Plants rely on tight coordination between nuclear, mitochondrial, and chloroplast genomes to form essential multi-enzyme cytonuclear complexes. Whole-genome duplication (WGD) doubles the nuclear genome, potentially disrupting cytonuclear stoichiometry unless organellar genomes respond accordingly. Targeted analyses of chloroplasts and mitochondria enabled us to dissect the extent and mechanisms of adjustments in both organelles immediately after WGD and across generations in Arabidopsis auto- and allopolyploids. We observed a substantial overcompensation of organellar genome copies in both organelles in early-generation autotetraploids primarily through multiplication of DNA copies within organelles rather than increasing the number of organelles. Despite higher DNA content, mitochondria maintained their volume, and chloroplasts were even smaller. In successive generations, chloroplast DNA copy numbers continued to rise, whereas mitochondrial DNA copies declined. Gene expression patterns also differed between chloroplasts and mitochondria and between auto- and allopolyploids. In autopolyploids, immediate transcriptional changes were minimal, but by the fourth generation after WGD, nuclear genes involved in mitochondria-nuclear complexes were downregulated. In allopolyploids, transcriptional changes appeared immediately in the first generation (chloroplast genes were upregulated and mitochondrial genes were downregulated). Our findings demonstrate that cytonuclear balance is restored through dynamic, organelle-specific, and polyploid-type-specific mechanisms. These insights advance our understanding of the evolution of polyploid genomes.

• Keywords
• chloroplasts, cytonuclear interactions, gene expression, interspecific hybridization, mitochondria, organellar DNA, stoichiometry, whole genome duplication,
• MeSH
• Arabidopsis * genetics   MeSH
• Cell Nucleus * genetics   MeSH
• Chloroplasts genetics   MeSH
• DNA, Chloroplast genetics   MeSH
• Genome, Chloroplast genetics   MeSH
• Genome, Plant genetics   MeSH
• DNA, Mitochondrial genetics   MeSH
• Mitochondria genetics   metabolism   MeSH
• Polyploidy * MeSH
• Gene Expression Regulation, Plant MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• DNA, Chloroplast MeSH
• DNA, Mitochondrial MeSH

BACKGROUND: The genus Allium is known for its high chromosomal variability, but most chromosome counts are based on a few individuals and genome size (GS) reports are limited in certain taxonomic groups. This is evident in the Allium sect. Codonoprasum, a species-rich (> 150 species) and taxonomically complex section with weak morphological differences between taxa, the presence of polyploidy and frequent misidentification of taxa. Consequently, a significant proportion of older karyological reports may be unreliable and GS data are lacking for the majority of species within the section. This study, using chromosome counting and flow cytometry (FCM), provides the first comprehensive and detailed insight into variation in chromosome number, polyploid frequency and distribution, and GS in section members, marking a step towards understanding the unresolved diversification and evolution of this group. RESULTS: We analysed 1578 individuals from 316 populations of 25 taxa and reported DNA ploidy levels and their GS, with calibration from chromosome counts in 22 taxa. Five taxa had multiple ploidy levels. First estimates of GS were obtained for 16 taxa. A comprehensive review of chromosome number and DNA-ploidy levels in 129 taxa of the section revealed that all taxa have x = 8, except A. rupestre with two polyploid series (x = 8, descending dysploidy x = 7), unique for this section. Diploid taxa dominated (72.1%), while di- & polyploid (12.4%) and exclusively polyploid (15.5%) taxa were less common. Ploidy diversity showed that diploid taxa dominated in the eastern Mediterranean and decreased towards the west and north, whereas only polyploid cytotypes of di- & polyploid taxa or exclusively polyploid taxa dominated in northern and northwestern Europe. A 4.1-fold variation in GS was observed across 33 taxa analysed so far (2C = 22.3-92.1 pg), mainly due to polyploidy, with GS downsizing observed in taxa with multiple ploidy levels. Intra-sectional GS variation suggests evolutionary relationships, and intraspecific GS variation within some taxa may indicate taxonomic heterogeneity and/or historical migration patterns. CONCLUSIONS: Our study showed advantages of FCM as an effective tool for detecting ploidy levels and determining GS within the section. GS could be an additional character in understanding evolution and phylogenetic relationships within the section.

