Search Results (452)

Transposable elements (TEs) serve as important drivers mediating polyploidization events and phenotypic diversification in plant genomes. However, the dynamic changes in various TE subclasses post-polyploidization and their mechanisms of influencing phenotypic variation require further investigation. The allopolyploid Gossypium species, originating from two diploid progenitors, provide an ideal model for studying TE dynamics following polyploidization. This study investigated TE dynamics post-polyploidization based on 21 diploid and 7 polyploid cotton genomes. The Tekay subclass of the Gypsy serves as a major driver of Gossypium genome evolution, as it underwent two burst events in the At-subgenome and its progenitor, exhibiting the highest abundance, longest length, and largest proportion among all TE subclasses. In contrast, the Gopia superfamily Tork subclass has lower abundance but greater genic association, facilitating environmental adaptation and phenotypic variation. Additionally, a pan-TE-related structural variation, the pan-TRV map, was constructed by integrating resequencing data from 256 accessions. Genome-wide analysis of 28 cotton genomes identified 142,802 TRVs, among which 72,116 showed polymorphisms in the 256 G. hirsutum accessions. The Gypsy superfamily, particularly the Tekay subclass, has been identified as a major source of TRVs, while Copia-type elements demonstrate significantly greater enrichment in gene-proximal genomic regions. A total of 334 TRVs exhibiting statistically significant associations with 10 key phenotypic traits, including 164 TRVs affecting yield components and 170 TRVs determining fiber quality. This investigation delineates the evolutionary significance of transposable elements in Gossypium genome diversification while simultaneously providing novel functional markers and potential editing targets for genetic dissection and molecular breeding of key agronomic traits in cotton. Full article

Polyploidisation is a very common phenomenon in the plant kingdom and plays a key role in plant evolution and breeding. It promotes speciation and the extension of biodiversity. It is estimated that approximately 47% of flowering plant species are polyploids, derived from two or more diploid ancestral species. In natural populations, the predominant methods of whole-genome multiplication are somatic cell polyploidisation, meiotic cell polyploidisation, or endoreduplication. The formation and maintenance of polyploidy is accompanied by a series of epigenetic and gene expression changes, leading to alterations in the structural, physiological, and biochemical characteristics of polyploids relative to diploids. This article provides information on the mechanisms of formation of natural and synthetic polyploids. It presents a number of examples of the effects of polyploidisation on the composition and content of secondary metabolites of polyploids, providing evidence of the importance of the phenomenon in plant adaptation to the environment, improvement of wild species, and crops. It aims to gather and systematise knowledge on the effects of polyploidisation on plant physiological traits, including stomatal conductance (Gs), transpiration rate (Tr), light saturation point (LSP), as well as the most important photosynthetic parameters determining biomass accumulation. The text also presents the latest findings on the adaptation of polyploids to biotic and abiotic stresses and explains the basic mechanisms of epigenetic changes determining resistance to selected stress factors. Full article

In this study, GH19 chitinase (Chi) gene family was systematically identified and characterized using genomic assemblies from four cotton species: Gossypium barbadense, G. hirsutum, G. arboreum, and G. raimondii. A suite of analyses was performed, including genome-wide gene identification, physicochemical property characterization of the encoded proteins, subcellular localization prediction, phylogenetic reconstruction, chromosomal mapping, promoter cis-element analysis, and comprehensive expression profiling using transcriptomic data and qRT-PCR (including tissue-specific expression, hormone treatments, and Fusarium oxysporum infection assays). A total of 107 GH19 genes were identified across the four species (35 in G. barbadense, 37 in G. hirsutum, 19 in G. arboreum, and 16 in G. raimondii). The molecular weights of GH19 proteins ranged from 9.9 to 97.3 kDa, and they were predominantly predicted to localize to the extracellular space. Phylogenetic analysis revealed three well-conserved clades within this family. In tetraploid cotton, GH19 genes were unevenly distributed across 12 chromosomes, often clustering in certain regions, whereas in diploid species, they were confined to five chromosomes. Promoter analysis indicated that GH19 gene promoters contain numerous stress- and hormone-responsive motifs, including those for abscisic acid (ABA), ethylene (ET), and gibberellin (GA), as well as abundant light-responsive elements. The expression patterns of GH19 genes were largely tissue-specific; for instance, GbChi23 was predominantly expressed in the calyx, whereas GbChi19/21/22 were primarily expressed in the roots and stems. Overall, this study provides the first comprehensive genomic and functional characterization of the GH19 family in G. barbadense, laying a foundation for understanding its role in disease resistance mechanisms and aiding in the identification of candidate genes to enhance plant defense against biotic stress. Full article

