Ploidy Level Research Articles

High mountains of central Europe as a refuge of surprising cytotype diversity of Huperzia selago (Lycopodiaceae)

AbstractPolyploidization is pivotal in plant speciation, affecting adaptability, ecological tolerance and specific geographical distribution patterns. While cytotype diversity has been extensively studied in angiosperms and ferns, knowledge in homosporous lycophytes remains very limited. Our study addresses this gap, focusing on the homosporous lycophyte Huperzia selago in Central Europe. The genome size of 1330 individuals from 208 populations were assessed via flow cytometry, revealing five distinct cytotypes (2x, 3x, 4x, 5x, 6x). Challenging chromosome counting using gemmae roots yielded average counts of 140 (2x), 204 (3x), and 262 (4x) chromosomes. The hexaploid genome size (29 pg) approached the upper limits reported for lycophytes. Tetraploids were the most abundant (72.7%), while triploids (21.3%) were less common, while the remaining cytotypes comprised less than 5% of the dataset. Geographical separation of cytotypes was not observed. However, uncommon cytotypes were associated with the Alps and triploids also occured in the highest parts of Western Carpathians. Around 27.3% of populations exhibited multiple cytotypes. Except for atypical diploids, spore abortion differed between even (21.8%) and odd ploidies (65.2%). Microcharacter (stoma, spore) proportions did not linearly correspond with increasing ploidy levels. The high ploidy-level diversity and cytotype coexistence in Central European H. selago match the well documented patterns in ferns and angiosperms. These findings provide valuable insights into lycophyte polyploidy, underscoring the necessity for broader geographical sampling and application of molecular studies to elucidate phylogenetic relationships and taxonomic classifications within the genus Huperzia.

Accession-specific parent-of-origin dependent and independent genome dosage effects on salt tolerance in Arabidopsis thaliana.

Improving the salt stress tolerance of crops is an important goal in plant breeding. Changes in the number of chromosome sets (i.e. ploidy level) cause genome dosage effects which can result in enhanced or novel traits. Maternal inheritance versus paternal inheritance of the same chromosome sets can have differential epigenetic effects on traits of F1 offspring. Hence, genome dosage effects can be parent-of-origin independent or dependent. The model plant Arabidopsis thaliana displays both genome dosage and parent-of-origin effects on plant growth under non-stress conditions. Using an isogenic ploidy series of diploid, triploid and tetraploid lines, we investigate the extent of genome dosage effects and their parent-of-origin dependency on in vitro salt stress tolerance of seedlings across 10 different A. thaliana accessions (genetic backgrounds). We detected genome dosage effects on salt stress tolerance for tetraploid lines in five accessions. In addition, through the generation of isogenic reciprocal F1 triploid lines, both parent-of-origin dependent and independent genome dosage effects on salt stress tolerance were detected. Thus, our results indicate not only that genome dosage balance effects can have significant impacts on abiotic stress tolerance in A. thaliana but also that parent-of-origin specific genome dosage effects can affect salt stress tolerance in plants.

Polyploidy and hybridization in the Mediterranean: unravelling the evolutionary history of Centaurium (Gentianaceae).

Polyploidy is considered one of the main mechanisms of plant evolution and speciation. In the Mediterranean basin, polyploidy has contributed to making this region a biodiversity hotspot, along with its geological and climatic history and other ecological and biogeographic factors. The Mediterranean genus Centaurium Hill (Gentianaceae) comprises ca. 25 species, of which 60% are polyploids, including tetraploids and hexaploids. To date, the evolutionary history of centauries has been studied using Sanger sequencing phylogenies, which have been insufficient to fully understand the phylogenetic relationships in this lineage. The goal of this study is to gain a better understanding of the evolutionary history of Centaurium by exploring the mechanisms that have driven its diversification, specifically hybridization and polyploidy. We aim at identifying the parentage of hybrid species, at the species or clade level, as well as assessing whether morphological traits are associated with particular ploidy levels. We sequenced RADseq markers from 42 samples of 28 Centaurium taxa, and performed phylogenomic analyses using maximum likelihood, summary coalescent SVDquartets and NeighborNet approaches. To identify hybrid taxa, we used Phylonetworks and the fastStructure algorithm. To infer the putative parental species of the allopolyploids, we employed genomic analyses (SNIPloid). The association between different traits and particular ploidy levels was explored with NMDS. Our phylogenetic analyses confirmed the long-suspected occurrence of recurrent hybridization. The allopolyploid origin of the tetraploid C. serpentinicola and the hexaploids C. mairei, C. malzacianum and C. centaurioides were also confirmed, unlike that of C. discolor. We inferred additional signatures of hybridization events within the genus and identified morphological traits differentially distributed in different ploidy levels. This study highlights the important role that hybridization has played in the evolution of a Mediterranean genus such as Centaurium, leading to a polyploid complex, which facilitated its diversification and may exemplify that of other Mediterranean groups.

