The genomes of many plants, animals, and fungi frequently comprise dispensable B chromosomes that rely upon various chromosomal drive mechanisms to counteract the tendency of non-essential genetic elements to be purged over time. The B chromosome of rye - a model system for nearly a century - undergoes targeted nondisjunction during first pollen mitosis, favouring segregation into the generative nucleus, thus increasing their numbers over generations. However, the genetic mechanisms underlying this process are poorly understood. Here, using a newly-assembled, ~430 Mb-long rye B chromosome pseudomolecule, we identify five candidate genes whose role as trans-acting moderators of the chromosomal drive is supported by karyotyping, chromosome drive analysis and comparative RNA-seq. Among them, we identify DCR28, coding a microtubule-associated protein related to cell division, and detect this gene also in the B chromosome of Aegilops speltoides. The DCR28 gene family is neo-functionalised and serially-duplicated with 15 B chromosome-located copies that are uniquely highly expressed in the first pollen mitosis of rye.
- MeSH
- Aegilops genetics metabolism MeSH
- Chromosomes, Plant * genetics MeSH
- Karyotyping MeSH
- Mitosis * genetics MeSH
- Nondisjunction, Genetic MeSH
- Pollen genetics MeSH
- Gene Expression Regulation, Plant MeSH
- Genes, Plant MeSH
- Plant Proteins genetics metabolism MeSH
- Secale * genetics MeSH
- Publication type
- Journal Article MeSH
Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.
- MeSH
- Adaptation, Physiological genetics MeSH
- Stress, Physiological MeSH
- Genome, Plant * MeSH
- Genetic Introgression MeSH
- Plant Immunity genetics MeSH
- Karyotype MeSH
- Chromosome Mapping methods MeSH
- Triticum genetics MeSH
- Gene Expression Regulation, Plant MeSH
- Plant Proteins genetics metabolism MeSH
- Plant Breeding methods MeSH
- Crops, Agricultural genetics immunology MeSH
- Secale genetics immunology MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
... Contents -- Preface XV -- Acknowledgements xviii -- 1 FUNDAMENTALS OF DNA, CHROMOSOMES, AND CELLS 1 - ... ... transcription, and the central dogma of molecular biology 7 -- 1.2 THE STRUCTURE AND -- FUNCTION OF CHROMOSOMES ... ... 8 -- Why we need highly structured chromosomes, and how they are organized 8 -- Chromosome function: ... ... in exons -- Translation: decoding messenger origins, centromeres, and telomeres.9 -- 1.3 DNA AND CHROMOSOMES ... ... Differences in DNA copy number between cells 10 -- The cell cycle and segregation of replicated chromosomes ...
2nd ed. 534 s. : il.
"Genetics and Genomics in Medicine is a new textbook written for undergraduate and graduate students, as well as medical researchers, which explains the science behind the uses of genetics and genomics in medicine today. It is not just about rare inherited and chromosomal disorders, but how genetics affects the whole spectrum of human health and disease. DNA technologies are explained, with emphasis on the modern techniques that have revolutionized the use of genetic information in medicine and are indicating the role of genetics in common complex diseases. The detailed, integrative coverage of genetic approaches to treatment and prevention includes pharmacogenomics and the prospects for personalized medicine. Cancers are essentially genetic diseases and are given a dedicated chapter that includes new insights from cancer genome sequencing. Clinical disorders are covered throughout and there are extensive end-of-chapter questions and problems"--Provided by publisher.
This study focused on the relationship between the asymmetry of initial motor symptoms of Parkinson's disease (PD) and premorbid handedness of patients. Structural equation modeling has been used for this purpose. The survey consisting of validated items measuring handedness and questions related to side of occurrence of initial symptoms was administered to 472 patients with PD [277 men, 195 women, mean age 66.5 (9.3), mean duration of the disease 10 (6.1) years]. The unidimensional model of handedness fits the data well (chi(2) = 37.86, df = 20, P = 0.009, Root Mean Square Error of Approximation = 0.044, Comparative Fit Index = 1.00, Standardized Root Mean Square Residual = 0.042) and side of initial motor symptoms is not significantly related to the factor of handedness (r =0.11, SE = 0.07, P = 0.14). In contrast to several other studies, the results indicate that the side of first occurrence of PD signs cannot be predicted from premorbid handedness of patients.
