailed analysis of the differently expressed genes corroborates the biochemical results observed in ROS production and suggests novel putative molecular mechanisms in the algal response to Hg2+. Moreover, we indicated that important transcription factor (TF) families associated with stress responses differentially expressed in C. velia cultures under Hg stress. Our study presents the first in-depth transcriptomic analysis of C. velia, focusing on the expression of genes involved in different detoxification defense systems in response to heavy metal stress.
- MeSH
- Alveolata účinky léků genetika růst a vývoj metabolismus MeSH
- chemické látky znečišťující vodu toxicita MeSH
- chlorofyl metabolismus MeSH
- peroxid vodíku metabolismus MeSH
- reaktivní formy dusíku metabolismus MeSH
- reaktivní formy kyslíku metabolismus MeSH
- rtuť toxicita MeSH
- transkriptom účinky léků MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
... regression -- Multiple, logistic, and proportional hazards regression -- Multiple regression traps -- Analysis ...
Completely rev. 2nd ed. xxvi, 447 s. : il. ; 24 cm
- MeSH
- biomedicínský výzkum metody MeSH
- biometrie * metody MeSH
- Publikační typ
- monografie MeSH
- Konspekt
- Statistika
- NLK Obory
- biologie
- statistika, zdravotnická statistika
Among the many diseases compromising the well-being of the honey bee (Apis mellifera) the chronic paralysis syndrome of adult honey bees is one of the best described. The causative agent, chronic bee paralysis virus (CBPV), is a positive sense, single-stranded RNA virus with a segmented genome. Segment 1 encodes three putative open reading frames (ORFs), including the RNA-dependent RNA polymerase and other non-structural protein coding regions. Segment 2 encodes four putative ORFs, which contain the genes of supposed structural proteins. In this study, we established a reverse genetic system for CBPV by molecular cloning of DNA copies of both genome segments. CBPV rescue was studied in imago and honey bee pupae infection models. Virus replication and progeny virus production was only initiated when capped RNAs of both genome segments were injected in honey bees. As injection of these clonal RNAs caused clinical symptoms similar to wild-type CBPV infection, we conclude that the novel molecular clone fulfilled Koch's postulates. Our virus clone will enable in-depth analysis of CBPV pathogenesis and help to increase knowledge about this important honey bee disease.
INTRODUCTION: Next-generation sequencing is now used on a routine basis for molecular testing but studies on copy-number variant (CNV) detection from next-generation sequencing data are underrepresented. Utilizing an existing whole-exome sequencing (WES) dataset, we sought to investigate the contribution of rare CNVs to the genetic causality of dystonia. METHODS: The CNV read-depth analysis tool ExomeDepth was applied to the exome sequences of 953 unrelated patients with dystonia (600 with isolated dystonia and 353 with combined dystonia; 33% with additional neurological involvement). We prioritized rare CNVs that affected known disease genes and/or were known to be associated with defined microdeletion/microduplication syndromes. Pathogenicity assessment of CNVs was based on recently published standards of the American College of Medical Genetics and Genomics and the Clinical Genome Resource. RESULTS: We identified pathogenic or likely pathogenic CNVs in 14 of 953 patients (1.5%). Of the 14 different CNVs, 12 were deletions and 2 were duplications, ranging in predicted size from 124bp to 17 Mb. Within the deletion intervals, BRPF1, CHD8, DJ1, EFTUD2, FGF14, GCH1, PANK2, SGCE, UBE3A, VPS16, WARS2, and WDR45 were determined as the most clinically relevant genes. The duplications involved chromosomal regions 6q21-q22 and 15q11-q13. CNV analysis increased the diagnostic yield in the total cohort from 18.4% to 19.8%, as compared to the assessment of single-nucleotide variants and small insertions and deletions alone. CONCLUSIONS: WES-based CNV analysis in dystonia is feasible, increases the diagnostic yield, and should be combined with the assessment of single-nucleotide variants and small insertions and deletions.
