Search Results (171)

Background/Objectives: The mutational dynamics of microsatellites over deep evolutionary timescales are poorly understood. This study aims to elucidate the life history of trinucleotide microsatellites by tracing orthologous loci across divergent vertebrate lineages and characterizing their mutational pathways. Methods: We developed a bioinformatic framework for identifying orthologous microsatellite loci using conserved flanking sequences. This approach was applied to three trinucleotide microsatellites located in exonic, intronic, and intergenic regions, respectively. These loci were amplified and sequenced across 126 individuals representing 64 vertebrate species, whose divergence times range from 6 to 150 million years ago (MYA). Results: Flanking sequences proved essential for reliable orthology assignment, while repeat motifs revealed distinct mutational pathways. Microsatellite decay occurs through two primary mechanisms: the complete loss of dominant repeats or their progressive reduction to solitary units (≤1 repeat). This degeneration process is facilitated by cryptic simple sequences (CSS), which act as genomic catalysts promoting birth–death transitions. Large intra-motif deletions were identified as the key mutational event driving contractions and eventual locus degeneration. Furthermore, mutational patterns were highly locus-specific, influenced by genomic context. Conclusions: Although the study focused on only three loci, limiting broader generalizations, our findings provide mechanistic insights into microsatellite evolution. These results establish a foundation for modeling complex microsatellite life histories and highlight the role of CSS in facilitating evolutionary turnover. Full article

Background: Indigofera pseudotinctoria, a traditional Chinese forage and medicine widely used in East Asia, holds significant economic and agricultural value. Despite this, genomic information regarding I. pseudotinctoria remains conspicuously lacking. Methods: In this study, we utilized genome survey sequencing to elucidate the complete genome sequence of this species. Results: The genome size of I. pseudotinctoria to be around 637–920 Mb with a heterozygosity rate of 0.98% and a repeat rate of 66.3%. A total of 240,659 simple sequence repeat (SSR) markers were predicted in the genome of I. pseudotinctoria. Substantial differences were observed among nucleotide repeat types, for instance, mononucleotide repeats were found to be predominant (62.47%), whereas pentanucleotide repeats were notably scarce (0.24%). Furthermore, among dinucleotide and trinucleotide repeats, sequence motifs AT/AT (66.57%) and AAT/ATT (54.15%) were found to be particularly abundant. Among the identified unigenes, 58,790 exhibited alignment with known genes in established databases, including 33,218 genes within the Gene Ontology (GO) database and 10,893 genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Conclusions: This study marks the first attempt to both sequence and delineate the genomic landscape of I. pseudotinctoria. Importantly, it will serve as a foundational reference for subsequent comprehensive genome-wide deep sequencing and the development of SSR molecular markers within the scope of I. pseudotinctoria research. Full article

Background: The mechanisms by which sporadic young-onset neurodegenerative processes develop are uncertain. Methods: We have previously proposed that stochastic processes involving sequence changes at a DNA, RNA, or protein level in critical genes and proteins might be important to this process. Further investigation points to the contribution of probabilistic states in other factors involved in neurodegenerative conditions, such as—in the case of young onset Alzheimer’s disease—head injury, apolipoprotein ε4 alleles and other elements that, by the interaction of conditional probabilities in these variables, influence the evolution of neurodegenerative conditions. Results: This proposal might help to explain why some autosomal dominant neurodegenerative conditions, such as trinucleotide repeat disorder (Huntington’s disease), might have variable ages of onset given the same disease-causing CAG repeat mutation length. Conclusions: The detection of somatic mutations in single brain cells provides some experimental support for these emerging concepts. Full article