- MeSH
- Behavioral Symptoms etiology MeSH
- Functional Laterality physiology MeSH
- Middle Aged MeSH
- Humans MeSH
- Statistics, Nonparametric MeSH
- Parkinsonian Disorders complications MeSH
- Motor Activity physiology MeSH
- Disability Evaluation MeSH
- Predictive Value of Tests MeSH
- Surveys and Questionnaires MeSH
- Psychiatric Status Rating Scales MeSH
- Retrospective Studies MeSH
- Chi-Square Distribution MeSH
- Aged MeSH
- Age of Onset MeSH
- Check Tag
- Middle Aged MeSH
- Humans MeSH
- Male MeSH
- Aged MeSH
- Female MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
OBJECTIVES: The objective was to make a contribution to deepening the knowledge of the etiopathogenesis of ADHD. DESIGN: In an association study design, an analysis of polymorphisms of selected genes was conducted in 119 hyperkinetic boys and a control group of boys, aged 7-13. Furthermore several psychologically determined subgroups were identified. A connection between psychological functions (endophenotypes) and genes were looked for. RESULTS: There was a statistically significant difference found in allelic and genotype frequencies of the TaqI A polymorphism of the DRD2 gene. The frequency of the allele A1 in hyperkinetic boys and the control subjects was 0.26 and 0.15, respectively (p<0.003). A statistically significant occurrence of atypical genotypes (8/10, 7/10 and 10/11) of the DAT1 gene was also found in hyperkinetic boys and a connection between the M235 polymorphism of the angiotensinogene gene and the positive family history of psychiatric illness was found in probands (p=0.031). Significant correlations between the results of some neuropsychological tests and genes for neuro-/immunomodulators (IL-6, TNF-alpha) and the gene for the brain-derived neurotrophic factor (BDNF) were found. CONCLUSION: The study showed a statistically significant prevalence of A1 allele of the DRD gene in the hyperkinetic group. We also found a significantly higher incidence of atypical DAT genotypes in the hyperkinetic group. Furthermore we found significant connections with particular gene polymorphisms which may hypothetically represent a neurodevelopmental risk factor in the etiopathogenesis of the disorder (IL-2, IL-6, TNF-alpha, BDNF). We further found a connection of the M235 polymorphism of the AGT (angiotensinogene) gene to positive family history of psychiatric illness (p=0.031). As for cognitive characteristics, we identified three subtypes with different cognitive performance profiles. This finding shows interindividual variability of cognitive style in the group of hyperkinetic boys.
- MeSH
- Biomarkers MeSH
- Discrimination, Psychological physiology MeSH
- Child MeSH
- Phenotype MeSH
- Financing, Organized MeSH
- Genetic Markers MeSH
- Genotype MeSH
- Attention Deficit Disorder with Hyperactivity epidemiology genetics metabolism MeSH
- Humans MeSH
- Methylphenidate therapeutic use MeSH
- Adolescent MeSH
- Neuropsychological Tests MeSH
- Polymorphism, Genetic genetics MeSH
- Attention physiology drug effects MeSH
- Psychiatric Status Rating Scales MeSH
- Psychomotor Performance physiology drug effects MeSH
- Receptors, Dopamine D2 genetics MeSH
- Central Nervous System Stimulants therapeutic use MeSH
- Form Perception physiology MeSH
- Check Tag
- Child MeSH
- Humans MeSH
- Adolescent MeSH
- Male MeSH
- Geographicals
- Czech Republic MeSH
The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules.
- MeSH
- Biotechnology methods MeSH
- Chromosomes, Plant genetics MeSH
- Genome, Plant * MeSH
- Chromosome Mapping methods MeSH
- Triticum genetics MeSH
- Sequence Analysis, DNA methods MeSH
- Tandem Repeat Sequences MeSH
- Chromosomes, Artificial, Bacterial MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
The house mouse hybrid zone (HMHZ) is a species barrier thought to be maintained by a balance between dispersal and natural selection against hybrids. While the HMHZ is characterized by frequency discontinuities for some sex chromosome markers, there is an unexpected large-scale regional introgression of a Y chromosome across the barrier, in defiance of Haldane's rule. Recent work suggests that a major force maintaining the species barrier acts through sperm traits. Here, we test whether the Y chromosome penetration of the species barrier acts through sperm traits by assessing sperm characteristics of wild-caught males directly in a field laboratory set up in a Y introgression region of the HMHZ, later calculating the hybrid index of each male using 1401 diagnostic single nucleotide polymorphisms (SNPs). We found that both sperm count (SC) and sperm velocity were significantly reduced across the natural spectrum of hybrids. However, SC was more than rescued in the presence of the invading Y. Our results imply an asymmetric advantage for Y chromosome introgression consistent with the observed large-scale introgression. We suggest that selection on sperm-related traits probably explains a large component of patterns observed in the natural hybrid zone, including the Y chromosome penetration.