Diploid Vaccinium fuscatum is a wild blueberry species with a low chilling requirement, an evergreen growth habit, and soil adaptability to southeast US growing regions. Regardless of its potential to improve the abiotic and biotic resilience of cultivated blueberries, this species has rarely been used for blueberry breeding. One hurdle is the ploidy barrier between diploid V. fuscatum and tetraploid cultivated highbush blueberries. To overcome the ploidy barrier, vegetative shoots micro-propagated from one genotype of V. fuscatum, selected because it grew vigorously in vitro and two southern highbush cultivars, ‘Emerald’ and ‘Rebel,’ were treated with colchicine. While shoot regeneration was severely repressed in ‘Emerald’ and ‘Rebel,’ shoot production from the V. fuscatum clone was not compromised at either 500 µM or 5000 µM colchicine concentrations. Due to the high number of shoots produced in vitro via the V. fuscatum clone shoots of this clone that had an enlarged stem diameter in vitro were subjected to flow cytometer analysis to screen for induced polyploidy. Sixteen synthetic tetraploid V. fuscatum, one synthetic octoploid ‘Emerald,’ and three synthetic octoploid ‘Rebel’ were identified. Growth rates of the polyploid-induced mutants were reduced compared to their respective wildtype controls. The leaf width and length of synthetic tetraploid V. fuscatum and synthetic octoploid ‘Emerald’ was increased compared to the wildtypes, whereas the leaf width and length of synthetic octoploid ‘Rebel’ were reduced compared to the wildtype controls. Significant increases in stem thickness and stomata guard cell length were found in the polyploidy-induced mutant lines compared to the wildtypes. In the meantime, stomata density was reduced in the mutant lines. These morphological changes may improve drought tolerance and photosynthesis in these mutant lines. Synthetic tetraploid V. fuscatum can be used for interspecific hybridization with highbush blueberries to expand the genetic base of cultivated blueberries. Full article

The European plum (Prunus domestica L.) is a hexaploid species that is grown worldwide for its tasty fruits. Many pomological forms and varieties exist, and thus it is important for genebank curators, breeders, growers, and/or control authorities to distinguish them with certainty. The purpose of this study was to select and verify a set of simple sequence repeat (SSR) markers for reliable genotyping, and to optimize their use in a one-reaction format for easy routine practice. After testing 78 SSR markers from different diploid Prunus species, 8 SSR markers were selected, multiplexed, and successfully verified as being able to distinguish all 242 unique genotypes tested. The selected markers were relatively easily scored and highly heterogenic, giving more than 35 alleles/genotype on average. The allele atlas was created to become a valuable tool for allele calling that should lead to standardized and reliable genotyping results between laboratories. The population analysis confirmed high diversity of the Czech germplasm collection used. The kit was also successfully tested for diploid “plums” of various origins and interspecies hybrids, as these are sometimes phenotypically indistinguishable from hexaploid European plums. The one-tube approach substantially simplified the plum genotyping laboratory workflow, minimizes errors, and saves labor, time, and money. Full article

Grass carp is an economically important cultured species in China. Triploid embryo production is widely applied in aquaculture to achieve reproductive sterility, improve somatic growth, and reduce ecological risks associated with uncontrolled breeding. In this study, a simple cold shock method for inducing triploid grass carp was developed. The triploid induction rate of 71.73 ± 5.00% was achieved by applying a cold treatment at 4 °C for 12 min, starting 2 min after artificial fertilization. Flow cytometry and karyotype analysis revealed that triploid individuals exhibited a 1.5-fold increase in DNA content compared to diploid counterparts, with a chromosomal composition of 3n = 72 (33m + 36sm + 3st). Additionally, embryonic transcriptome analysis demonstrated that, in the cold shock-induced embryos, genes associated with abnormal mesoderm and dorsal–ventral axis formation, zygotic genome activation (ZGA), and anti-apoptosis were downregulated, whereas pro-apoptotic genes were upregulated, which may contribute to the higher abnormal mortality observed during embryonic development. Overall, this study demonstrates optimized conditions for inducing triploidy in grass carp via cold shock and provides insights into the transcriptomic changes that take place in cold shock-induced embryos, which could inform future grass carp genetic breeding programs. 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

