The Application of Flow Cytometry for Estimating Genome Size, Ploidy Level Endopolyploidy, and Reproductive Modes in Plants

The genome sequence of fat-hen, Chenopodium album L

We present a genome assembly from an individual Chenopodium album (fat-hen; Streptophyta; Magnoliopsida; Caryophyllales; Chenopodiaceae). The genome sequence has a total length of 1,593.80 megabases. Most of the assembly (99.61%) is scaffolded into 27 chromosomal pseudomolecules suggesting the individual is an allohexaploid (2 n = 6 x = 54). The mitochondrial and plastid genome assemblies have lengths of 312.95 kilobases and 152.06 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 50,077 protein-coding genes.

The genome sequence of the Black Medic, Medicago lupulina L

We present a genome assembly from a specimen of Black Medic, Medicago lupulina (Streptophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence has a total length of 575.40 megabases. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 294.12 kilobases and 123.99 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 27,424 protein-coding genes.

The genome sequence of barren brome, Bromus sterilis L. (Poaceae)

We present a genome assembly from an individual Bromus sterilis (the barren brome; Streptophyta; Magnoliopsida; Poales; Poaceae). The genome sequence has a total length of 2,677.90 megabases. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 523.28 kilobases and 136.96 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 29,147 protein-coding genes.

The genome sequence of wood avens, Geum urbanum L., 1753

We present a genome assembly from an individual Geum urbanum the (wood avens; Streptophyta; Magnoliopsida; Rosales; Rosaceae). The genome sequence is 1,304.9 megabases in span. Most of the assembly is scaffolded into 21 chromosomal pseudomolecules. The mitochondrial and plastid genomes have also been assembled and are 335.5 and 156.1 kilobases in length respectively. Gene annotation of this assembly on Ensembl identified 50,336 protein-coding genes.

A 160 Gbp fork fern genome shatters size record for eukaryotes

Vascular plants are exceptional among eukaryotes due to their outstanding genome size diversity which ranges ∼2,400-fold, including the largest genome so far recorded in the angiosperm Paris japonica (148.89 Gbp/1C). Despite available data showing that giant genomes are restricted across the Tree of Life, the biological limits to genome size expansion remain to be established. Here, we report the discovery of an even larger eukaryotic genome in Tmesipteris oblanceolata, a New Caledonian fork fern. At 160.45 Gbp/1C, this record-breaking genome challenges current understanding and opens new avenues to explore the evolutionary dynamics of genomic gigantism.

The genome sequence of the tree-moss, Climacium dendroides (Hedw.) F.Weber & D.Mohr (Climaciaceae)

We present a genome assembly from an individual Climacium dendroides gametophyte (the tree-moss; Bryophyta; Bryopsida; Leucodontales; Climaciaceae). The genome sequence is 413.1 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 104.86 kilobases and 124.96 kilobases in length, respectively.

The genome sequence of purple glasswort, Salicornia ramosissima Woods (Amaranthaceae)

We present a genome assembly from an individual Salicornia ramosissima (purple glasswort; Tracheophyta; Magnoliopsida; Caryophyllales; Chenopodiaceae). The genome sequence is 529.1 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 328.55 kilobases and 153.3 kilobases in length, respectively.

The genome sequence of lesser trefoil or Irish shamrock, Trifolium dubium Sibth. (Fabaceae)

We present a genome assembly from an individual Trifolium dubium (lesser trefoil; Tracheophyta; Magnoliopsida; Fabales; Fabaceae) as part of a collaboration between the Darwin Tree of Life and the European Reference Genome Atlas. The genome sequence is 679.1 megabases in span. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules. The two mitochondrial genomes have lengths of 133.86 kb and 182.32 kb, and the plastid genome assembly has a length of 126.22 kilobases.

The genome sequence of black poplar, Populus nigra subsp. betulifolia L., 1753 (Salicaceae)

We present a genome assembly from an individual Populus nigra subsp. betulifola (black poplar; Tracheophyta; Malpighiales; Salicaceae). The genome sequence is 413.2 megabases in span. Most of the assembly (99.73%) is scaffolded into 19 chromosomal pseudomolecules. Mitochondrial and plastid genomes were also assembled. Three mitochondrial assemblies have lengths of 281.85, 335.57 and 186.15 kilobases, and the plastid genome has a length of 156.37 kilobases.

