Search Results (171)

The bZIP gene family play a crucial role in plant growth, development, and stress responses, functioning as transcription factors. While this gene family has been studied in several plant species, its roles in the endangered woody plant Phoebe bournei remain largely unclear. This study comprehensively analyzed the PbbZIP gene family in P. bournei, identifying 71 PbbZIP genes distributed across all 12 chromosomes. The amino acid count in these genes ranged from 74 to 839, with molecular weights varying from 8813.28 Da to 88,864.94 Da. Phylogenetic analysis categorized the PbbZIP genes into 12 subfamilies (A-K, S). Interspecific collinearity analysis revealed homologous PbbZIP genes between P. bournei and Arabidopsis thaliana. A promoter cis-acting element analysis indicated that PbbZIP genes contain various elements responsive to plant hormones, stress signals, and light. Additionally, expression analysis of public RNA-seq data showed that PbbZIP genes are distributed across multiple tissues, exhibiting distinct expression patterns specific to root bark, root xylem, stem bark, stem xylem, and leaves. We also performed qRT-PCR analysis on five representative PbbZIP genes (PbbZIP14, PbbZIP26, PbbZIP32, PbbZIP67, and PbbZIP69). The results demonstrated significant differences in the expression of PbbZIP genes under various abiotic stress conditions, including salt stress, heat, and drought. Notably, PbbZIP67 and PbbZIP69 exhibited robust responses under salt or heat stress conditions. This study confirmed the roles of the PbbZIP gene family in responding to various abiotic stresses, thereby providing insights into its functions in plant growth, development, and stress adaptation. The findings lay a foundation for future research on breeding and enhancing stress resistance in P. bournei. Full article

This study identifies and classifies resistance gene analogues (RGAs) in the genomes of Brassica nigra, Sinapis arvensis and Sinapis alba using the RGAugury pipeline. RGAs were categorised into four main classes: receptor-like kinases (RLKs), receptor-like proteins (RLPs), nucleotide-binding leucine-rich repeat (NLR) proteins and transmembrane-coiled-coil (TM-CC) genes. A total of 4499 candidate RGAs were detected, with species-specific proportions. RLKs were the most abundant across all genomes, followed by TM-CCs and RLPs. The sub-classification of RLKs and RLPs identified LRR-RLKs, LRR-RLPs, LysM-RLKs, and LysM-RLPs. Atypical NLRs were more frequent than typical ones in all species. Atypical NLRs were more frequent than typical ones in all species. We explored the relationship between chromosome size and RGA count using regression analysis. In B. nigra and S. arvensis, larger chromosomes generally harboured more RGAs, while S. alba displayed the opposite trend. Exceptions were observed in all species, where some larger chromosomes contained fewer RGAs in B. nigra and S. arvensis, or more RGAs in S. alba. The distribution and density of RGAs across chromosomes were examined. RGA distribution was skewed towards chromosomal ends, with patterns differing across RGA types. Sequence hierarchical pairwise similarity analysis revealed distinct gene clusters, suggesting evolutionary relationships. The study also identified homologous genes among RGAs and non-RGAs in each species, providing insights into disease resistance mechanisms. Finally, RLKs and RLPs were co-localised with reported disease resistance loci in Brassica, indicating significant associations. Phylogenetic analysis of cloned RGAs and QTL-mapped RLKs and RLPs identified distinct clusters, enhancing our understanding of their evolutionary trajectories. These findings provide a comprehensive view of RGA diversity and genomics in these Brassicaceae species, providing valuable insights for future research in plant disease resistance and crop improvement. Full article

Polyploidy in plants can enhance stress resistance and secondary metabolite production, offering potential benefits for Clausena lansium (L.) Skeel, a medicinally valuable species. However, systematic studies of polyploidy-induced morphological, anatomical, and metabolic changes in this species are lacking. This study aimed to induce and characterize polyploid C. lansium lines, assess ploidy-dependent variations, and evaluate their impact on bioactive metabolite accumulation. Three cultivars were hybridized, treated with colchicine, and bred, yielding 13 stable polyploid lines confirmed by flow cytometry and chromosome counting. The polyploids exhibited distinct traits, including larger pollen grains, altered leaf margins, increased leaflet numbers, enlarged guard cells with reduced stomatal density, and thicker leaf tissues. Metabolomic analysis revealed that tetraploids accumulated significantly higher levels of flavonoids, alkaloids, and phenolic acids compared to diploids, while triploids showed moderate increases. These findings demonstrate that polyploidization, particularly tetraploidy, enhances C. lansium’s medicinal potential by boosting pharmacologically active compounds. The study expands germplasm resources and supports the development of high-quality cultivars for pharmaceutical applications. Full article