Friedreich’s ataxia (FRDA) is an autosomal recessive neurodegenerative disorder characterized by ataxia, sensory loss and pyramidal signs. While the majority of FRDA cases are caused by biallelic GAA trinucleotide repeat expansions in intron 1 of FXN, there is a subset of patients harboring a heterozygous pathogenic small variant compound-heterozygous with a GAA repeat expansion. We report on the diagnostic journey of a 21-year-old patient who was clinically suspected of having FRDA at the age of 12 years. Genetic testing included fragment analysis, gene panel analysis and exome sequencing, which only detected one pathogenic heterozygous missense variant (c.389 G>T,p.Gly130Val) in FXN. Although conventional repeat analyses failed to detect GAA expansions in our patient, subsequent short-read genome sequencing (GS) indicated a potential GAA repeat expansion. This finding was confirmed by long-read GS, which in addition revealed a complex pattern of interruptions. Both large and small GAA expansions with divergent interruptions containing G, A, GA, GAG and/or GAAG sequences were present within one allele, indicating mosaic sequence variations. Our findings underscore the complexity of repeat expansions which can exhibit both interruptions and somatic instability. We also highlight the utility of long-read GS in unraveling intricate genetic profiles, ultimately contributing to more accurate diagnoses in clinical practice. Full article

Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability and a major genetic contributor to autism spectrum disorder. It is caused by a CGG trinucleotide repeat expansion in the FMR1 gene, resulting in gene silencing and the loss of FMRP, an RNA-binding protein essential for synaptic plasticity. This review covers over 80 years of FXS research, highlighting key milestones, clinical features, genetic and molecular mechanisms, the FXS mouse model, disrupted molecular pathways, and current therapeutic strategies. Additionally, we discuss recent advances including AI-driven combination therapies, CRISPR-based gene editing, and antisense oligonucleotides (ASOs) therapies. Despite these scientific breakthroughs, translating preclinical findings into effective clinical treatments remains challenging. Clinical trials have faced several difficulties, including patient heterogeneity, inconsistent outcome measures, and variable therapeutic responses. Standardized preclinical testing protocols and refined clinical trial designs are required to overcome these challenges. The development of FXS-specific biomarkers could also improve the precision of treatment assessments. Ultimately, future therapies will need to combine pharmacological and behavioral interventions tailored to individual needs. While significant challenges remain, ongoing research continues to offer hope for transformative breakthroughs that could significantly improve the quality of life for individuals with FXS and their families. Full article

Blackcurrant (Ribes nigrum L.) has high nutritional value for human health due to its abundant vitamin C, flavonoids, and organic acids. However, its breeding and genetic research have been severely hindered by the lack of scientific tools such as molecular markers. Here, we identified 14,258 EST-SSR loci from 9531 CDS sequences with lengths greater than 1 kb, which comprised 6211 mononucleotide repeats, 4277 dinucleotide repeats, and 2469 trinucleotide repeats. We then randomly selected 228 EST-SSR loci for PCR amplification and gel electrophoresis imaging in the Ribes collection of Northeast Agricultural University (95 blackcurrant cultivars and 12 other Ribes accessions). As a result, 31 pairs of markers produced clear and reproducible bands of the expected size. Based on the 107 Ribes accessions, the allele number (Na), information index (I), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphic information content (PIC) of the 31 markers were 2–5, 0.23–1.32, 0.07–0.71, 0.11–0.68, and 0.14–0.67, respectively. For the blackcurrant gene pool, neighbor-joining and population structure analysis revealed three clusters, which did not align well with their geographical origins. Based on the results, two sets with 21 and 19 blackcurrant cultivars were identified by Power Core (PC) and Core Hunter (CH) programs. The integrated core germplasm (IC) set with 27 cultivars derived from the PC and CH sets harbored abundant genetic diversity, where the allele retention rate accounted for 98.9% of the blackcurrant gene pool. The SSR markers, data, and core germplasms presented in this study lay a solid foundation for the phylogenetic study, molecular breeding, and conservation genetics of Ribes, especially Ribes nigrum. Full article