Trematode infections caused by Fasciolidae and Paramphistomidae remain widespread in livestock, resulting in substantial economic losses. The two distinct fluke families are difficult to distinguish morphologically, and molecular identification provides the most reliable means of accurate diagnosis. In Ecuador, however, molecular data on these parasites are scarce. In this study, we collected trematodes from cattle rumen and bile ducts, molecularly identified them, and assessed their phylogenetic relationship to Fasciola hepatica to determine their introduction pathways into South America. Genomic DNA was extracted, and PCR was used to amplify the ITS2 (~500 bp) and COXI (~266 bp) regions; all amplicons were Sanger-sequenced. Phylogenetic trees for both markers were constructed using a Maximum Likelihood approach with 1000 bootstrap replicates in CIPRES v3.3. The rumen fluke exhibited 99% ITS2 and COXI similarity to an Indian Cotylophoron cotylophorum strain, while the bile-duct fluke showed 99% ITS2 and 100% COXI similarity to F. hepatica isolates from Australia and Nigeria, respectively. Distinct single-nucleotide polymorphisms (SNPs) in the ITS2 chromatograms suggest a diploid genome structure in both trematode species. This is the first report of C. cotylophorum in Ecuador, and its presence may be linked to the late 19th-century introduction of Zebu cattle (Bos taurus indicus) from India. Full article

Soil salinization threatens agriculture by inducing osmotic stress, ion toxicity, and oxidative damage. SnRK2 genes are involved in plant stress responses, but their roles in salt stress response regulation of tobacco remain unclear. Through genome-wide analysis, we identified 54 SnRK2 genes across four Nicotiana species (N. tabacum, N. benthamiana, N. sylvestris, and N. tomentosiformis). Phylogenetic reconstruction clustered these genes into five divergent groups, revealing lineage-specific expansion in diploid progenitors (N. tomentosiformis) versus polyploidy-driven gene loss in N. tabacum. In silico promoter analysis uncovered regulatory networks involving light, hormones, stress, and developmental signals, with prevalent ABA-responsive elements (ABREs) supporting conserved stress-adaptive roles. Structural analysis highlighted functional diversification through variations in intron–exon architecture and conserved kinase motifs. This study provides a genomic atlas of SnRK2 evolution in Nicotiana, offering a foundation for engineering salt-tolerant crops. 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

The genus Vigna Savi (Leguminosae Juss.) comprises approximately 150 species, classified into five subgenera, most of which exhibit a diploid chromosome number of 2n = 22. However, the wild species Vigna lasiocarpa (Benth) Verdc. (V. subg. Lasiospron) is notable for its dysploid chromosome number of 2n = 20. This study aimed to elucidate the chromosomal events involved in the karyotype evolution of V. lasiocarpa (Vla). We used oligopainting probes from chromosomes 1, 2, 3, and 5 of Phaseolus vulgaris L. and two barcode probes from the genome of V. unguiculata (L.) Walp. Additionally, bacterial artificial chromosomes (BACs) from V. unguiculata and P. vulgaris, along with a telomeric probe from Arabidopsis thaliana (L.) Heynh., were hybridized to V. lasiocarpa metaphase chromosomes to characterize Vla3, Vla7/5, and Vla9. Our findings revealed conserved oligo-FISH patterns on chromosomes 2, 6, 8, 10, and 11 between V. unguiculata and V. lasiocarpa. Paracentric and pericentric inversions were identified for Vla3 and Vla9, respectively. Our integrative approach revealed that the dysploid chromosome originated from an “end-to-end fusion” of homoeologous chromosomes 5 and 7. This is the first report on the chromosomal mechanisms underlying descending dysploidy in Vigna, providing new insights into the evolutionary dynamics of the genus. Full article

Cannabis sativa L. is a dioecious species known to produce over 1600 chemical constituents, including more than 180 cannabinoids classified into 11 structural groups. These bioactive compounds are predominantly synthesised in the glandular trichomes of female inflorescences. However, sex determination in C. sativa is influenced by both genetic and environmental factors, often leading to the development of male flowers on female plants. This unintended fertilisation reduces cannabinoid yield and increases genetic heterogeneity and challenges in medical cannabis production. Haploid and doubled haploid (DH) technologies offer a promising solution by rapidly generating homozygous lines from gametophytic (e.g., unpollinated ovaries and ovules) or sporophytic tissues (e.g., anthers and microspores) via in vitro culture or chromosome reduction during hybridisation. In land plants, the life cycle alternates between a diploid sporophyte and a haploid gametophyte generation, both capable of mitotic division to form multicellular bodies. A single genome regulates this phase transition and encodes the molecular, genetic, and epigenetic mechanisms that precisely control the developmental processes unique to each generation. While the application of haploid technology in C. sativa remains limited, through recent progress in haploid induction (HI) and CRISPR-based genome editing, the direct modification of haploid gametes or embryos enables the creation of null homozygous lines following chromosome doubling, improving genetic uniformity. Understanding the molecular mechanisms of spontaneous chromosome doubling may further facilitate the development of elite cannabis genotypes. Ultimately, enhancing the efficiency of DH production and optimising genome editing approaches could significantly increase the speed of genetic improvement and cultivar development in Cannabis sativa. Full article