Distribution, diversity and genetic structure of alders (Alnus lusitanica and A. glutinosa) in Spain

Alders (Alnus spp., Betulaceae) are keystone pioneer species in riparian habitats. In the Mediterranean Basin, where the diploid Alnus glutinosa coexists with the recently discovered tetraploid A. lusitanica, the distribution, diversity and genetic structure of alder species is unknown. The main objectives of this study were to report the distribution of A. glutinosa and A. lusitanica, quantify the local genetic diversity of populations and explore the presence of putative hybrids resulting from the coexistence of A. lusitanica and A. glutinosa individuals in Spain. We assessed 627 individuals from 22 natural alder populations by combining chromosome counts, flow cytometry and microsatellite markers (SSRs) analyses. The ploidy analysis, validated through chromosome counts, revealed the presence of 92 diploid and 535 tetraploid trees from three A. glutinosa and 18 A. lusitanica pure populations, respectively. Notably, no hybrids were detected, not even in Assa, the only population where both species co-occur. The occurrence of mixed ploidy level in alder is reported for the first time in Spain (Assa, Logroño, within the Ebro basin). SSR analysis revealed robust genetic differentiation between the two species and distinctive patterns of variation within A. glutinosa. The high level of differentiation observed was supported by the most probable population clustering determined through pca and structure analyses, along with the identification of a high number of private alleles. For A. lusitanica, the results revealed three distinct genetic groups, geographically distributed. Positive genetic and geographical distance correlations indicated that differentiation could have been driven by isolation by distance. In light of the results, A. lusitanica is the most representative, widespread and genetically variable alder species in Spain, and A. glutinosa is restricted to the north-east of the country. The Ebro riverbank is a contact zone between A. lusitanica and A. glutinosa species, in which no evidence of hybridization was detected yet. Finally, with focus on management, our findings may suggest considering A. lusitanica as a new species, which should be regulated by the forest reproductive material legislation.

Селекционна оценка на някои показатели за качеството на фуража при многогодишнишни житни треви – пасищен райграс (Lolium perenne L.)

The chemical composition of 21 accessions of Lolium perenne L. from the collection nursery of Institute of Forage Crops - Pleven, for three cuts each year, for the period 2017-2018, was evaluated as follows: crude protein (CP), % – according to Kjeldahl‘s method; crude fiber (CF), % – by Weende analysis; water-soluble carbohydrates (WSC) – according to Ermakov et al. Statistical processing of the data was performed, which included regression, correlation, two-factor ANOVA a nd cluster a nalyses. There is a t rend i n both years for the first cut to be lowest in crude protein (CP); relatively high in crude fiber (CF) and highest in water soluble carbohydrates (WSC) content. In the second and third cuts, crude protein increases; crude fiber content varies within different limits, but generally decreases; and the amount of water-soluble carbohydrates also decreases. The genotype–environment (accessions x cuts) interaction had insignificant variance in all three studied traits. In terms of CP, the maximum value was reported for the Iljo variety (18.8%) and the minimum for China (14.6%). No significant differences were observed between the check Tetrany (16.1%) and the other accessions. Only two cases of significant differences were observed for CF and WSC between accessions. The cluster analysis arranges the accessions into three groups, with the second cluster of 8 accessions being the most interesting for the selection. The analysis well differentiates the accessions regarding the optimal combination of the three traits in one genotype, as well as their ploidy level. A significant negative correlation was observed between crude protein and crude fiber content (r=-0.744).