Narenga porphyrocoma (Hance) Bor is a close relative of sugarcane, with traits such as drought resistance, robustness, early maturity, and disease resistance. In this study, we report the first genome assembly of N. porphyrocoma (Hance) Bor GXN1, a diploid species with a chromosomal count of 2n = 30. We assembled the genome into 15 pseudochromosomes with an N50 of 128.80 Mp, achieving a high level of completeness (99.0%) using benchmarking universal single-copy orthologs (BUSCO) assessment. The genome was approximately 1.8 Gb. Our analysis identified a substantial proportion of repetitive sequences, primarily long terminal repeats (LTRs), contributing to 69.12% of the genome. In total, 70,680 protein-coding genes were predicted and annotated, focusing on genes related to drought resistance. Transcriptome analysis under drought stress revealed the key gene families involved in plant physiological rhythms and hormone signal transduction, including aquaporins, late embryogenesis abundant proteins, and heat shock proteins. This research reveals the genome of the diploid wild sugarcane relative N. porphyrocoma (Hance) Bor, encouraging future studies on gene function, genome evolution, and genetic improvement of sugarcane. Full article

Polyploidy plays a significant role in loquat breeding, particularly in triploid breeding for seedless fruit production. Currently, loquat polyploid breeding primarily relies on natural seedling selection and sexual hybridization approaches. In this study, unfertilized ovules from four loquat varieties were in vitro cultured. Gynogenesis and embryoid regeneration were achieved in ‘Xingning 1’ and ‘Huabai 1’, with ‘Xingning 1’ demonstrating the highest gynogenesis efficiency (21.63%). Flow cytometry and chromosome counting revealed that the obtained embryoid lines included haploid, diploid, tetraploid, hexaploid, and chimeric ploidy types. Further characterization of ‘Xingning 1’-derived embryoid lines through SSR markers and whole-genome resequencing confirmed that the haploid, diploid, tetraploid, and hexaploidy embryoid originated from haploid–somatic chimeras, diploid, doubled diploid and tripled diploid, respectively. Metabolic analysis showed a positive correlation between ploidy level and the content of both soluble sugars and organic acids. This study explored a novel platform for polyploid induction in loquat and may provide methodological insights for improvement of other perennial fruit trees. Full article

This study investigated the effects of oryzalin treatments on the induction of polyploids and variants, as well as their subsequent morphological and physiological characteristics, in Lysimachia xiangxiensis, a perennial herbaceous plant belonging to the Primulaceae family that is known for its ornamental value. A total of 52 of the 162 treated stem segments survived after treatments and further developed into plantlets, and significant morphological changes in leaf color and growth status were observed. Using flow cytometry and chromosome counting, plants are categorized into the three variant types (VT1, VT2, and VT3), that is, VT1 and VT2 were diploid aneuploids, while VT3 was triploid. The optimized polyploid induction scheme involved treatment with 0.001% oryzalin for 4 days, resulting in an induction rate of up to 100%. Higher concentrations and longer exposure durations resulted in lower survival and polyploid induction rates of all stem segments during the above-mentioned processing. Observation of morphological features indicated that triploid VT3 vines were longer, with larger and thicker leaves and more guard cells, but lower stomatal density, compared with diploid aneuploids or the wild type. Polyploids outperformed other types in terms of chlorophyll content, net photosynthesis rate, stomatal conductance, and intercellular CO₂ concentration, but had a lower flavonoid content. The results demonstrate that oryzalin can effectively induce polyploidy and variants in L. xiangxiensis, resulting in beneficial changes in morphology and physiological characteristics; this should provide valuable insight into the improvement of excellent varieties in plants. Full article