Chestnut trees are an essential source of both food and timber. However, the severe threats from invasive pests and diseases compromise their existence and productivity. In Europe, chestnut hybridization programs have been initiated to produce resilient rootstocks in response to ink disease. However, the gap in the identification of these hybrid plants is typically based on field observations and morphological features and remains a challenge. Our study presents a marker set for distinguishing between chestnut hybrid CA90 (Castanea sativa × Castanea crenata), a hybrid with demonstrated resistance to Phytophthora cinnamomi, and other varieties using microsatellite (SSR) markers and bioinformatics tools. We used 35 chestnut samples, including three CA90 controls, hybrids sampled within Portugal, with an aim to define the profiles of the chestnut hybrids and varieties in this study based on band patterns and SSR motifs. We selected and modified nine distinct SSR primers with null allelic features from 43 already developed simple sequence repeat (SSR) markers. PCR amplification and agarose gel electrophoresis were used to amplify and visualize the DNA bands. To confirm genetic variations, 27 amplified bands were sequenced by Sanger sequencing. This analysis identified 31 SSRs across 22 SSR-containing sequences, with trinucleotide (67.74%) repeats being the most common, followed by repeats of dinucleotide (22.58%), mononucleotide (6.45%), and hexanucleotide (3.23%). A total of 18 alleles were observed for the nine loci. The alleles ranged from one to three per locus for the 35 samples. The novel locus CP4 could only be found in CA90 hybrids. This tool can aid in identifying and selecting disease-resistant hybrids, thereby contributing to chestnut production and management strategies. Full article

Nightlily (Hemerocallis citrina Baroni) is an important vegetable with edible floral organs. It possesses considerable economic value due to its edibility, ornamental, and medicinal properties. However, the genetic linkage map construction and quantitative trait locus (QTL) mapping of nightlily have not been performed. This study used two varieties ‘Dongzhuanghuanghua’ and ‘Chonglihua’ of nightlily as cross parents to establish an intraspecific hybridization population of 120 F₁ progenies. The ‘Datonghuanghua’ (female) variety of nightlily and ‘Lullaby Baby’ (male) variety of daylily were selected to construct an interspecific hybridization population of 55 F₁ progenies. A total of 965 expressed sequence tag–simple sequence repeats (EST-SSRs), along with 20 SSR markers from various sources, were used for genetic mapping. Among these markers, CT/TC (9.24%) of the dinucleotide and GGA/GAG/AGG (4.67%) of the trinucleotide repeat motifs were most abundant. In the intraspecific hybridization genetic map, a total of 124 markers were resolved into 11 linkage groups, with a total map length of 1535.07 cM and an average interval of 12.38 cM. Similarly, the interspecific hybridization map contained 11 linkage groups but with 164 markers, a total map length of 2517.06 cM, and an average interval of 15.35 cM. The two constructed maps had 48 identical markers and demonstrated good collinearity. The collinearity analysis showed that 161 markers hit the genomic sequence of the published H. citrina genome, indicating that the two constructed genetic maps had high accuracy. Phenotypic data were investigated over two consecutive years (2018 and 2019) for flower bud fresh weight, dry weight, and bud length in two hybridization populations. A total of nine QTLs associated with flower bud-related traits were identified, among which those located on linkage group 8 of the intraspecific genetic map and linkage group 4 of the interspecific genetic map showed good stability. All nine QTLs had LOD values of not less than 4 and PVE values of not less than 15% over two years. This is the first report about the intra- and interspecific genetic map construction and QTL mapping of the flower bud-related traits in nightlily based on a genetic map. The results promote marker-assisted breeding and offer insights into the mechanisms underlying important traits of the genus Hemerocallis. Full article

Fragile X-associated tremor/ataxia syndrome (FXTAS) is a late-onset neurodegenerative disorder caused by moderately expanded CGG trinucleotide repeats in the 5′ untranslated region (UTR) of the FMR1 gene. Characterized by motor deficits such as action tremor and cerebellar gait ataxia, FXTAS is further distinguished by ubiquitin-positive intranuclear inclusions in neurons and glia. However, its clinical spectrum often overlaps with other neurodegenerative conditions such as Parkinson’s disease (PD). Sensorimotor gating deficits, commonly associated with disorders affecting the nigrostriatal pathway such as PD, have been reported in FXTAS, but the underlying connection between these two phenotypes remains undetermined. In this study, we used the P90CGG mouse model of FXTAS, which expresses 90 CGG repeats upon doxycycline induction, to investigate sensorimotor gating deficits and their relationship to nigrostriatal degeneration. After induction, the P90CGG model exhibited late-onset impairments in prepulse inhibition (PPI), a cross-species measure of sensorimotor gating. These deficits coincided with pronounced nigrostriatal degeneration but occurred without evidence of inclusion formation in the substantia nigra. Our findings highlight nigrostriatal degeneration, which has not previously been reported in animal models of FXTAS, and suggest a potential link to sensorimotor gating dysfunction within the context of the disorder. Full article

