Genes最新文献

The manuscript "Hearing Loss: Genetic Testing, Current Advances and the Situation in Latin America" by De Rosa et al [...].

Background/objectives: Crassula aquatica (L.) Schonl. is a very small annual plant growing along riverbanks. Chloroplast (cp) genomes, crucial for photosynthesis, are highly conserved and play a key role in understanding plant evolution. In this study, we conducted cp genome analysis of C. aquatica, aiming to elucidate its phylogenetic position and structural variations. We analyzed and described the features of the complete cp genome of C. aquatica and conducted comparative analysis with the cp genomes of closely related taxa.

Rsults: The cp genome was 144,503 bp in length and exhibited the typical quadripartite structure, consisting of a large single-copy region (LSC; 77,993 bp), a small single-copy region (SSC; 16,784 bp), and two inverted repeats (24,863 bp). The cp genome of C. aquatica comprised 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNAs, and 4 rRNA genes. Comparative genomic analysis of 13 other Crassula species and six outgroups demonstrated highly conserved gene content and order among Crassula species. However, notable differences were observed, including the complete loss of the rpoC1 intron in C. aquatica and several closely related species, which may serve as a synapomorphic trait supporting the monophyly of the subgenus Disporocarpa. We analyzed the nucleotide diversity among 14 Crassula cp genomes and identified five highly variable regions (pi > 0.08) in the IGS regions. Phylogenetic analysis based on 78 PCGs confirmed the monophyly of Crassula and its division into two subgenera: Crassula and Disporocarpa. Although the phylogenetic tree supported the subgeneric classification system, the sectional classification system requires reassessment.

Conclusions: In this study, we conducted a comparative analysis of the cp genome of the genus Crassula. We inferred evolutionary trends within the Crassula cp genome and provided molecular evidence supporting the integration of the genus Tillaea into the genus Crassula. However, as this study does not represent all species within the genus Tillaea, further comprehensive phylogenetic analyses are requrired.

Background/objectives: Acute promyelocytic leukemia (APL) is an aggressive subtype of acute myeloid leukemia (AML), characterized by the hallmark translocation t(15;17) resulting in a PML::RARA fusion. Once diagnosed, APL is now considered to be one of the most treatable forms of AML. However, without early detection and treatment, the disease is associated with rapid deterioration and lethal side effects. Methods: We describe a case of diagnostic APL presenting with a normal karyotype, normal RARA break-apart FISH, and unclear, atypical PML/RARA FISH findings. We used optical genome mapping (OGM) to characterize this atypical PML/RARA fusion. Results: OGM allowed for detection of a PML::RARA fusion resulting from a cryptic and complex insertion of PML::RARA into RARA on 17q21.2 whereby a segment of 15q24.1 was inserted into the 17q21.2. The recipient breakpoint of the insertion was at intron 2 of the RARA gene and the donor breakpoint of the insertion was at exon 5/intron 6 of the PML gene. Conclusions: This is the first report of an insertional PML::RARA fusion into the RARA gene on 17q detected by OGM. OGM has demonstrated its utility in a clinical cytogenetics environment, allowing for clearer characterization and diagnosis of various neoplasms.

Neuromuscular disorders (NMDs) encompass a broad range of hereditary and acquired conditions that affect motor units, significantly impacting patients' quality of life and reproductive health. This narrative review aims to explore in detail the reproductive challenges associated with major hereditary NMDs, including Charcot-Marie-Tooth disease (CMT), dystrophinopathies, Myotonic Dystrophy (DM), Facioscapulohumeral Muscular Dystrophy (FSHD), Spinal Muscular Atrophy (SMA), Limb-Girdle Muscular Dystrophy (LGMD), and Amyotrophic Lateral Sclerosis (ALS). Specifically, it discusses the stages of diagnosis and genetic testing, recurrence risk estimation, options for preimplantation genetic testing (PGT) and prenatal diagnosis (PND), the reciprocal influence between pregnancy and disease, potential obstetric complications, and risks to the newborn.

Background: Febrile seizures (FSs) are the most common form of epilepsy in children aged between six months and five years. The exact cause is unknown, but several studies have demonstrated the importance of genetic predisposition, with increasing involvement of receptors and ion channels. The present study aims to identify novel pathogenic variants in Italian patients with FSs.

Methods: We performed targeted panel sequencing in a cohort of 21 patients with FSs. In silico analysis was performed to predict the pathogenic role of the resulting variants.

Results: We found two novel variants segregating in two families with FSs: c.1021C>G (p.Leu341Val) in the CHRNA2 gene and c.140A>G (p.Glu47Gly) in SCN2A.

Conclusions: The c.1021C>G (p.Leu341Val) variant leads to a codon change of highly conserved leucine to valine at position 341 and is located in segments M3 of the subunit, which is important for channel gating. The c.140A>G (p.Glu47Gly) variant causes a substitution of glutamic acid with glycine at position 47 of the protein, which is highly conserved across the species. Moreover, it is located in the N-terminal domain, a region commonly affected in ASD, which impacts the inactivation kinetics and voltage dependence of steady-state activation. Further analyses are needed to better explain the role of CHRNA2 and SCN2A in the development of febrile seizures.

Background: The differing floret opening times between subsp. indica and subsp. japonica in rice limit the potential for increased hybrid seed production.

Objectives: To elucidate the physiological basis underlying the differences in floret opening time between indica and japonica rice.

Materials: A comparative analysis involved nine indica and ten japonica rice varieties.

Methods: Using paraffin sectioning, transcriptome sequencing, RT-PCR, and endogenous substance quantification, we investigated the structural variations in floral organs, the differences in the initiation timing of floret opening regulatory pathways, and endogenous regulators.

Results: The results indicated insignificant differences in lemma thickness, lodicule thickness, lodicule area, and the coupling-lodicule length between indica and japonica rice. However, japonica rice exhibited larger lodicule-lemma gaps and more vascular bundles compared to indica rice. Within the 9:00 a.m. to 10:00 a.m. interval, the expression of OsAOS1 in α-linolenic acid metabolism and OsISA3 in starch and sucrose metabolism notably increased in indica rice, with no significant change in japonica rice. Additionally, the endogenous JA and α-amylase surged more significantly in indica rice than in japonica rice. The increase in soluble carbohydrate in indica rice is greater than in japonica rice, but the difference is not significant.

Conclusions: These findings suggest that in the process of the floret opening, the α-linolenic acid metabolism and starch and sucrose metabolism are initiated earlier in indica rice, accompanied by a more pronounced elevation in endogenous JA and α-amylase. Furthermore, the smaller lodicule-lemma gap in indica rice contributes to earlier floret opening compared to japonica rice.

Accurate phylogenetic tree construction for species without reference genomes often relies on de novo transcriptome assembly to identify single-copy orthologous genes. However, challenges such as whole-genome duplication (WGD), heterozygosity, gene duplication, and loss can hinder the selection of these genes, leading to limited data for constructing reliable species trees. To address these issues, we developed a new analytical pipeline, OHDLF (Orthologous Haploid Duplication and Loss Filter), which filters orthologous genes from transcript data and adapts parameter settings based on genomic characteristics for further phylogenetic tree construction. In this study, we applied OHDLF to the genus Camellia and evaluated its effectiveness in constructing phylogenetic trees. The results highlighted the pipeline's ability to handle challenges like high heterozygosity and recent gene duplications by selectively retaining genes with a missing rate and merging duplicates with high similarity. This approach ensured the preservation of informative sites and produced a highly supported consensus tree for Camellia. Additionally, we evaluate the accuracy of the OHDLF phylogenetic trees for different species, demonstrating that the OHDLF pipeline provides a flexible and effective method for selecting orthologous genes and constructing accurate phylogenetic trees, adapting to the genomic characteristics of various plant groups.

Background: The cashmere goat is a biological resource that mainly produces cashmere. Cashmere has a soft hand feel and good luster, with high economic value. The quality and yield of cashmere are determined by the process of hair follicle development during the embryonic period.