Unveiling the epigenetic landscape of plants using flow cytometry approach

Plants are sessile creatures that have to adapt constantly changing environmental circumstances. Plants are subjected to a range of abiotic stressors as a result of unpredictable climate change. Understanding how stress-responsive genes are regulated can help us better understand how plants can adapt to changing environmental conditions. Epigenetic markers that dynamically change in response to stimuli, such as DNA methylation and histone modifications are known to regulate gene expression. Individual cells or particles' physical and/or chemical properties can be measured using the method known as flow cytometry. It may therefore be used to evaluate changes in DNA methylation, histone modifications, and other epigenetic markers, making it a potent tool for researching epigenetics in plants. We explore the use of flow cytometry as a technique for examining epigenetic traits in this thorough discussion. The separation of cell nuclei and their subsequent labeling with fluorescent antibodies, offering information on the epigenetic mechanisms in plants when utilizing flow cytometry. We also go through the use of high-throughput data analysis methods to unravel the complex epigenetic processes occurring inside plant systems.

The genome sequence of rosebay willowherb Chamaenerion angustifolium (L.) Scop., 1771 (syn. Epilobium angustifolium L., 1753) (Onagraceae)

We present a genome assembly from an individual Chamaenerion angustifolium (fireweed; Tracheophyta; Magnoliopsida; Myrtales; Onagraceae). The genome sequence is 655.9 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 495.18 kilobases and 160.41 kilobases in length, respectively.

The genome sequence of the Lesser Skullcap, Scutellaria minor Huds., 1762 (Lamiaceae)

We present a genome assembly from an individual Scutellaria minor (Tracheophyta; Magnoliopsida; Lamiales; Lamiaceae). The genome sequence is 341.8 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 376.64 kilobases and 152.59 kilobases in length, respectively.

The genome sequence of field madder, Sherardia arvensis L., 1753 (Rubiaceae)

We present a genome assembly from an individual Sherardia arvensis (field madder; Tracheophyta; Magnoliopsida; Gentianales; Rubiaceae). The genome sequence is 440.9 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 203.98 kilobases and 152.73 kilobases in length, respectively.

The genome sequence of common knotgrass, Polygonum aviculare L. (Polygonaceae)

We present a genome assembly from an individual Polygonum aviculare (common knotgrass; Eudicot; Magnoliopsida; Caryophyllales; Polygonaceae). The genome sequence is 351.6 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 333.39 kilobases and 163.28 kilobases in length, respectively.

The genome sequence of great wood-rush, Luzula sylvatica (Huds) Gaudin

We present a genome assembly from an individual specimen of Luzula sylvatica (great wood-rush; Tracheophyta; Magnoliopsida; Poales; Juncaceae). The genome sequence is 444.5 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 633.36 kilobases and 201.32 kilobases in length, respectively.

The genome sequence of the Annual Mercury, Mercurialis annua L., 1753 (Euphorbiaceae)

We present a genome assembly from a diploid female Mercurialis annua (the Annual Mercury; Tracheophyta; Magnoliopsida; Malpighiales; Euphorbiaceae). The genome sequence is 453.2 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules, including the X chromosome. The organelle genomes have also been assembled, and the mitochondrial genome is 435.28 kilobases in length, while the plastid genome is 169.65 kilobases in length.

The genome sequence of the English holly, Ilex aquifolium L. (Aquifoliaceae)

We present a genome assembly from an individual Ilex aquifolium (the English holly; Eudicot; Magnoliopsida; Aquifoliales; Aquifoliaceae). The genome sequence is 800.0 megabases in span. Most of the assembly is scaffolded into 20 chromosomal pseudomolecules. The assembled mitochondrial and plastid genomes have lengths of 538.43 kilobases and 157.52 kilobases in length, respectively.