• Keywords
• Chromosome number, Cytogeography, DNA ploidy level, Flow cytometry, Genome size, Polyploidy,
• Publication type
• Journal Article MeSH

Quinoa (Chenopodium quinoa) is an important crop for the future challenges of food and nutrient security. Deep characterization of quinoa diversity is needed to support the agronomic improvement and adaptation of quinoa as its worldwide cultivation expands. In this study, we report the construction of chromosome-scale genome assemblies of eight quinoa accessions covering the range of phenotypic and genetic diversity of both lowland and highland quinoas. The assemblies were produced from a combination of PacBio HiFi reads and Bionano Saphyr optical maps, with total assembly sizes averaging 1.28 Gb with a mean N50 of 71.1 Mb. Between 43,733 and 48,564 gene models were predicted for the eight new quinoa genomes, and on average, 66% of each quinoa genome was classified as repetitive sequences. Alignment between the eight genome assemblies allowed the identification of structural rearrangements including inversions, translocations, and duplications. These eight novel quinoa genome assemblies provide a resource for association genetics, comparative genomics, and pan-genome analyses for the discovery of genetic components and variations underlying agriculturally important traits.

• MeSH
• Chenopodium quinoa * genetics   MeSH
• Genetic Variation MeSH
• Genome, Plant * MeSH
• Publication type
• Journal Article MeSH
• Dataset MeSH

The integration of nanoparticles into plant cryopreservation protocols holds great promise for improving the survival rates and recovery potential of explants. This study aimed to verify the effect of nanoparticles on the ex-vitro performance of cryopreservation-derived plants. Lamprocapnos spectabilis (L.) Fukuhara (bleeding heart) 'Gold Heart' and 'Valentine' cultivars were used as the plant material. The encapsulation-vitrification cryopreservation protocol of shoot tips included the preculture, encapsulation, dehydration, storage in liquid nitrogen, rewarming, and recovery steps. Gold (AuNPs), silver (AgNPs), or zinc oxide (ZnONPs) nanoparticles were added at varying concentrations, either into the preculture medium or the protective bead matrix during encapsulation. After the in vitro recovery, the plants were transferred to the glasshouse and subjected to detailed biometrical, biochemical and cytogenetic analyses. Nanoparticles had no evident effect on the acclimatization efficiency (80-100% survival) and leaf number in L. spectabilis 'Gold Heart'. Nonetheless, shoots developed from alginate beads supplemented with 5 ppm AuNPs were twice as long as the control, while the leaves of plants grown on the preculture medium with ZnONPs contained significantly more chlorophyll and had higher Leaf Soil-Plant Analysis Development (SPAD) values. Moreover, several NPs treatments stimulated the development of leaves, including their surface area, length, and perimeter. Higher ZnONPs levels enhanced also the replication process, resulting in higher nuclear DNA content. As for L. spectabilis 'Valentine', alginate augmentation with 5 ppm AgNPs or 5 ppm ZnONPs stimulated the elongation of shoots. There was also a tendency suggesting a positive influence of 5 ppm AgNPs in the alginate bead matrix on foliar growth. The effect of nanoparticles on the content of flavonoids, anthocyanins, and stress markers in the plants varied depending on the treatment and cultivar, but also on the organ studied (leaf or stem). Overall, L. spectabilis 'Gold Heart' was more stress-tolerant and genetically stable than 'Valentine' judging by the activity of Photosystem II (PSII) and flow cytometric analyses, respectively. The complex effects of nanoparticles on survival, biometric parameters, physiological responses, and cytogenetic events underscore the intricate interplay between nanoparticles and plant systems. Nonetheless, our research confirmed the positive effect of nanoparticles on the ex-vitro growth and development of L. spectabilis plants after cryostorage.