Background: The genus Dugesia (Platyhelminthes: Tricladida) includes a large diversity of free-living freshwater flatworms and is important for studies on regeneration and evolution. This study aims to describe a newly discovered asexual planarian species from southern China and explore its genetic characteristics and regenerative abilities. Methods: An integrative taxonomic analysis was conducted using morphology, karyology, histology, molecular phylogeny (18S, 28S, COI, mitogenome), and genome size estimation via flow cytometry. Regeneration was assessed by standardized amputations, and long-term asexual propagation was observed under laboratory conditions for three years. Results: Phylogenetic analyses using nuclear (18S, 28S rDNA) and mitochondrial (COI, mitogenome) markers confirmed that Dugesia cantonensis Guang Yang & Zhinan Yin, sp. nov. forms a distinct clade within Dugesia. Its 18,125 bp mitogenome contains 36 genes but lacks atp8. D. cantonensis displays a distinctive morphology, notably a pharynx located near the head. All body fragments regenerated into complete individuals within nine days. Remarkably, one individual produced ~10⁵ clonal descendants over three years via repeated amputation, maintaining stable regenerative ability and growth across generations. Karyological analysis revealed a diploid karyotype (2n = 16) consisting of eight chromosome pairs. The nuclear genome size was estimated at approximately 2.5 Gb using Danio rerio as an internal standard. Histological examination showed no detectable reproductive organs, confirming the species as an exclusively asexual lineage. Conclusions: D. cantonensis represents a new planarian strain with stable propagation and regeneration. These features make it a valuable resource for regenerative biology and comparative genomic studies. Full article

Interspecific and intersectional crosses have introduced valuable genetic traits for blueberry (Vaccinium sect. Cyanococcus) cultivar improvement. Introgression from Vaccinium species at the diploid, tetraploid, and hexaploid levels has been found in cultivated blueberries. Continued efforts to integrate wild blueberry genetic resources into blueberry breeding are essential to broaden the genetic diversity of cultivated blueberries. However, performing heteroploid crosses among Vaccinium species is challenging. Polyploid induction through tissue culture has been useful in bridging ploidy barriers. Mixoploid or chimeric shoots often are produced, along with solid polyploid mutants. These chimeras are mostly discarded because of their genome instability and the difficulty in identifying periclinal mutants carrying germline mutations. Since induced polyploidy in blueberries often results in a low frequency of solid mutant lines, it is important to recover solid polyploids through chimera dissociation. In this study, two vegetative propagation methods, i.e., axillary and adventitious shoot induction, were evaluated for their efficiency in chimera dissociation. Significantly higher rates of chimera dissociation were found in adventitious shoot induction compared to axillary shoot induction. Approximately 89% and 82% of the adventitious shoots induced from mixoploid lines 145.11 and 169.40 were solid polyploids, respectively, whereas only 25% and 53% of solid polyploids were recovered through axillary shoot induction in these lines. Effective chimera dissociation provides useful and stable genetic materials to enhance blueberry breeding. Full article

Sphaerophoria rueppellii is a Palearctic hoverfly widely used as a native biocontrol agent against aphid pests in Mediterranean agroecosystems. In this study, we present a cytogenetic analysis and characterization of the mitochondrial genome of this species. Chromosomal preparations, obtained from third-instar larvae, were used for conventional staining, DAPI staining and C-banding techniques, and major ribosomal DNA (rDNA) location by fluorescence in situ hybridization (FISH). Karyotype analysis revealed a diploid number of 2n = 10, with heterochromatic blocks in the pericentromeric regions of all autosomes and rDNA clusters on both sex chromosomes. The complete mitochondrial genome (16,605 bp) was sequenced and annotated using next-generation sequencing and assembly pipelines. It contains the typical 37 mitochondrial genes and a highly A + T-rich control region with tandem repeats. Gene order and codon usage were conserved compared with other Syrphidae. Phylogenetic reconstruction based on mitochondrial protein-coding genes clarifies the species’ placement within the Syrphini tribe. Our results contribute valuable genomic and cytogenetic information that supports comparative analyses and may aid in taxonomic clarification within the genus. These findings also offer key data that could guide the genetic optimization of S. rueppellii as an efficient, environmentally safe biological control agent in sustainable agriculture. Full article