Methods: In this study, the skin of the Inner Mongolia cashmere goat at different embryonic stages (45, 55, 65, and 75d) was collected, and the differentially expressed lncRNA MSTRG.20890.1 at 75d was obtained by screening. Dual luciferase reporter gene system, qRT-PCR, and EDU experiments were used to verify further the regulatory role and molecular mechanism of the lncRNA in dermal fibroblasts.

Results: Based on the transcriptome database of Inner Mongolia cashmere goat skin at different embryonic stages, which was previously constructed by our group, according to the characteristics of hair follicle development in the embryonic stage, we screened out the lncRNA MSTRG.20890.1 that was down-expressed on the 75-SHFINI day of the embryonic stage. We found that lncRNA MSTRG.20890.1 was mainly located in the cytoplasm of cells, and it could inhibit the proliferation and directional migration of dermal fibroblasts through the chi-miR-24-3p/ADAMTS3 signaling axis, thereby inhibiting the formation of dermal papilla structure at embryonic stage.

Conclusions: This study revealed that lncRNA MSTRG.20890.1 regulated secondary hair follicle morphogenesis and development in cashmere goats through the chi-miR-24-3p/ADAMTS3 signaling axis.

Background: Strawberries are bright in color, sweet and sour in taste, and rich in nutrients and flavonoid compounds such as anthocyanins and proanthocyanidins. The synthesis and accumulation of anthocyanins are the decisive factors that make strawberries appear bright red. From the perspective of plant breeding, a change in flesh color is an important goal.

Methods: In this study, two strawberry plants with different flesh colors were selected, and transcriptome and metabolome analyses were performed during the color change period (S1) and ripening period (S2).

Results: RNA-seq revealed a total of 13,341 differentially expressed genes (DEGs) between and within materials, which were clustered into 5 clusters. A total of 695 metabolites were detected via metabolome analysis, and 243 differentially regulated metabolites (DRMs) were identified. The anthocyanin biosynthesis, starch and sucrose metabolism and glycolysis/gluconeogenesis pathways were determined to be important regulatory pathways for changes in strawberry flesh color through a joint analysis of RNA-seq data and the metabolome. The leucoanthocyanidin reductase (LAR) and chalcone synthase (CHS) gene is a key gene related to anthocyanins, cinnamic acid, and phenylalanine. In addition, through joint RNA-seq and metabolome analyses combined with weighted gene co-expression network analysis (WGCNA), we identified 9 candidate genes related to strawberry flesh color.

Conclusions: Our research findings have laid the groundwork for a more comprehensive understanding of the molecular mechanisms governing the color transformation in strawberry flesh. Additionally, we have identified novel genetic resources that can be instrumental in advancing research related to strawberry color change.

Background: Substance use disorder in the United States represents a complex and growing public health crisis, marked by increasing rates of overdose deaths and the misuse of prescription medications. There is a critical need for furthering the understanding of the molecular and genetic mechanisms that can lead to substance use disorder. Identifying significant variants in the kynurenine pathway could help identify therapeutic targets for intervention.

Methods: The All of Us cohort builder evaluated the frequency of variants of four genes, TDO2, IDO1, IDO2, and KMO, encoding enzymes in the kynurenine pathway. The samples were broken into six cohorts: alcohol, cannabis, cocaine, opioid, other use disorder, and control. Using Chi-square analysis, the frequency of at least one copy of a variant allele was calculated.

Results: Chi-square analysis showed a significant variation in genetic frequency (p-value < 0.005) in 14 of 18 polymorphisms analyzed. The cocaine cohort had the most significant variants (13), cannabis had 11, opioids had 3, other use disorders had 2, and alcohol had 1 significant variant.

Conclusions: This study found associations of polymorphisms in the TDO2, IDO1, IDO2, and KMO genes of individuals with a substance use disorder. These results provide evidence of potential predictors of increased susceptibility to substance use disorder.