• MeSH
• Chlorophyll metabolism   MeSH
• Metal Nanoparticles * chemistry   MeSH
• Cryopreservation * methods   MeSH
• Plant Leaves drug effects   MeSH
• Silver pharmacology   MeSH
• Plant Shoots drug effects   growth & development   MeSH
• Gold chemistry   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Chlorophyll MeSH
• Silver MeSH
• Gold MeSH

The identification of genes involved in salinity tolerance has primarily focused on model plants and crops. However, plants naturally adapted to highly saline environments offer valuable insights into tolerance to extreme salinity. Salicornia plants grow in coastal salt marshes, stimulated by NaCl. To understand this tolerance, we generated genome sequences of two Salicornia species and analyzed the transcriptomic and proteomic responses of Salicornia bigelovii to NaCl. Subcellular membrane proteomes reveal that SbiSOS1, a homolog of the well-known SALT-OVERLY-SENSITIVE 1 (SOS1) protein, appears to localize to the tonoplast, consistent with subcellular localization assays in tobacco. This neo-localized protein can pump Na+ into the vacuole, preventing toxicity in the cytosol. We further identify 11 proteins of interest, of which SbiSALTY, substantially improves yeast growth on saline media. Structural characterization using NMR identified it as an intrinsically disordered protein, localizing to the endoplasmic reticulum in planta, where it can interact with ribosomes and RNA, stabilizing or protecting them during salt stress.

• MeSH
• Chenopodiaceae * metabolism   genetics   drug effects   MeSH
• Sodium Chloride pharmacology   metabolism   MeSH
• Endoplasmic Reticulum metabolism   MeSH
• Proteomics MeSH
• Gene Expression Regulation, Plant drug effects   MeSH
• Plant Proteins * metabolism   genetics   MeSH
• Salinity MeSH
• Salt Stress MeSH
• Nicotiana metabolism   genetics   drug effects   MeSH
• Salt Tolerance * genetics   MeSH
• Transcriptome MeSH
• Vacuoles metabolism   MeSH
• Publication type
• Journal Article MeSH

BACKGROUND AND AIMS: The Greater Cape Floristic Region is one of the world's biodiversity hotspots and is considered poor in polyploids. To test this assumption, ploidy variation was investigated in a widespread Cape shrub, Dicerothamnus rhinocerotis (renosterbos, Asteraceae). The aim was to elucidate the cytotype distribution and population composition across the species range, and to assess differences in morphology, environmental niches and genetics. METHODS: Ploidy level and genome size were determined via flow cytometry and cytotype assignment was confirmed by chromosome counting. Restriction site-associated DNA sequencing (RADseq) analyses were used to infer genetic relationships. Cytotype climatic and environmental niches were compared using a range of environmental layers and a soil model, while morphological differences were examined using multivariate methods. KEY RESULTS: The survey of 171 populations and 2370 individuals showed that the species comprises diploid and tetraploid cytotypes, no intermediates and only 16.8 % of mixed populations. Mean 2C values were 1.80-2.06 pg for diploids and 3.48-3.80 pg for tetraploids, with very similar monoploid genome sizes. Intra-cytotype variation showed a significant positive correlation with altitude and longitude in both cytotypes and with latitude in diploids. Although niches of both cytotypes were highly equivalent and similar, their optima and breadth were shifted due to differences mainly in isothermality and available water capacity. Morphometric analyses showed significant differences in the leaves and corolla traits, the number of florets per capitulum, and cypsela dimensions between the two cytotypes. Genetic analyses revealed four groups, three of them including both cytotypes. CONCLUSIONS: Dicerothamnus rhinocerotis includes two distinct cytotypes that are genetically similar. While tetraploids arise several times independently within different genetic groups, morphological and ecological differences are evident between cytotypes. Our results open up new avenues for questions regarding the importance of ploidy in the megadiverse Cape flora, and exemplify the need for population-based studies focused on ploidy variation.

• Keywords
• Elytropappus rhinocerotis, Stoebe clade, Asteraceae, Compositae, Gnaphalieae, RADseq, South Africa, flow cytometry, ploidy level, renosterbos, renosterveld,
• MeSH
• Asteraceae * genetics   MeSH
• Genome Size MeSH
• Diploidy * MeSH
• Ecosystem * MeSH
• Genetic Variation MeSH
• Genome, Plant MeSH
• Tetraploidy * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Chamaecrista is a Pantropical legume genus of the tribe Cassieae, which includes six other genera. In contrast to most of the other Cassieae genera, Chamaecrista shows significant variability in chromosome number (from 2n = 14 to 2n = 56), with small and morphologically similar chromosomes. Here, we performed a new cytomolecular analysis on chromosome number, genome size, and rDNA site distribution in a molecular phylogenetic perspective to interpret the karyotype trends of Chamaecrista and other two genera of Cassieae, seeking to understand their systematics and evolution. Our phylogenetic analysis revealed that Chamaecrista is monophyletic and can be divided into four major clades corresponding to the four sections of the genus. Chromosome numbers ranged from 2n = 14, 16 (section Chamaecrista) to 2n = 28 (sections Absus, Apoucouita, and Baseophyllum). The number of 5S and 35S rDNA sites varied between one and three pairs per karyotype, distributed on different chromosomes or in synteny, with no obvious phylogenetic significance. Our data allowed us to propose x = 7 as the basic chromosome number of Cassieae, which was changed by polyploidy generating x = 14 (sections Absus, Apoucouita, and Baseophyllum) and by ascending dysploidy to x = 8 (section Chamaecrista). The DNA content values supported this hypothesis, with the genomes of the putative tetraploids being larger than those of the putative diploids. We hypothesized that ascending dysploidy, polyploidy, and rDNA amplification/deamplification are the major events in the karyotypic diversification of Chamaecrista. The chromosomal marks characterized here may have cytotaxonomic potential in future studies.

• Keywords
• trnL-trnF, C-value, Genome size, ITS1–5.8S–ITS2, Karyotype evolution, Ribosomal DNA,
• MeSH
• Chamaecrista * genetics   MeSH
• Chromosomes, Plant genetics   MeSH
• Fabaceae * genetics   MeSH
• Phylogeny MeSH
• Genome, Plant MeSH
• Karyotype MeSH
• Polyploidy MeSH
• DNA, Ribosomal genetics   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• DNA, Ribosomal MeSH

INTRODUCTION: Despite the wealth of studies dealing with the invasions of alien plants, invasions of alien genotypes of native species (cryptic invasions) have been vastly neglected. The impact of cryptic invasions on the biodiversity of plant communities can, however, be significant. Inland saline habitats and halophytes (i.e., salt-tolerant plant species) are especially threatened by this phenomenon as they inhabit fragmented remnants of largely destroyed habitats, but at the same time some of these halophytic species are rapidly spreading along salt-treated roads. To study potential cryptic invasion of halophytes, the patterns of genome size and ploidy variation in the Puccinellia distans complex (Poaceae), the most rapidly spreading roadside halophyte in Central Europe, were investigated. METHODS: DNA flow cytometry with confirmatory chromosome counts were employed to assess ploidy levels of 1414 individuals from 133 populations of the P. distans complex. In addition, climatic niche modelling was used to predict the distributions of selected cytotypes. RESULTS: Eight groups differing in ploidy level and/or genome size were discovered, one diploid (2x; 2n = 14), two tetraploid (4xA, 4xB; 2n = 28), one pentaploid (5x; 2n = 35), three hexaploid (6xA, 6xB, 6xC; 2n = 42), and one heptaploid (7x; 2n = 49). The hexaploids (mostly the 6xC cytotype) were widespread through the study area, spreading intensively in both anthropogenic and natural habitats and probably hybridizing with the natural habitat dwelling tetraploids. In contrast, the non-hexaploid cytotypes rarely spread and were predominantly confined to natural habitats. DISCUSSION: The extensive spread of the hexaploid cytotypes along roadsides has most likely facilitated their incursion into natural habitats. The colonization of new natural habitats by the hexaploids may pose a threat to the indigenous Puccinellia populations by compromising their genetic integrity and/or by outcompeting them.