Comparative assessment of morphological, cytological, and reproductive characteristics of the spontaneous mixoploid ‘MM 2×/4×’ and its diploid counterpart ‘Miss Manilla’ in Bougainvillea (Bougainvillea × buttiana Honlttum & Standl.)

Polyploidization-triggered chromosome multiplication typically leads to improved agronomic and ornamental characteristics in plants. However, mixoploidy may sometimes occur in spontaneous and artificially induced polyploidization events, and the deficiency of basic information about mixoploidy limits its application in breeding. In this study, the ploidy stability of spontaneous mixoploidy Bougainvillea × buttiana ‘Miss Manila’ (‘MM 2×/4×’) was validated through chromosome counting and flow cytometry analysis. Compared with its diploid counterpart ‘MM 2×’, ‘MM 2×/4×’ exhibited significantly larger size in the morphological characters related to leaf, bract, thorn, and perianth tube. The average length, width, and density of stomata in ‘MM 2×/4×’ were also significantly larger than in ‘MM 2×’, while the stomatal density of mesophyll cells decreased. The anthers of ‘MM 2×/4×’produced both 1n and 2n pollen grains, which in vitro germinated reached 8.92 %, significantly higher than ‘MM 2×’ (0.36 %). The seed setting rate of the crossing combinations ‘MM 2×/4×’ × ‘Chitra’, ‘Chitra’ × ‘MM 2×/4×’ and ‘MM 2×/4×’ × ‘Bixi’ were 65.47 %, 32.36 %, and 53.17 %, respectively, and the ploidy levels among different offspring individuals of the same genetic population are relatively consistent. While ‘MM 2×’ could not be hybrid with either the tetraploid ‘Chitra’ or diploid ‘Bixi’. Therefore, the mixoploid ‘MM 2×/4×’ partially restored the fertility of gametes and might be employed for both ploidy breeding directly and creating hybrid segregation populations in bougainvillea for trait genetic dissection.

Macromorphological and foliar epidermal anatomical characteristics of Lilium rosthornii (Liliaceae): Implications for morphological adaptations and taxonomic significance.

This research is to examine the macromorphological and foliar epidermal anatomical features of Lilium rosthornii Diels and its ability to plastically adapt to environmental forces, which is crucial for its taxonomic classification. L. rosthornii has macromorphological characteristics such as linear to lanceolate leaves of up to 20 cm in length and 2-3 cm in breadth, grouped in a whorled pattern. The blooms are voluminous and conspicuous, measuring up to 15 cm in diameter and are supported by a towering stalk that grows up to 1 m in height. The foliar epidermal structure of L. rosthornii exhibits a stomatal length of 82.02 ± 5.77 μm and a width of 29.19 ± 1.39 μm. These measurements suggest that the plant's stomata are influenced by its ploidy levels and may serve as adaptive mechanisms to enhance water consumption efficiency. The leaf structure shows a significant thickness of 398.74 ± 97.96 μm, which might potentially contribute to its ability to withstand environmental challenges. Additionally, the presence of defensive adaptations in the top and lower epidermal layers further supports this observation. The palisade tissue measurement (58.87 ± 9.56 m) and spongy tissue measurement (32.42 ± 12.72 μm) indicate a potential for photosynthetic optimization. Furthermore, there is a possible correlation between the vascular bundle width (28.15 ± 6.52 °m) and the efficiency of nutrition delivery. The results of this study emphasize the notable diversity in the foliar structures of L. rosthornii, offering valuable understanding of its morphological adaptations that have ecological and taxonomic significance. The findings provide a deeper comprehension of the potential impact of anatomical characteristics on plant function and categorization, hence providing significant insights to the domain of plant morphology and systematics. RESEARCH HIGHLIGHTS: Examines Lilium rosthornii's anatomical features and environmental adaptability for taxonomic relevance. Leaf thickness and epidermal defenses indicate resilience to environmental stress. Highlights the diversity in L. rosthornii's foliar structures, with implications for ecological and taxonomic significance Offers insights into the impact of anatomical characteristics on plant function and classification.