- MeSH
- Y Chromosome * MeSH
- Species Specificity MeSH
- Phenotype MeSH
- Hybridization, Genetic * MeSH
- Polymorphism, Single Nucleotide MeSH
- Models, Genetic MeSH
- Mice physiology MeSH
- Selection, Genetic MeSH
- Spermatozoa physiology MeSH
- Animals MeSH
- Check Tag
- Male MeSH
- Mice physiology MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
It is widely accepted that chromosomes occupy more or less fixed positions in mammalian interphase nucleus. However, relation between large-scale order of chromosome positioning and gene activity remains unclear. We used the model of the human ribosomal genes to address specific aspects of this problem. Ribosomal genes are organized at particular chromosomal sites in clusters termed nucleolus organizer regions (NORs). Only some NORs, called competent are generally accepted to be transcriptionally active during interphase. Importantly in this respect, the regularities in distribution of competent, and non-competent NORs among the specific chromosomes were already established in two human-derived cell lines: transformed HeLa and primary LEP cells. In the present study, using FISH and immunocytochemistry, we found that in HeLa and LEP cells the large-scale positioning of the NOR-bearing chromosomes with regard to nucleoli is linked to the transcription activity of rDNA. Namely, the tendency of rDNA-bearing chromosomes to associate with nucleoli correlates with the number of transcriptionally competent NORs in the respective chromosome homologs. Regarding the position of NORs, we found that not only competent but also most of the non-competent NORs are included in the nucleoli. Some intranucleolar NORs (supposedly non-competent) are situated on elongated chromatin protrusions connecting nucleoli with respective chromosome territories spatially distanced from nucleoli.
Our novel Python-based tool EVANGELIST allows the visualization of GC and repeats percentages along chromosomes in sequenced genomes and has enabled us to perform quantitative large-scale analyses on the chromosome level in fish and other vertebrates. This is a different approach from the prevailing analyses, i.e., analyses of GC% in the coding sequences that make up not more than 2% in human. We identified GC content (GC%) elevations in microchromosomes in ancient fish lineages similar to avian microchromosomes and a large variability in the relationship between the chromosome size and their GC% across fish lineages. This raises the question as to what extent does the chromosome size drive GC% as posited by the currently accepted explanation based on the recombination rate. We ascribe the differences found across fishes to varying GC% of repetitive sequences. Generally, our results suggest that the GC% of repeats and proportion of repeats are independent of the chromosome size. This leaves an open space for another mechanism driving the GC evolution in vertebrates.
- MeSH
- Chromosomes genetics MeSH
- Cytogenetics * MeSH
- Genome genetics MeSH
- Evolution, Molecular * MeSH
- Vertebrates classification genetics MeSH
- Birds classification genetics MeSH
- Recombination, Genetic genetics MeSH
- Repetitive Sequences, Nucleic Acid MeSH
- Fishes classification genetics MeSH
- Base Composition genetics MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the progenitor of wheat. We performed chromosome-based survey sequencing of the 14 chromosomes, examining repetitive sequences, protein-coding genes, miRNA/target pairs and tRNA genes, as well as syntenic relationships with related grasses. We found considerable differences in the content and distribution of repetitive sequences between the A and B subgenomes. The gene contents of individual chromosomes varied widely, not necessarily correlating with chromosome size. We catalogued candidate agronomically important loci, along with new alleles and flanking sequences that can be used to design exome sequencing. Syntenic relationships and virtual gene orders revealed several small-scale evolutionary rearrangements, in addition to providing evidence for the 4AL-5AL-7BS translocation in wild emmer wheat. Chromosome-based sequence assemblies contained five novel miRNA families, among 59 families putatively encoded in the entire genome which provide insight into the domestication of wheat and an overview of the genome content and organization.
- MeSH
- Chromosomes, Plant genetics MeSH
- Genetic Loci genetics MeSH
- Genome, Plant genetics MeSH
- Conserved Sequence genetics MeSH
- Poaceae genetics MeSH
- MicroRNAs genetics MeSH
- RNA, Untranslated genetics MeSH
- Polyploidy MeSH
- Flow Cytometry MeSH
- Triticum genetics MeSH
- Repetitive Sequences, Nucleic Acid genetics MeSH
- Genes, Plant genetics MeSH
- Tetraploidy MeSH
- High-Throughput Nucleotide Sequencing MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH