The global distribution of angiosperm genome size is shaped by climate

Angiosperms, which inhabit diverse environments across all continents, exhibit significant variation in genome sizes, making them an excellent model system for examining hypotheses about the global distribution of genome size. These include the previously proposed large genome constraint, mutational hazard, polyploidy-mediated, and climate-mediated hypotheses. We compiled the largest genome size dataset to date, encompassing 16 017 (> 5% of known) angiosperm species, and analyzed genome size distribution using a comprehensive geographic distribution dataset for all angiosperms. We observed that angiosperms with large range sizes generally had small genomes, supporting the large genome constraint hypothesis. Climate was shown to exert a strong influence on genome size distribution along the global latitudinal gradient, while the frequency of polyploidy and the type of growth form had negligible effects. In contrast to the unimodal patterns along the global latitudinal gradient shown by plant size traits and polyploid proportions, the increase in angiosperm genome size from the equator to 40-50°N/S is probably mediated by different (mostly climatic) mechanisms than the decrease in genome sizes observed from 40 to 50°N northward. Our analysis suggests that the global distribution of genome sizes in angiosperms is mainly shaped by climatically mediated purifying selection, genetic drift, relaxed selection, and environmental filtering.

Taxonomy and distribution of Taraxacum sect. Erythrosperma (Asteraceae) in Poland

The dandelions from Taraxacumsect.Erythrosperma are taxonomically well distinguished and ecologically restricted to warm and sunlit habitats of steppes, dry and sandy grasslands, and distributed in temperate regions of Europe and Central Asia, with some being introduced to North America. Despite the long tradition of botanical research, the taxonomy and distribution of dandelions of T.sect.Erythrosperma is still underexplored in central Europe. In this paper, by combining traditional taxonomic studies supported by micromorphological, molecular and flow cytometry analyses as well as potential distribution modelling we shed light on taxonomical and phylogenetical relationships between members of T.sect.Erythrosperma in Poland. We also provide an identification key, species-checklist, detailed descriptions of morphology and occupated habitats as well as distribution maps for 14 Polish erythrosperms (T.bellicum, T.brachyglossum, T.cristatum, T.danubium, T.disseminatum, T.dissimile, T.lacistophyllum, T.parnassicum, T.plumbeum, T.proximum, T.sandomiriense, T.scanicum, T.tenuilobum, T.tortilobum). Finally, conservation assessments performed using the IUCN method and threat categories for all the examined species are proposed.

Ploidy Status, Nuclear DNA Content and Start Codon Targeted (SCoT) Genetic Homogeneity Assessment in Digitalis purpurea L., Regenerated In Vitro

Digitalis purpurea L. is a therapeutically important plant that synthesizes important cardiotonics such as digitoxin and digoxin. The present work reports a detailed and efficient propagation protocol for D. purpurea by optimizing various PGR concentrations in Murashige and Skoog (MS) medium. The genetic homogeneity of in vitro regenerants was assessed by the flow cytometric method (FCM) and Start Codon Targeted (SCoT) marker technique. Firstly, the seeds inoculated in full MS medium added with 0.5 mg/L GA₃ produced seedlings. Different parts such as hypocotyl, nodes, leaves and apical shoots were used as explants. The compact calli were obtained on BAP alone or in combinations with 2, 4-D/NAA. The hypocotyl-derived callus induced somatic embryos which proliferated and germinated best in 0.75 mg/L BAP-fortified MS medium. Scanning electron microscopic (SEM) images confirmed the presence of various developmental stages of somatic embryos. Shoot regeneration was obtained in which BAP at 1.0 mg/L and 2.0 mg/L BAP + 0.5 mg/L 2,4-D proved to be the best treatments of PGRs in inducing direct and indirect shoot buds. The regenerated shoots showed the highest rooting percentage (87.5%) with 24.7 ± 1.9 numbers of roots/shoot in 1.0 mg/L IBA augmented medium. The rooted plantlets were acclimatized in a greenhouse at a survival rate of 85-90%. The genome size and the 2C nuclear DNA content of field-grown, somatic embryo-regenerated and organogenic-derived plants were estimated and noted to be 3.1, 3.2 and 3.0 picogram (pg), respectively; there is no alteration in ploidy status and the DNA content, validating genetic uniformity. Six SCoT primers unveiled 94.3%-95.13% monomorphic bands across all the plant samples analyzed, further indicating genetic stability among in vitro clones and mother plants. This study describes for the first time successful induction of somatic embryos from hypocotyl callus; and flow cytometry and SCoT marker confirmed the genetic homogeneity of regenerated plants.

Biotechnology of the Tree Fern Cyathea smithii (J.D. Hooker; Soft Tree Fern, Katote) II Cell Suspension Culture: Focusing on Structure and Physiology in the Presence of 2,4-D and BAP

The aim of our research was to describe the structure and growth potential of a cell suspension of the tree fern Cyathea smithii. Experiments were performed on an established cell suspension with ½ MS medium supplemented with 9.05 µM 2,4-D + 0.88 µM BAP. In the experiments, attention was paid to the microscopic description of cell suspension, evaluation of cell growth dependent on the initial mass of cells and organic carbon source in the medium, the length of the passage, the content of one selected flavonoid in the post-culture medium, nuclear DNA content, ethylene production, and the antimicrobial value of the extract. For a better understanding of the cell changes that occurred during the culture of the suspension, the following structures of the cell were observed: nucleus, lipid bodies, tannin deposits, starch grains, cell walls, primary lamina, and the filaments of metabolites released into the medium. The nuclear DNA content (acriflavine-Feulgen staining) of cell aggregates distinctly indicated a lack of changes in the sporophytic origin of the cultured cell suspension. The physiological activity of the suspension was found to be high because of kinetics, intensive production of ethylene, and quercetin production. The microbiological studies suggested that the cell suspension possessed a bactericidal character against microaerobic Gram-positive bacteria. A sample of the cell suspension showed bacteriostatic activity against aerobic bacteria.

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.

Plant material selection, collection, preservation, and storage for nuclear DNA content estimation

In theory, any plant tissue providing intact nuclei in sufficient quantity is suitable for nuclear DNA content estimation using flow cytometry (FCM). While this certainly opens a wide variety of possible applications of FCM, especially when compared to classical karyological techniques restricted to tissues with active cell division, tissue selection and quality may directly affect the precision (and sometimes even reliability) of FCM measurements. It is usually convenient to first consider the goals of the study to either aim for the highest possible accuracy of estimates (e.g., for inferring genome size, detecting homoploid intraspecific genome size variation, aneuploidy, among others), or to decide that histograms of reasonable resolution provide sufficient information (e.g., ploidy level screening within a single model species). Here, a set of best practices guidelines for selecting the optimal plant tissue for FCM analysis, sampling of material, and material preservation and storage are provided. In addition, factors potentially compromising the quality of FCM estimates of nuclear DNA content and data interpretation are discussed.

Genome Size, Chromosome Number and Morphological Data Reveal Unexpected Infraspecific Variability in Festuca (Poaceae)

Polyploidy has played an important evolutionary role in the genus Festuca (Poaceae), and several ploidy levels (ranging from 2n = 2x = 14 to 2n = 12x = 84) have been detected to date. This study aimed to estimate the genome size and ploidy level of two subspecies belonging to the F. yvesii polyploid complex by flow cytometry and chromosome counting. The phenotypic variation of the cytotypes was also explored, based on herbarium material. The genome size of F. yvesii subsp. lagascae has been estimated for the first time. Nuclear 2C DNA content of F. yvesii subsp. summilusitana ranged from 21.44 to 31.91 pg, while that of F. yvesii subsp. lagascae was from 13.60 to 22.31 pg. We report the highest ploidy level detected for Festuca (2n = 14x = 98) and previously unknown cytotypes. A positive correlation between holoploid genome size and chromosome number counts shown herein was confirmed. The morphometric approach showed a slight trend towards an increase in the size of some organs consistent with the variation in the ploidy level. Differences in characters were usually significant only among the most extreme cytotypes of each subspecies, but, even in this case, the high overlapping ranges prevent their distinction.

Genome Size Diversity in Rare, Endangered, and Protected Orchids in Poland

Orchidaceae is one of the largest and the most widespread plant families with many species threatened with extinction. However, only about 1.5% of orchids’ genome sizes have been known so far. The aim of this study was to estimate the genome size of 15 species and one infraspecific taxon of endangered and protected orchids growing wild in Poland to assess their variability and develop additional criterion useful in orchid species identification and characterization. Flow cytometric genome size estimation revealed that investigated orchid species possessed intermediate, large, and very large genomes. The smallest 2C DNA content possessed Liparis loeselii (14.15 pg), while the largest Cypripedium calceolus (82.10 pg). It was confirmed that the genome size is characteristic to the subfamily. Additionally, for four species Epipactis albensis, Ophrys insectifera, Orchis mascula, Orchis militaris and one infraspecific taxon, Epipactis purpurata f. chlorophylla the 2C DNA content has been estimated for the first time. Genome size estimation by flow cytometry proved to be a useful auxiliary method for quick orchid species identification and characterization.