Lantana camara L. is sold worldwide for ornamental purposes, although it is also characterized by high invasiveness potential. Genetic and molecular data available for L. camara are still poor, and breeding is performed through conventional methods. This study focused on a molecular genotyping analysis through the ddRADseq method on an experimental collection of lantana clonal lines to evaluate the potential of molecular techniques in performing marker-assisted breeding, in favour of variety registration and in guaranteeing plant variety protection for the species. Although high genetic uniformity was observed in the population, a unique molecular profile was assigned to every line, indicating the effectiveness of the approach used. Interestingly, low degrees of heterozygosity were observed. In addition, the possibility of inferring ploidy levels through SNP profiles was assessed since it would avoid the necessity of previous biological knowledge and the use of fresh materials. Ploidy analysis is of high interest for lantana breeding to obtain less invasive triploids. Flow cytometry and chromosome counting were used for inference assessment. An nQuack framework provided correct results for the majority of the clonal lines, confirming its effectiveness. These findings encourage the adoption of molecular systems to help breed minor species such as L. camara. Full article

In vitro anther culture is a technique used to produce haploid plants when regenerating varieties with specific traits. To generate haploid plants with preferred characteristics, an anther culture technique was established for Lilium longiflorum “Show Up”. Morphological characteristics were recorded, including the flower bud length and anther color corresponding to different stages of microspore development. The effects of different flower bud lengths, various concentrations of exogenous plant growth regulators (PGRs), low-temperature pretreatment at 4 °C, and incubation under dark conditions on the induction of callus formation were studied. When the flower buds were 2.2–2.4 cm in length and the microspores were in the mononuclear development phase, callus induction reached the highest rate (15.6%). Callus was not induced when the PGRs 2,4-dichlorophenoxyacetic acid (2,4-D) and kinetin (KT) were added separately to the growth medium, but the highest callus induction rate occurred when anthers were cultured on the medium containing 2,4-D (0.75–1.0 mg/L) and KT (4 mg/L). The low-temperature pretreatment significantly enhanced the induction rate of anthers, but prolonged low-temperature pretreatment reduced the induction rate. The optimal period of cultivation in darkness was 6 d. After 15 days of cultivation, the number of swollen anthers was recorded, and these were transferred onto the differentiation medium Murashige and Skoog (MS) + 1-naphthaleneacetic acid (NAA) (2.0 mg/L), sucrose (30 g/L), and agar (7 g/L) at pH 5.8, whereon 100% differentiation was recorded. Overall, 14 regenerated lines were obtained by in vitro anther culture. Chromosome ploidy was determined by counting chromosomes in the root tips of ten regenerated plants, and four were found to be haploids. This study lays the foundation for anther culture in lilies to shorten the breeding cycle, improve selection efficiency, facilitate efficient genetic transformation, and enable the effective production of both haploid and double-haploid plants. Full article

In Europe, there is a growing concern for animal welfare, encompassing both their rights and health. Consequently, identifying biomarkers that predict serious pathological conditions has become crucial in veterinary medicine. The Buccal Micronucleus Cytome (BMCyt) assay is a minimally invasive method that uses biomarkers to evaluate DNA damage and chromosomal instability, using exfoliated buccal cells. A rising frequency of anomalies, such as micronuclei formation, strongly indicates an elevated risk of cancer, neurodegenerative diseases, or accelerated aging, potentially originating from exposure to genotoxins and cytotoxins. This method has been validated in humans, but very little research has been conducted on animals. This work aims to provide a detailed description of an optimized method for collecting buccal exfoliated cells in dogs and to characterize a biomarker related to genomic damage using optical and fluorescent microscopy. Samples from dogs in breeding kennels, including pregnant animals, were tested for chromosomal instability. By following procedures similar to those used in humans, we were able to detect and count major nuclear abnormalities. The percentage of micronuclei was higher compared to other studies. Technical aspects, such as avoiding artifacts and ensuring prior training of the operator, must be taken into account. This work validated the BMCyt method for collecting and processing samples in dogs, potentially enhancing the understanding of micronuclei as biomarkers for pre-pathological states in canines. Full article

A QTL on chromosome 4D of the Juglans microcarpa × J. regia genome that co-located resistance against Agrobacterium tumefaciens, Phytophthora pini, and Phytophthora cinnamomi disease scores was investigated for additional traits. Phenotypic data for Pratylenchus vulnus counts and tree height were analyzed in this study for the same hybrids previously used to identify this QTL. Using the same GBS genotype data, the same co-located QTL for A. tumefaciens and Phytophthora spp. disease scores were reproduced and the QTL for P. vulnus counts and tree height were co-located with resistance to A. tumefaciens and Phytophthora spp. Moreover, we found GBS genotype data to harbor additional genetic variation unrelated to any of the traits analyzed. Marker-assisted and genomic selection models were created and assessed for their performance in selection. The ability to predict traits using SNP data was strongest with two-year tree height, followed by A. tumefaciens disease score, three-year tree height, Phytophthora spp. disease score, and P. vulnus counts. These results suggest a shared mechanism of action that links disease to tree height. Moreover, deploying these selection models would assist efforts in walnut improvement for rootstock genotypes. Full article