The study of Reticulitermes chinensis offers valuable insights into insect aging and longevity, focusing on telomere biology and simple sequence repeats (SSRs). Telomeres, the protective cap at chromosome ends, are often linked to cellular aging and lifespan. Through transcriptomic analysis using the RepeatExplorer tool, a total of 10,740 SSR loci were identified, encompassing di-, tri-, tetra-, penta-, and hexa-nucleotide motifs. Among these, tri-nucleotide repeats were the most prevalent (2702), with prominent motifs including AC/GT (21.91%), AAG/CTT (8.49%), and AGC/CTG (8.2%). The identified SSRs serve as valuable genetic markers for taxonomy, phylogenetic, and population genetics. A telomeric sequence array featuring the TTAGG repeat motif was also discovered, with fluorescence in situ hybridization (FISH) confirming its localization at chromosome ends. Telomere lengths R. chinensis ranged from tens to hundreds of kilobases but showed no significant correlation with lifespan differences among termite castes. All castes had the same telomere length. This finding suggests that R. chinensis may possess a unique telomere maintenance mechanism, decoupling telomere length from aging and challenging the conventional view that shorter telomeres are indicative aging. It is hypothesized that telomerase activity plays a critical role in preserving telomere integrity in this species. These findings underscore the complexity and evolutionary adaptations of telomere biology in social insects. Moreover, the variation and organization of SSRs in R. chinensis provide a rich genetic resource for genome mapping, evolutionary research, and population genetics. This study sheds light on telomere dynamics and genetic diversity in termites, opening new pathways for research in evolutionary biology and the molecular mechanisms of aging. Full article

Background: Childhood-onset progressive ataxias are rare neurodegenerative disorders characterized by cerebellar signs, sometimes associated with other neurological or extra-neurological features. The autosomal dominant forms, known as spinocerebellar ataxias (SCAs), linked to trinucleotide (i.e., CAG) repeat disorders, are ultra-rare in children. We describe three patients from two unrelated families affected by spinocerebellar ataxia type 2 (SCA2) and present a literature review of pediatric cases. Methods: The patients’ clinical and genetic data were collected retrospectively. Results: The first case was a 9.5-year-old boy, affected by ataxia with oculomotor apraxia and cerebellar atrophy, subcortical myoclonus, and peripheral axonal sensitive polyneuropathy caused by a pathologic expansion in ATXN2, inherited from his asymptomatic father. Two brothers with familial SCA2 presented neurodegeneration leading to early death in one case and progressive ataxia, parkinsonism, and epilepsy with preserved ambulation at age 18 years in the second. To date, 19 pediatric patients affected by SCA2 have been reported, 3 of whom had a phenotype consistent with progressive ataxia with shorter CAG repeats, while 16 had more severe early-onset encephalopathy, with longer alleles. Conclusions: Although they are ultra-rare, trinucleotide repeat disorders must be considered in differential diagnosis of hereditary progressive ataxias in children, especially considering that they require targeted genetic testing and can manifest even before a parental carrier becomes symptomatic. Thus, they must also be taken into account with negative family history and when Next-Generation Sequencing (NGS) results are inconclusive. Notably, the association between cerebellar ataxia and other movement disorders should raise suspicion of SCA2 among differential diagnoses. Full article

It is known that a number of neurodegenerative diseases, also called diseases of waiting, are associated with the expansion of the polyQ tract in the first exon of the ATXN2 gene. In the expanded polyQ tract, the probability of occurrence of non-canonical configurations (hairpins, G-quadruplexes, etc.) is significantly higher than in the normal one. Obviously, for their formation, the occurrence of open states (OSs) is necessary. Calculations were made for these processes using the angular mechanical model of DNA. It has been established that the probability of the large OS zones genesis in a DNA segment depends not only on the “strength” of the nucleotide sequence but also on the factors determining the dynamics of DNA; localization of the energy in the DNA molecule and the potential energy of interaction between pairs of nitrogenous bases also depend on environmental parameters. The potential energy of hydrogen bonds does not remain constant, and oscillatory movements lead to its redistribution and localization. In this case, OSs effectively dissipate the energy of oscillations. Thus, mathematical modeling makes it possible to calculate the localization of mechanical energy, which is necessary for the OSs formation, and to predict the places of their origin, taking into account the mechanical oscillations of the DNA molecule. Full article