The genome sequence of the silverweed cinquefoil, Potentilla anserina L., 1753

We present a genome assembly from a specimen of Potentilla anserina (the silverweed cinquefoil; Streptophyta; eudicotyledons; Rosales; Potentilleae). The haploid genome sequence is 237 megabases in span. Most of the assembly is scaffolded into seven chromosomal pseudomolecules. The mitochondrial and plastid genomes have also been assembled and are 294.6 and 155.6 kilobases in length respectively.

The genome sequence of black horehound, Ballota nigra L. subsp. foetida (Lam.) Hayek (Lamiaceae)

We present a genome assembly from a specimen of Ballota nigra (black horehound; Tracheophyta; Magnoliopsida; Lamiales; Lamiaceae). The genome sequence is 1186.8 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules. Three mitochondrial chromosomes were assembled, with lengths of 148,17, 121,67 and 125,74 kilobases. The chloroplast genome has been assembled and is 151.91 kilobases in length.

The genome sequence of common fleabane, Pulicaria dysenterica (L.) Bernh. (Asteraceae)

We present a genome assembly from an individual Pulicaria dysenterica (common fleabane; Tracheophyta; Magnoliopsida; Asterales; Asteraceae). The genome sequence is 833.2 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial and plastid genomes were assembled and have lengths of 375.47 kilobases and 150.94 kilobases respectively.

The genome sequence of bittersweet, Solanum dulcamara L. (Solanaceae)

We present a genome assembly from an individual Solanum dulcamara (bittersweet; Eudicot; Magnoliopsida; Solanales; Solanaceae). The genome sequence is 946.3 megabases in span. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules. The mitochondrial and plastid genomes have also been assembled, with lengths of 459.22 kilobases and 161.98 kilobases respectively.

The genome sequence of the common toadflax, Linaria vulgaris Mill., 1768

We present a genome assembly from a Linaria vulgaris specimen (common toadflax; Streptophyta; Magnoliopsida; Lamiales; Plantaginaceae). The genome sequence is 760.5 megabases in span. Most of the assembly is scaffolded into six chromosomal pseudomolecules. Two mitochondrial genomes were assembled, which were 330.8 and 144.0 kilobases long. The plastid genome was also assembled and is 156.7 kilobases in length.

The genome sequence of common ivy, Hedera helix L., 1753

We present a genome assembly from a specimen of Hedera helix (common ivy; Streptophyta; Magnoliopsida; Apiales; Araliaceae). The genome sequence is 1,199.4 megabases in span. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules. The mitochondrial and plastid genomes have also been assembled and are 609.2 and 162.2 kilobases in length respectively.

The genome sequence of the tree of heaven, Ailanthus altissima (Mill.) Swingle, 1916

We present a genome assembly from an individual Ailanthus altissima (tree of heaven; Streptophyta; Magnoliopsida; Sapindales; Simaroubaceae). The genome sequence is 939 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies are 661.1 kilobases and 161.1 kilobases long, respectively.

Are chromosome number and genome size associated with habit and environmental niche variables? Insights from the Neotropical orchids

BACKGROUND AND AIMS

The entangled relationship of chromosome number and genome size with species distribution has been the subject of study for almost a century, but remains an open question due to previous ecological and phylogenetic knowledge constraints. To better address this subject, we used the clade Maxillariinae, a widely distributed and karyotypically known orchid group, as a model system to infer such relationships in a robust methodological framework.

METHODS

Based on the literature and new data, we gathered the chromosome number and genome size for 93 and 64 species, respectively. We built a phylogenetic hypothesis and assessed the best macroevolutionary model for both genomic traits. Additionally, we collected together ecological data (preferences for bioclimatic variables, elevation and habit) used as explanatory variables in multivariate phylogenetic models explaining genomic traits. Finally, the impact of polyploidy was estimated by running the analyses with and without polyploids in the sample.

KEY RESULTS

The association between genomic and ecological data varied depending on whether polyploids were considered or not. Without polyploids, chromosome number failed to present consistent associations with ecological variables. With polyploids, there was a tendency to waive epiphytism and colonize new habitats outside humid forests. The genome size showed association with ecological variables: without polyploids, genome increase was associated with flexible habits, with higher elevation and with drier summers; with polyploids, genome size increase was associated with colonizing drier environments.