• Keywords
• Puccinellia distans agg., cryptic invasion, cytogeography, flow cytometry, genetic pollution, halophyte, polyploidy,
• Publication type
• Journal Article MeSH

Odd ploidy-level cytotypes in sexually reproducing species are considered a dead end due to absent or reduced fertility. If sterility is only partial, however, their contribution to the population gene pool can be augmented by longevity and clonal growth. To test this, we investigated the cytotype origin and spatial pattern, and pollen viability in three relict shrub species of the genus Daphne (Thymelaeaceae Juss.) in central Europe. Daphne cneorum subsp. cneorum is a widespread European species that has a broad ecological amplitude, whereas D. cneorum subsp. arbusculoides and D. arbuscula are narrow endemics of the western Pannonian Plain and the Western Carpathians, respectively. Our study confirmed that all three taxa are diploid. However, of more than a thousand analysed individuals of D. cneorum subsp. cneorum, five in four different populations were triploid. Our data indicate that these triploids most likely originate from recurrent autopolyploidization events caused by the fusion of reduced and unreduced gametes. High pollen viability was observed in all three taxa and in both diploid and triploid cytotypes, ranging from 65 to 100 %. Our study highlights the significant role of odd ploidy-level cytotypes in interploidy gene flow, calling for more research into their reproduction, genetic variability, and overall fitness. Interestingly, while the endemic D. arbuscula differs from D. cneorum based on genetic and genome size data, D. cneorum subsp. arbusculoides was indistinguishable from D. cneorum subsp. cneorum. However, our study reveals that the subspecies differ in the number of flowers per inflorescence. This is the first comprehensive cytogeographic study of this intriguing genus at a regional scale, and in spite of its karyological stability, it contributes to our understanding of genomic evolution in plant species with a wide ecological amplitude.

• Keywords
• Carpathians, Daphne, ITS, Pannonian Basin, endemics, genome size stasis, pollen fertility, polyploidy, relicts, triploids,
• Publication type
• Journal Article MeSH

Flow cytometry has emerged as a uniquely flexible, accurate, and widely applicable technology for the analysis of plant cells. One of its most important applications centers on the measurement of nuclear DNA contents. This chapter describes the essential features of this measurement, outlining the overall methods and strategies, but going on to provide a wealth of technical details to ensure the most accurate and reproducible results. The chapter is aimed to be equally accessible to experienced plant cytometrists as well as those newly entering the field. Besides providing a step-by-step guide for estimating genome sizes and DNA-ploidy levels from fresh tissues, special attention is paid to the use of seeds and desiccated tissues for such purposes. Methodological aspects regarding field sampling, transport, and storage of plant material are also given in detail. Finally, troubleshooting information for the most common problems that may arise during the application of these methods is provided.

• Keywords
• Best practices, DAPI, DNA-ploidy level, Desiccated tissues, Flow cytometry, Genome size, Plant nuclei isolation, Plant tissues, Propidium iodide, Seeds,
• MeSH
• Cell Nucleus * genetics   chemistry   MeSH
• Genome Size MeSH
• DNA, Plant genetics   analysis   MeSH
• Genome, Plant MeSH
• Ploidies MeSH
• Flow Cytometry methods   MeSH
• Plants * genetics   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• DNA, Plant MeSH