A cyclical switch of gametogenic pathways in hybrids depends on the ploidy level

The cellular and molecular mechanisms governing sexual reproduction are conserved across eukaryotes. Nevertheless, hybridization can disrupt these mechanisms, leading to asexual reproduction, often accompanied by polyploidy. In this study, we investigate how ploidy level and ratio of parental genomes in hybrids affect their reproductive mode. We analyze the gametogenesis of sexual species and their diploid and triploid hybrids from the freshwater fish family Cobitidae, using newly developed cytogenetic markers. We find that diploid hybrid females possess oogonia and oocytes with original (diploid) and duplicated (tetraploid) ploidy. Diploid oocytes cannot progress beyond pachytene due to aberrant pairing. However, tetraploid oocytes, which emerge after premeiotic genome endoreplication, exhibit normal pairing and result in diploid gametes. Triploid hybrid females possess diploid, triploid, and haploid oogonia and oocytes. Triploid and haploid oocytes cannot progress beyond pachytene checkpoint due to aberrant chromosome pairing, while diploid oocytes have normal pairing in meiosis, resulting in haploid gametes. Diploid oocytes emerge after premeiotic elimination of a single-copied genome. Triploid hybrid males are sterile due to aberrant pairing and the failure of chromosomal segregation during meiotic divisions. Thus, changes in ploidy and genome dosage may lead to cyclical alteration of gametogenic pathways in hybrids.

Polyploidisation pleiotropically buffers ageing in hepatocytes

Polyploidy in hepatocytes has been proposed as a genetic mechanism to buffer against transcriptional dysregulation. Here, we aim to demonstrate the role of polyploidy in modulating gene regulatory networks in hepatocytes during ageing. We performed single-nucleus RNA-sequencing in hepatocyte nuclei of different ploidy levels isolated from young and old wild-type mice. Changes in the gene expression and regulatory network were compared to three independent haploinsufficient strains for HNF4A, CEBPA or CTCF, representing non-deleterious perturbations. Phenotypic characteristics of the liver section were additionally evaluated histologically, whereas the genomic allele composition of hepatocytes was analysed by BaseScope. We observed that ageing in wild-type mice results in nuclei polyploidy and marked increase in steatosis. Haploinsufficiency of liver-specific master regulators (HFN4A or CEBPA) results in the enrichment of hepatocytes with tetraploid nuclei at a young age, affecting the genomic regulatory network, and dramatically suppressing ageing-related steatosis tissue-wide. Notably, these phenotypes are not the result of subtle disruption to liver-specific transcriptional networks, since haploinsufficiency in CTCF insulator protein resulted in the same phenotype. Further quantification of genotypes of tetraploid hepatocytes in young and old HFN4A haploinsufficient mice revealed that during ageing, tetraploid hepatocytes lead to the selection of wild-type alleles, restoring non-deleterious genetic perturbation. ConclusionsOur results suggest a model whereby polyploidisation leads to fundamentally different cell states. Polyploid conversion enables pleiotropic buffering against age-related decline via non-random allelic segregation to restore a wild-type genome.

A cryptic syngameon within Betula shrubs revealed: Implications for conservation in changing subarctic environments.

Arctic and subarctic ecosystems are rapidly transforming due to global warming, emphasizing the need to understand the genetic diversity and adaptive strategies of northern plant species for effective conservation. This study focuses on Betula glandulosa, a native North American tundra shrub known as dwarf birch, which demonstrates an apparent capacity to adapt to changing climate conditions. To address the taxonomic challenges associated with shrub birches and logistical complexities of sampling in the northernmost areas where species' ranges overlap, we adopted a multicriteria approach. Incorporating molecular data, ploidy level assessment and leaf morphology, we aimed to distinguish B. glandulosa individuals from other shrub birch species sampled. Our results revealed three distinct species and their hybrids within the 537 collected samples, suggesting the existence of a shrub birch syngameon, a reproductive network of interconnected species. Additionally, we identified two discrete genetic clusters within the core species, B. glandulosa, that likely correspond to two different glacial lineages. A comparison between the nuclear and chloroplast SNP data emphasizes a long history of gene exchange between different birch species and genetic clusters. Furthermore, our results highlight the significance of incorporating interfertile congeneric species in conservation strategies and underscores the need for a holistic approach to conservation in the context of climate change, considering the complex dynamics of species interactions. While further research will be needed to describe this shrub birches syngameon and its constituents, this study is a first step in recognizing its existence and disseminating awareness among ecologists and conservation practitioners. This biological phenomenon, which offers evolutionary flexibility and resilience beyond what its constituent species can achieve individually, may have significant ecological implications.