CONCLUSIONS

The chromosome number and genome size variations, essential but neglected traits in the ecological niche, are shaped in the Maxillariinae by both neutral and adaptive evolution. Both genomic traits are partially correlated to bioclimatic variables and elevation, even when controlling for phylogenetic constraints. While polyploidy was associated with shifts in the environmental niche, the genome size emerges as a central trait in orchid evolution by the association between small genome size and epiphytism, a key innovation to Neotropical orchid diversification.

Genome size of alpine plants does not predict temperature resistance

Genome size of alpine plants is not related to their resistance against frost and heat. Genome size is a variable trait in angiosperms, and it was suggested that large genome size represents a constraint in stressful environments. We measured genome size and resistance to frost and heat in 89 species of plants from tropical and temperate alpine habitats. Genome size of the species, ranging from 0.49 pg to 25.8 pg across the entire dataset, was not related to either frost or heat resistance in either group of plants. Genome size does not predict resistance to extreme temperatures in alpine plants and is thus not likely to predict plant responses to climate changes.

In vitro Induction and Phenotypic Variations of Autotetraploid Garlic (Allium sativum L.) With Dwarfism

Garlic (Allium sativum L.) is a compelling horticultural crop with high culinary and therapeutic values. Commercial garlic varieties are male-sterile and propagated asexually from individual cloves or bulbils. Consequently, its main breeding strategy has been confined to the time-consuming and inefficient selection approach from the existing germplasm. Polyploidy, meanwhile, plays a prominent role in conferring plants various changes in morphological, physiological, and ecological properties. Artificial polyploidy induction has gained pivotal attention to generate new genotype for further crop improvement as a mutational breeding method. In our study, efficient and reliable in vitro induction protocols of autotetraploid garlic were established by applying different antimitotic agents based on high-frequency direct shoot organogenesis initiated from inflorescence explant. The explants were cultured on solid medium containing various concentrations of colchicine or oryzalin for different duration days. Afterward, the ploidy levels of regenerated plantlets with stable and distinguished characters were confirmed by flow cytometry and chromosome counting. The colchicine concentration at 0.2% (w/v) combined with culture duration for 20 days was most efficient (the autotetraploid induction rate was 21.8%) compared to the induction rate of 4.3% using oryzalin at 60 μmol L-1 for 20 days. No polymorphic bands were detected by simple sequence repeat analysis between tetraploid and diploid plantlets. The tetraploids exhibited a stable and remarkable dwarfness effect rarely reported in artificial polyploidization among wide range of phenotypic variations. There are both morphological and cytological changes including extremely reduced plant height, thickening and broadening of leaves, disappearance of pseudostem, density reduction, and augmented width of stomatal. Furthermore, the level of phytohormones, including, indole propionic acid, gibberellin, brassinolide, zeatin, dihydrozeatin, and methyl jasmonate, was significantly lower in tetraploids than those in diploid controls, except indole acetic acid and abscisic acid, which could partly explain the dwarfness in hormonal regulation aspect. Moreover, as the typical secondary metabolites of garlic, organosulfur compounds including allicin, diallyl disulfide, and diallyl trisulfide accumulated a higher content significantly in tetraploids. The obtained dwarf genotype of autotetraploid garlic could bring new perspectives for the artificial polyploids breeding and be implemented as a new germplasm to facilitate investigation into whole-genome doubling consequences.