The anthrax pathogen Bacillus anthracis can remain dormant as spores in soil for many years. This applies to both natural foci and to sites of anthropogenic activity such as tanneries, abattoirs, or wool factories. The A.Br.075 (A-branch) clade (also known as A.Br.Sterne) is prominent not only because it comprises several outbreak strains but even more so because spore preparations of its namesake, the Sterne strain, are counted among the most utilized anthrax animal vaccines. In this study, we genome-sequenced and analyzed 56 additional B. anthracis isolates of the A.Br.075 clade. Four of these we recently retrieved from soil samples taken from a decades-long abandoned tannery. The other 52 strains originated from our archival collection from the 20th century. Notably, the extended phylogeny of the A.Br.075 clade indicated that many of the newly added chromosomes represent basal members, some of which are among the most basal strains from this lineage. Twelve new strains populate a very deep-branching lineage we have named A.Br.Ortho-Sterne (also known as A.Br.076). A further 11 isolates amend the clade named A.Br.Para-Sterne (A.Br.078). Finally, some of the terminal clusters of the clade named A.Br.Eu-Sterne appear to be replete with (near) identical isolates, possibly a result of widespread use of the Sterne vaccine and of its re-isolation from vaccination-related animal anthrax outbreaks. From the accrued new phylogenetic information, we designed and tested a variety of new SNP-PCR assays for rapid and facile genotyping of unassigned B. anthracis genomes. Lastly, the successful isolation of live B. anthracis from a long-abandoned tannery reemphasizes the need for continued risk awareness of such sites. Full article

Acute lymphoblastic leukaemia is the most common childhood malignancy that remains a leading cause of death in childhood. It may be characterised by multiple known recurrent genetic aberrations that inform prognosis, the most common being hyperdiploidy and t(12;21) ETV6::RUNX1. We aimed to assess the applicability of a new imaging flow cytometry methodology that incorporates cell morphology, immunophenotype, and fluorescence in situ hybridisation (FISH) to identify aneuploidy of chromosomes 4 and 21 and the translocation ETV6::RUNX1. We evaluated this new “immuno-flowFISH” platform on 39 cases of paediatric ALL of B-lineage known to have aneuploidy of chromosomes 4 and 21 and the translocation ETV6::RUNX1. After identifying the leukaemic population based on immunophenotype (i.e., expression of CD34, CD10, and CD19 antigens), we assessed for copy numbers of loci for the centromeres of chromosomes 4 and 21 and the ETV6 and RUNX1 regions using fluorophore-labelled DNA probes in more than 1000 cells per sample. Trisomy 4 and 21, tetrasomy 21, and translocations of ETV6::RUNX1, as well as gains and losses of ETV6 and RUNX1, could all be identified based on FISH spot counts and digital imagery. There was variability in clonal makeup in individual cases, suggesting the presence of sub-clones. Copy number alterations and translocations could be detected even when the cell population comprised less than 1% of cells and included cells with a mature B-cell phenotype, i.e., CD19-positive, lacking CD34 and CD10. In this proof-of-principle study of 39 cases, this sensitive and specific semi-automated high-throughput imaging flow cytometric immuno-flowFISH method has been able to show that alterations in ploidy and ETV6::RUNX1 could be detected in the 39 cases of paediatric ALL. This imaging flow cytometric FISH method has potential applications for diagnosis and monitoring disease and marrow regeneration (i.e., distinguishing residual ALL from regenerating haematogones) following chemotherapy. Full article