Triploid brown trout, Salmo trutta, develop functional gonads with age and are able to interbreed with diploid counterparts.

The study investigated if gonad maturation in triploid brown trout, Salmo trutta, was entirely suppressed or only delayed, and if triploids could interbreed with diploid counterparts. Ten percent of the total number of 3-year-old triploid S. trutta, 15% of 4-year-old fish, and 17% of 5-year-old fish produced semen. Three and 4 years old triploid fish did not produce eggs, but 15% of the 5-year-old fish did so. The quantity and sperm motility of triploid semen did not differ from diploids, but the sperm concentration was significantly lower. When diploid eggs were fertilized with triploid semen (3n × 2n crosses), the percentage of eyed stage embryos, of hatched larvae, and of normal-shaped larvae did not differ from the diploid controls. Circa 90% of 3n × 2n crosses had a ploidy level of 2.4n. In the remaining percentage of 3n × 2n crosses, the ploidy level was ≥2n and <2.4n. In sperm competition experiments where diploid eggs were fertilized with a mixture of diploid and triploid semen, 52% of the originating larvae had a ploidy level of 2n, 43% of 2.4n, and 5% of the fish were not exactly classified. From the start of feeding to an age of 248 days, the mortality rate of 3n × 2n interploid crosses and of 2n × 2n controls was similar. The growth of interploid crosses was significantly higher than that of controls. In triploid mature females, the egg mass per kilogram of body weight was significantly lower than in diploids. The mass of the non-hardened eggs and the percentile weight increase during hardening did not differ from diploid eggs. When triploid eggs were fertilized with diploid semen (2n × 3n crosses), the development rate to normal hatched larvae was less than 10%. All originating larvae had a ploidy level of 3n. From the start of feeding to an age of 248 days, 2n × 3n crosses had a higher mortality rate (15%) than diploid controls (<5%). Growth of this type of interploid crosses was reduced in comparison to controls. Therefore, triploids introduced into natural waters for recreational fisheries or escaping from farms may interbreed with diploid counterparts. This not only alters the genotypes of local populations but also changes the ploidy levels.

Variations in Fruit Ploidy Level and Cell Size between Small- and Large-Fruited Olive Cultivars during Fruit Ontogeny.

Olive (Olea europaea L.) is one of the major oil fruit tree crops worldwide. However, the mechanisms underlying olive fruit growth remain poorly understood. Here, we examine questions regarding the interaction of endoreduplication, cell division, and cell expansion with olive fruit growth in relation to the final fruit size by measuring fruit diameter, pericarp thickness, cell area, and ploidy level during fruit ontogeny in three olive cultivars with different fruit sizes. The results demonstrate that differences in the fruit size are related to the maximum growth rate between olive cultivars during early fruit growth, about 50 days post-anthesis (DPA). Differences in fruit weight between olive cultivars were found from 35 DPA, while the distinctive fruit shape became detectable from 21 DPA, even though the increase in pericarp thickness became detectable from 7 DPA in the three cultivars. During early fruit growth, intense mitotic activity appeared during the first 21 DPA in the fruit, whereas the highest cell expansion rates occurred from 28 to 42 DPA during this phase, suggesting that olive fruit cell number is determined from 28 DPA in the three cultivars. Moreover, olive fruit of the large-fruited cultivars was enlarged due to relatively higher cell division and expansion rates compared with the small-fruited cultivar. The ploidy level of olive fruit pericarp between early and late growth was different, but similar among olive cultivars, revealing that ploidy levels are not associated with cell size, in terms of different 8C levels during olive fruit growth. In the three olive cultivars, the maximum endoreduplication level (8C) occurred just before strong cell expansion during early fruit growth in fruit pericarp, whereas the cell expansion during late fruit growth occurred without preceding endoreduplication. We conclude that the basis for fruit size differences between olive cultivars is determined mainly by different cell division and expansion rates during the early fruit growth phase. These data provide new findings on the contribution of fruit ploidy and cell size to fruit size in olive and ultimately on the control of olive fruit development.

MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction.

Constructing a phylogenetic tree requires calculating the evolutionary distance between samples or species via large-scale resequencing data, a process that is both time-consuming and computationally demanding. Striking the right balance between accuracy and efficiency is a significant challenge. To address this, we introduce a new algorithm, MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard coefficient. Simulation results highlight the superior speed of MIKE compared to existing state-of-the-art methods. We used MIKE to reconstruct a phylogenetic tree, incorporating 238 yeast, 303 Zea, 141 Ficus, 67 Oryza, and 43 Saccharum spontaneum samples. MIKE demonstrated accurate performance across varying evolutionary scales, reproductive modes, and ploidy levels, proving itself as a powerful tool for phylogenetic tree construction. MIKE is publicly available on Github at https://github.com/Argonum-Clever2/mike.git.

Hybridization, polyploidization, and morphological convergence make dozens of taxa into one chaotic genetic pool: a phylogenomic case of the Ficus erecta species complex (Moraceae).

The Ficus erecta complex, characterized by its morphological diversity and frequent interspecific overlap, shares pollinating fig wasps among several species. This attribute, coupled with its intricate phylogenetic relationships, establishes it as an exemplary model for studying speciation and evolutionary patterns. Extensive researches involving RADseq (Restriction-site associated DNA sequencing), complete chloroplast genome data, and flow cytometry methods were conducted, focusing on phylogenomic analysis, genetic structure, and ploidy detection within the complex. Significantly, the findings exposed a pronounced nuclear-cytoplasmic conflict. This evidence, together with genetic structure analysis, confirmed that hybridization within the complex is a frequent occurrence. The ploidy detection revealed widespread polyploidy, with certain species exhibiting multiple ploidy levels, including 2×, 3×, and 4×. Of particular note, only five species (F. abelii, F. erecta, F. formosana, F. tannoensis and F. vaccinioides) in the complex were proved to be monophyletic. Species such as F. gasparriniana, F. pandurata, and F. stenophylla were found to encompass multiple phylogenetically distinct lineages. This discovery, along with morphological comparisons, suggests a significant underestimation of species diversity within the complex. This study also identified F. tannoensis as an allopolyploid species originating from F. vaccinioide and F. erecta. Considering the integration of morphological, molecular systematics, and cytological evidences, it is proposed that the scope of the F. erecta complex should be expanded to the entire subsect. Frutescentiae. This would redefine the complex as a continuously evolving group comprising at least 33 taxa, characterized by blurred species boundaries, frequent hybridization and polyploidization, and ambiguous genetic differentiation.

In vitro multiplication and phytochemical evaluation of Apios americana Medik for enhanced production of the staple food and tissues with versatile bioactivities

Apios americana Medik tissues, including tubers, flowers, leaves, and vines have both nutritional and therapeutic benefits. These tissues are extensively used in products like beverages and food supplements, driving an exponential increase in worldwide demand for the plant. However, conventional propagation of A. americana through seeds and tubers faces several challenges, including limited seed sets under manual pollination, resulting in reduced production. To overcome these challenges, micropropagation emerges as a promising solution. The current research study has developed an effective in vitro propagation strategy for A. americana using direct regeneration from apical segment explants. Full-strength Quoirin and Lepoivre (QL) medium, supplemented with vitamins and 2.0 mg/L benzylaminopurine (BAP), yielded the highest number of shoots (7.50 ± 0.06) per apical segment explant. QL medium fortified with 1.0 mg/L indole-3-butyric acid (IBA) demonstrated the highest root number (2.80 ± 0.30), length (85.80 ± 7.49 mm), and surface area (10.40 ± 0.82 cm2) in regenerated A. americana shoots. The survival rate of the regenerants in the ex vitro environment was 92.7% after acclimatization. In vitro-regenerated A. americana plants and mother plants exhibited similar ploidy level, chlorophyll content, photosynthetic rate, phytochemical composition, and antioxidant capacity, indicating similarity in their physiological and biochemical properties. This protocol offers a rapid and scalable method for generating high-quality, A. americana plant stocks with stable genome size/ploidy level, meeting the exponentially growing demand for plant tissues. Additionally, it holds potential applications in A. americana breeding and germplasm preservation.

Transcriptome analysis reveals polyploidy-related differential gene expression among diploid, triploid, and tetraploid Pacific oysters (Crassostrea gigas) based on growth-related phenotypes

Tetraploid oysters hold a significant position in the global oyster industry, particularly as core germplasm resources for the production of triploids. Triploids exhibit desirable characteristics such as reduced gonadal development, larger adult size, and superior flesh quality compared with diploids. However, tetraploids often face challenges of slow growth and chromosomal instability during the breeding process, and the mechanisms underlying the formation of these polyploid characteristics remain unclear. This study aimed to elucidate these mechanisms by constructing a polyploid oyster system and comparing the differences in growth-related phenotypes and gene expression among diploids, triploids, and tetraploids. We identified 1404 differentially expressed genes (DEGs) between diploids and triploids, 1814 DEGs between triploids and tetraploids, and 933 DEGs between diploids and tetraploids. Furthermore, we observed distinct gene expression patterns related to innate immunity response and biomineralization between different ploidy levels. Through trend analysis, we clustered genes with similar expression level changes across different ploidy levels and conducted gene ontology (GO) enrichment analysis on genes with different expression profiles. The results indicated that genes associated with the innate immunity response exhibited significantly upregulated expression with increasing ploidy, while genes related to biomineralization showed higher or lower expression levels in triploid oysters. As biomineralization is closely linked to oyster shell growth, this highlights the crucial role of genes associated with biomineralization in regulating the rapid shell growth observed in triploid oysters. Confronted with environmental challenges, tetraploid oysters may display a stronger innate immune response than diploids and triploids. Our study provides valuable resources for investigating the functional aspects of genes related to polyploid phenotype differences and offers new insights into the molecular mechanisms of existing issues in tetraploid oyster breeding.

Hybridization in the Subtribe Alopecurinae Dumort. (Poaceae) According to Molecular Phylogenetic Analysis: Different Ploidy Level Tells Different Origin of the Groups.

We performed next-generation sequencing of the 18S rDNA-ITS1-5.8S rDNA region along with traditional Sanger sequencing of rbcL, matK, ndhF, and ITS1-5.8S rDNA-ITS2 to clarify the hybridization pattern in the subtribe Alopecurinae and in the genus Alopecurus in particular. Our data support the hybrid origin of Alopecurus × brachystylus from hybridization between A. geniculatus (sect. Alopecurium) and A. pratensis (sect. Alopecurus). Moreover, in the rDNA of hybrid A. × brachystylus, only A. aequalis-like ribotypes from tetraploid A. geniculatus participated. Surprisingly, we found the traces of introgression of A. arundinaceus-like ribotypes not only in hybrid A. × marssonii (A. geniculatus × A. arundinaceus) but in A. aequalis s. str. as well. A high-polyploid group from the section Alopecurus, A. aggr. alpinus has undoubted hybrid origin: e. g., A. brachystachyus has rDNA from the sect. Alopecurium. Alopecurus alpinus, with its allies, is clearly distinct from other members of the sect. Alopecurus (especially by maternal line) and thus we can re-establish a previous opinion about the separate group to which A. alpinus belongs. Species from the section Colobachne (presumably Alpine grasses from Ancient Mediterranean region) probably hybridized with the A. alpinus group. Even A. myosuroides (sect. Pseudophalaris) that could be referred to the separate genus has ribotypes common with the species of the section Alopecurium (A. aequalis, A. geniculatus) in one of the accessions. Additionally, we found that the possible polyphyletic origin of the genus Limnas. Limnas stelleri is very close to Alopecurus magellanicus according to NGS data, while L. malyschevii is more or less distinct from other studied species of the genus Alopecurus.