Background: Huntington’s disease (HD) is a multifaceted neurological disorder characterized by the progressive deterioration of motor, cognitive, and psychiatric functions. Despite a limited understanding of its pathogenesis, research has implicated abnormal trinucleotide cytosine-adenine-guanine CAG repeat expansion in the huntingtin gene (HTT) as a critical factor. The development of innovative strategies is imperative for the early detection of predictive biomarkers, enabling timely intervention and mitigating irreversible cellular damage. Lipidomics, a comprehensive analytical approach, has emerged as an indispensable tool for systematically characterizing lipid profiles and elucidating their role in disease pathology. Method: A MedLine search was performed to identify studies that use lipidomics for the characterization of HD. Search terms included “Huntington disease”; “lipidomics”; “biomarker discovery”; “NMR”; and “Mass spectrometry”. Results: This review highlights the significance of lipidomics in HD diagnosis and treatment, exploring changes in brain lipids and their functions. Recent breakthroughs in analytical techniques, particularly mass spectrometry and NMR spectroscopy, have revolutionized brain lipidomics research, enabling researchers to gain deeper insights into the complex lipidome of the brain. Conclusions: A comprehensive understanding of the broad spectrum of lipidomics alterations in HD is vital for precise diagnostic evaluation and effective disease management. The integration of lipidomics with artificial intelligence and interdisciplinary collaboration holds promise for addressing the clinical variability of HD. Full article

FMR1 (Fragile X messenger ribonucleoprotein 1), located on the X-chromosome, encodes the multi-functional FMR1 protein (FMRP), critical to brain development and function. Trinucleotide CGG repeat expansions at this locus cause a range of neurological disorders, collectively referred to as Fragile X-related conditions. The most well-known of these is Fragile X syndrome, a neurodevelopmental disorder associated with syndromic facial features, autism, intellectual disabilities, and seizures. However, CGG expansions of different sizes also confer a risk of neuropsychiatric and neurodegenerative disorders throughout the lifespan, through distinct molecular mechanisms. Although Fragile X syndrome is associated with downstream synaptic deficits and neuronal hyperexcitability, work in the past decade has demonstrated that both the causative FMR1 trinucleotide repeat expansion and FMRP itself play important roles in nuclear function and regulation, including non-canonical nucleic acid structure formation and chromatin dynamics. These effects are critical to cellular pathophysiology, although the full extent of their contribution to clinical phenotypes is only just emerging. Here, we present a focused review on some of the nuclear consequences of FMR1/FMRP dysregulation, including parallels in other repeat expansion disorders, ranging from studies in model systems to human cells and tissues. Full article

The yellowfin seabream (Acanthopagrus latus) is an economically important commercial mariculture fish in China and Southeast Asia. Only a few simple sequence repeats (SSRs) of A. latus have been isolated and reported, which has hindered breeding progress. A total of 318,862 SSRs were isolated and characterized from the A. latus genome in this study. All SSRs were 9,069,670 bp in length, accounting for 1.32% of the genome. The density and frequency of SSRs were 468.40 loci/Mb and 13,323.19 bp/Mb, respectively. The major SSRs were dinucleotides (accounting for 76.92%), followed by trinucleotides (15.75%). The most abundant SSR motif was (AC)n (168,390, accounting for 53%), with the highest frequency (245.78 loci/Mb) and density (7304.18 bp/Mb). Most SSRs were located in non-coding regions, such as intergenic regions (34.54%) and introns (56.91%). SSR-containing exons were distributed into 51 gene ontology (GO) terms and significantly enriched in immunity- and growth-related pathways. A total of 217,791 SSR markers were successfully designed. Nine SSR markers were amplified in 29 A. latus individuals, and eight of them possess high polymorphism. The cross-species transferability of 33 out of the 37 tested loci were successfully amplified in Acanthopagrus schlegelii. These results lay the foundation for the molecular marker-assisted breeding and genetic information assessment of A. latus. Full article