N6-methyladenosine (m6A) modification is a key methylation modification involved in reproductive processes. Myostatin gene editing (MT) in cattle is known to enhance muscle mass and productivity. However, the changes in m6A modification in MT bull sperm remain poorly understood. In the MT and wild-type (WT) groups, we identified 25,542 and 22,253 m6A peaks, respectively, mainly concentrated in the coding sequence (CDS) and 3′ untranslated region (UTR) of genes. The MT group showed an increase in gene transcription, but there was no significant difference in the overall m6A peaks pattern. There was also no significant difference in m6A motif and chromosome distribution between MT and WT groups. Most genes had less m6A modification sites. A total of 1120 m6A peaks were significantly different, corresponding to 1053 differentially m6A-methylated genes (DMMGs). These DMMGs are mainly associated with G protein-coupled receptor signaling pathways and the overall composition of the cell membrane. Furthermore, an MCL clustering analysis of 111 differentially m6A-methylated and expressed genes identified seven key genes (RHOA, DAAM1, EXOC4, GNA12, PRICKLE1, SCN1A, and STXBP5L), with the cytoskeleton and migration-related gene, RHOA, being the most important gene located at the center of the gene network. However, the analysis of sperm morphology and motility indicated no significant changes in semen volume, sperm count, sperm viability, plasma membrane integrity, acrosome membrane integrity, or mitochondrial membrane integrity. This study provides a map of m6A methylation in spermatozoa from MT and WT bulls, identifies key differential m6A genes that are affected by the myostatin gene but do not affect sperm morphology and viability in MT bulls, and provides a theoretical basis for the breeding quality of MT bulls. Full article

Deletion and duplication in the human 16p11.2 chromosomal region are closely linked to neurodevelopmental disorders, specifically autism spectrum disorder. Data from neuroimaging studies suggest white matter microstructure aberrations across these conditions. In 16p11.2 deletion and duplication carriers, potential gene dosage effects may impact white matter organisation, contributing to phenotypes including impaired cognition. However, the biological mechanisms underlying this white matter pathology remain unclear. To bridge this knowledge gap, we utilised mouse models of 16p11.2 deletion and duplication to explore changes in corpus callosum oligodendrocytes, myelination, axon caliber, and astrocytes. Immunofluorescence staining was employed to measure lineage and mature oligodendrocyte numbers, as well as myelin basic protein and glial fibrillary acidic protein fluorescence intensity. Transmission electron microscopy was utilised to evaluate axonal structural alterations related to myelin, such as myelinated axon percentage, diameter, myelin thickness, and g-ratio. Our findings reveal changes in the number of mature oligodendrocytes, myelination levels, axon diameter, and astrocytes in the corpus callosum of mice with 16p11.2 deletion and duplication. Deletion mice displayed a tendency toward reduced counts of mature oligodendrocytes and myelination levels, while duplication mice exhibited a notable increase. Axon diameter variations included a significant increase in axon diameter and myelin thickness in both deletion and duplication mice, but with irregular structure in duplication mice. Variances in astrocytes between genotypes showed significant early increases in development for both deletion and duplication mice compared to wild-type mice, with this rise sustained in duplication mice but significantly diminished in deletion mice at a later stage. Our research reveals changes in the biological mechanisms impacting white matter. Comparison of reciprocal trends in 16p11.2 deletion and duplication mice with wild-type mice suggests the possibility of gene dosage effects. Identification of these mechanisms offers an initial step in unveiling therapeutic targets for associated neurodevelopmental disorder phenotypes. Full article

Background/Objectives: All 11 metallothionein protein-coding genes are located on human chromosome 16q13. It is unique among human genetics to have an entire pathway’s genes clustered in a short chromosomal region. Since solid tumors, particularly high-grade serous ovarian cancer (HGSC), exhibit high rates of monoallelic aneuploidy, this region is commonly lost. Studies have not yet been performed to determine what vulnerability may be created in cancer cells with low metallothionein expression. Here, a screen of FDA-approved cancer small molecule drugs for those best targeting low metallothionein ovarian cancer was completed. Methods: Screening methods were tested and compared using vehicle-treated negative controls and cadmium chloride, a positive control for cell loss selective for low metallothionein cells. CAOV3 cells, which are unique in their expression of only two metallothionein isoforms, were used, with or without shRNA knockdown of the predominantly expressed MT2A gene. A library of FDA-approved molecules was then screened. Results: The optimal assay utilized Hoechst 33342 nuclear staining and mechanized fluorescent microscope counting of cell content. Encorafenib, an RAF inhibitor, was identified as the most selective for enhanced cytotoxicity in MT2A knockdown cells compared to scrambled controls. Conclusions: The nuclear stain Hoechst 33342, assessed by fluorescence microscopy, provides a low variance, moderate throughput platform for cancer cell loss screens. Low metallothionein ovarian cancer cells exhibit a vulnerability to the RAF inhibitor encorafenib. Full article