The variability of nuclear DNA content of different Pelargonium species estimated by flow cytometry

Pelargonium is a versatile genus mainly from the Cape Region, South Africa. The genus is divided into four subgenera and 16 sections characterized by several groups of chromosomes sizes and numbers. The DNA content of species from all subgenera and sections of Pelargonium, except for the sections Subsucculentia and Campylia was estimated using flow cytometry. Nuclei of Pelargonium samples (leaf or petal tissue) and an internal plant standard (leaf tissue) were isolated together and stained with propidium iodide. The DNA content was estimated providing that the 2C peaks of sample and standard be in linearity in the flow cytometer histograms. In total, 96 Pelargonium accessions of 60 species (22 Pelargonium species for the first time) were analyzed. The 2C DNA content ranged from 0.84 pg (P. longifolium, section Hoarea) to 6.69 pg (P. schizopetalum, section Magnistipulacea) and the corresponding 1Cx DNA content from 0.42 pg (P. longifolium) to 1.72 pg (P. transvaalense. This demonstrates the high plasticity within the genus Pelargonium. Some species, such as P. peltatum accessions revealed a pronounced endopolyploidization in leaves but not in petals underlining the importance to choose the right tissue as sample for the flow cytometry analysis. The reported genome sizes are a step forward towards the characterization of the Pelargonium collection within the German Gene Bank for Ornamental Plants and a valuable base for future sequencing programs of the Pelargonium genomes.

Chromosome Number and Genome Size Evolution in Brasolia and Sobralia (Sobralieae, Orchidaceae)

Despite the clear circumscription of tribe Sobralieae (Orchidaceae), its internal relationships are still dubious. The recently delimited genus Brasolia, based on previous Sobralia species, is now assumed to be paraphyletic, with a third genus, Elleanthus, nested in it. The morphology of these three genera is significantly different, indicating the necessity of new data for a better genera delimitation. Though morphology and molecular data are available, cytogenetics data for Sobralieae is restricted to two Sobralia and one Elleanthus species. Aiming to evaluate the potential of cytogenetic data for Brasolia-Elleanthus-Sobralia genera delimitation, we present chromosome number and genome size data for 21 and 20 species, respectively, and used such data to infer the pattern of karyotype evolution in these genera. The analysis allowed us to infer x = 24 as the base chromosome number and genome size of average 1C-value of 5.0 pg for the common ancestor of Brasolia-Elleanthus-Sobralia. The recurrent descending dysploidy in Sobralieae and the punctual genome upsize suggest a recent diversification in Sobralieae but did not allow differing between Brasolia and Sobralia. However, the basal position of tribe Sobralieae in the subfamily Epidendroideae makes this tribe of interest to further studies clarifying the internal delimitation and pattern of karyotype evolution.

A taxonomic, genetic and ecological data resource for the vascular plants of Britain and Ireland

The vascular flora of Britain and Ireland is among the most extensively studied in the world, but the current knowledge base is fragmentary, with taxonomic, ecological and genetic information scattered across different resources. Here we present the first comprehensive data repository of native and alien species optimized for fast and easy online access for ecological, evolutionary and conservation analyses. The inventory is based on the most recent reference flora of Britain and Ireland, with taxon names linked to unique Kew taxon identifiers and DNA barcode data. Our data resource for 3,227 species and 26 traits includes existing and unpublished genome sizes, chromosome numbers and life strategy and life-form assessments, along with existing data on functional traits, species distribution metrics, hybrid propensity, associated biomes, realized niche description, native status and geographic origin of alien species. This resource will facilitate both fundamental and applied research and enhance our understanding of the flora's composition and temporal changes to inform conservation efforts in the face of ongoing climate change and biodiversity loss.

Application-based guidelines for best practices in plant flow cytometry

Flow cytometry (FCM) is currently the most widely-used method to establish nuclear DNA content in plants. Since simple, 1-3-parameter, flow cytometers, which are sufficient for most plant applications, are commercially available at a reasonable price, the number of laboratories equipped with these instruments, and consequently new FCM users, has greatly increased over the last decade. This paper meets an urgent need for comprehensive recommendations for best practices in FCM for different plant science applications. We discuss advantages and limitations of establishing plant ploidy, genome size, DNA base composition, cell cycle activity, and level of endoreduplication. Applications of such measurements in plant systematics, ecology, molecular biology research, reproduction biology, tissue cultures, plant breeding, and seed sciences are described. Advice is included on how to obtain accurate and reliable results, as well as how to manage troubleshooting that may occur during sample preparation, cytometric measurements, and data handling. Each section is followed by best practice recommendations; tips as to what specific information should be provided in FCM papers are also provided.