- MeSH
- dospělí MeSH
- dystonické poruchy diagnóza genetika MeSH
- dystonie diagnóza genetika MeSH
- kohortové studie MeSH
- lidé MeSH
- sekvenování exomu * MeSH
- variabilita počtu kopií segmentů DNA * genetika MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Sage reference publication
3 sv. : il. ; 29 cm
- MeSH
- politika MeSH
- sociální vědy metody MeSH
- vládní programy MeSH
- vytváření politiky MeSH
- výzkum MeSH
- výzkumné techniky MeSH
- Publikační typ
- encyklopedie MeSH
- Konspekt
- Sociologie
- NLK Obory
- sociologie
- statistika, zdravotnická statistika
Cílem studie bylo retrospektivně zhodnotit vybrané parametry ovlivňující pooperační vizus do blízka v souboru pseudofakických očí pacientů s nekorigovaným visem do dálky (UDVA) a na základě získaných výsledků stanovit ty, které nejvíce ovlivnily dobrou nekorigovanou zrakovou ostrost do blízka (UNVA) po implantaci monofokální IOL. Celkem bylo sledováno 122 pseudofakických očí 65 pacientů, přičemž u 57 z nich byly operovány obě oči. Hodnocena četnost zrakové ostrosti pro trojici skupin operovaných očí kategorizovaných dle stěžejního parametru – axiální délky oka (krátká, průměrná, dlouhá). U každé skupiny byly stanoveny průměrné parametry (věk, axiální délka, keratometrie i hloubka přední komory) a relativní četnost pooperační zrakové ostrosti do blízka bez korekce na konvenčně využívaných čtecích tabulkách. Vyšetření vizu do blízka bylo pro každé oko zvlášť prováděno v jeho horizontální poloze pomocí tabulky Zeiss. Studie nepotvrdila jednoznačnou závislost pooperačního vizu do blízka na věku pacienta, hloubce přední komory a ani implantovaném modelu IOL. Potvrzen byl předpoklad optimálního vizu do blízka pro oči s axiální délkou kratší než 23,5 mm, přičemž byla mezi oběma parametry nalezena slabá negativní korelace. Naopak zjištěna střední pozitivní korelace mezi nekorigovanou ostrostí do blízka a centrální optickou mohutností rohovky u očí s axiální délkou 22,5–23,5 mm. Studie potvrdila, že vyšší hodnoty centrální optické mohutnosti rohovky a horní hranice axiální délky oka do 23,5 mm jsou předpokladem optimální pooperační nekorigované zrakové ostrosti do blízka po implantaci monofokální IOL.
Aim of the study was to evaluate retrospectively selected parameters, which influence the postoperative near visual acuity in a group of pseudophakic eyes of patients with Uncorrected Distance Visual Acuity (UDVA) and according to acquired results establish those, which mostly influenced good Uncorrected Near Visual Acuity (UNVA) after the implantation of monofocal IntraOcular Lens (IOL). Altogether, 122 pseudophakic eyes of 65patients were followed up, out of them in 57 patients both eyes were operated on. The frequency of visual acuity for three groups of operated eyes categorized according to the crucial parameter – eye’s axial length (short, average, long) was evaluated. In each of groups, the average parameters (age, axial length, keratometry, and depth of the anterior chamber) were established, as well as relative frequency of postoperative uncorrected near visual acuity on conventionally used reading tables. The near visual acuity assessment for each eye separately was preformed in its horizontal position using the Zeiss table. The study did not confirm positive correlation of postoperative near visual acuity on the age of the patient, depth of the anterior chamber, nor the implanted IOL type. It was confirmed the presumption of optimal near visual acuity for eyes with axial length shorter than 23.5 mm, and in the process, between both parameters slightly negative correlation was found. On the other hand, middle positive correlation between uncorrected near visual acuity and central corneal power (in dioptres) in eyes with the axial length 22.5 – 23.5 mm was found. The study confirmed, that higher values of the central corneal power (in dioptres) and the high borderline value of the axial length up to 23.5 mm are the condition for optimal postoperative uncorrected near visual acuity after the implantation of monofocal intraocular lens.
- Klíčová slova
- nekorigovaný pooperační vizus do blízka, UNVA, monofokální IOL, pseudo-akomodace,
- MeSH
- axiální délka oka MeSH
- extrakce katarakty * MeSH
- implantace nitrooční čočky * statistika a číselné údaje MeSH
- interpretace statistických dat MeSH
- lidé středního věku MeSH
- lidé MeSH
- přední komora oční MeSH
- rohovka fyziologie MeSH
- rohovková topografie MeSH
- senioři MeSH
- statistika jako téma MeSH
- věkové faktory MeSH
- zraková ostrost * fyziologie MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- senioři MeSH
- Publikační typ
- hodnotící studie MeSH