Polyploid goldback and silverback ferns (Pentagramma) occupy a wider, colder, and wetter bioclimatic niche than diploid counterparts.

The western North American fern genus Pentagramma (Pteridaceae) is characterized by complex patterns of ploidy variation, an understanding of which is critical to comprehending both the evolutionary processes within the genus and its current diversity. We undertook a cytogeographic study across the range of the genus, using a combination of chromosome counts and flow cytometry to infer ploidy level. Bioclimatic variables and elevation were used to compare niches. We found that diploids and tetraploids are common and widespread, and triploids are rare and sporadic; in contrast with genome size inferences in earlier studies, no hexaploids were found. Diploids and tetraploids show different geographic ranges: only tetraploids were found in the northernmost portion of the range (Washington, Oregon, and British Columbia) and only diploids were found in the Sierra Nevada of California. Diploid, triploid, and tetraploid cytotypes were found to co-occur in relatively few localities: in the southern (San Diego County, California) and desert Southwest (Arizona) parts of the range, and along the Pacific Coast of California. Tetraploids occupy a wider bioclimatic niche than diploids both within P. triangularis and at the genus-wide scale. It is unknown whether the wider niche of tetraploids is due to their expansion upon the diploid niche, if diploids have contracted their niche due to competition or changing abiotic conditions, or if this wider niche occupancy is due to multiple origins of tetraploids.

Divergence of 10 satellite repeats in Artemisia (Asteraceae: Anthemideae) based on sequential fluorescence in situ hybridization analysis: evidence for species identification and evolution.

Artemisia is a large genus encompassing about 400 diverse species, many of which have considerable medicinal and ecological value. However, complex morphological information and variation in ploidy level and nuclear DNA content have presented challenges for evolution studies of this genus. Consequently, taxonomic inconsistencies within the genus persist, hindering the utilization of such large plant resources. Researchers have utilized satellite DNAs to aid in chromosome identification, species classification, and evolutionary studies due to their significant sequence and copy number variation between species and close relatives. In the present study, the RepeatExplorer2 pipeline was utilized to identify 10 satellite DNAs from three species (Artemisia annua, Artemisia vulgaris, Artemisia viridisquama), and fluorescence in situ hybridization confirmed their distribution on chromosomes in 24 species, including 19 Artemisia species with 5 outgroup species from Ajania and Chrysanthemum. Signals of satellite DNAs exhibited substantial differences between species. We obtained one genus-specific satellite from the sequences. Additionally, molecular cytogenetic maps were constructed for Artemisia vulgaris, Artemisia leucophylla, and Artemisia viridisquama. One species (Artemisia verbenacea) showed a FISH distribution pattern suggestive of an allotriploid origin. Heteromorphic FISH signals between homologous chromosomes in Artemisia plants were observed at a high level. Additionally, the relative relationships between species were discussed by comparing ideograms. The results of the present study provide new insights into the accurate identification and taxonomy of the Artemisia genus using molecular cytological methods.

LocoGSE, a sequence-based genome size estimator for plants.

Extensive research has focused on exploring the range of genome sizes in eukaryotes, with a particular emphasis on land plants, where significant variability has been observed. Accurate estimation of genome size is essential for various research purposes, but existing sequence-based methods have limitations, particularly for low-coverage datasets. In this study, we introduce LocoGSE, a novel genome size estimator designed specifically for low-coverage datasets generated by genome skimming approaches. LocoGSE relies on mapping the reads on single copy consensus proteins without the need for a reference genome assembly. We calibrated LocoGSE using 430 low-coverage Angiosperm genome skimming datasets and compared its performance against other estimators. Our results demonstrate that LocoGSE accurately predicts monoploid genome size even at very low depth of coverage (<1X) and on highly heterozygous samples. Additionally, LocoGSE provides stable estimates across individuals with varying ploidy levels. LocoGSE fills a gap in sequence-based plant genome size estimation by offering a user-friendly and reliable tool that does not rely on high coverage or reference assemblies. We anticipate that LocoGSE will facilitate plant genome size analysis and contribute to evolutionary and ecological studies in the field. Furthermore, at the cost of an initial calibration, LocoGSE can be used in other lineages.