Is the evolution of carnivory connected with genome size reduction?

PREMISE

As repeatedly shown, the remarkable variation in the genome size of angiosperms can be shaped by extrinsic selective pressures, including nutrient availability. Carnivory has evolved independently in 10 angiosperm clades, but all carnivorous plants share a common affinity to nutrient-poor habitats. As such, carnivory and genome reduction could be responses to the same environmental pressure. Indeed, the smallest genomes among flowering plants are found in the carnivorous family Lentibulariaceae, where a unique mutation in cytochrome c oxidase (COX) is suspected to promote genome miniaturization. Despite these hypotheses, a phylogenetically informed test of genome size and nutrient availability across carnivorous clades has so far been missing.

METHODS

Using linear mixed models, we compared genome sizes of 127 carnivorous plants from 7 diverse angiosperm clades with 1072 of their noncarnivorous relatives. We also tested whether genome size in Lentibulariaceae reflects the presence of the COX mutation.

RESULTS

The genome sizes of carnivorous plants do not differ significantly from those of their noncarnivorous relatives. Based on available data, no significant association between the COX mutation and genome miniaturization could be confirmed, not even when considering polyploidy.

CONCLUSIONS

Carnivory alone does not seem to significantly affect genome size decrease. Plausibly, it might actually counterbalance the effect of nutrient limitation on genome size evolution. The role of the COX mutation in genome miniaturization needs to be evaluated by analysis of a broader data set because current knowledge of its presence across Lentibulariaceae covers less than 10% of the species diversity in this family.

Cytogenetic and pollen identification of genus Gagnepainia (Zingiberaceae) in Thailand

Gagnepainia godefroyi K. Schumann, 1904 and G. harmandii K. Schumann, 1904 belong to the genus Gagnepainia K. Schumann, 1904 of the Ginger family. They have the potential to be developed as medicinal and attractive ornamental plants. To date, the knowledge on the cytological and reproductive aspects of Gagnepainia have not been publicly available. Therefore, the aims of this research are to investigate the cytogenetic and pollen characters of Gagnepainia species using light, fluorescence, and scanning electron microscopes. The regular meiotic figures of 15 bivalents are found in both species and presented for the first time. These evidences indicate that Gagnepainia is diploid and contains 2n = 2x = 30 with basic number of x = 15. The mean nuclear DNA contents range from 1.986 pg in Gagnepainia sp., 2.090 pg in G. godefroyi to 2.195 pg in G. harmandii. Pollens of all species are monad, inaperturate, prolate with bilateral symmetry, and thick wall with fossulate exine sculpturing. The pollen size of G. harmandii (74.506 ± 5.075 μm, 56.082 ± 6.459 μm) is significantly larger than that of G. godefroyi (59.968 ± 3.484 μm, 45.439 ± 2.870 μm). Both 2C DNA content and pollen size are the effective characteristics for species discrimination. The reproductive evidence of high meiotic stability and normal pollen production indicate that both Gagnepainia species have high fertility and seed productivity, which are in accordance with the broad distribution. The present study provides good cytogenetic and pollen characters not only for plant identification, but also plant fertility assessment through plant genetic resource management and improvement of Gagnepainia.

One Major Challenge of Sequencing Large Plant Genomes Is to Know How Big They Really Are

Any project seeking to deliver a plant or animal reference genome sequence must address the question as to the completeness of the assembly. Given the complexity introduced particularly by the presence of sequence redundancy, a problem which is especially acute in polyploid genomes, this question is not an easy one to answer. One approach is to use the sequence data, along with the appropriate computational tools, the other is to compare the estimate of genome size with an experimentally measured mass of nuclear DNA. The latter requires a reference standard in order to provide a robust relationship between the two independent measurements of genome size. Here, the proposal is to choose the human male leucocyte genome for this standard: its 1C DNA amount (the amount of DNA contained within unreplicated haploid chromosome set) of 3.50 pg is equivalent to a genome length of 3.423 Gbp, a size which is just 5% longer than predicted by the most current human genome assembly. Adopting this standard, this paper assesses the completeness of the reference genome assemblies of the leading cereal crops species wheat, barley and rye.

Ploidy and domestication are associated with genome size variation in Palms

PREMISE OF THE STUDY

The genome size of a species (C-value) is associated with growth, development and adaptation to environmental changes. Angiosperm C-values range 1200-fold and frequently vary within species, although little is known about the impacts of domestication on genome size. Genome size variation among related species of palms is of evolutionary significance because changes characterize clades and may be associated with polyploidy, transposon amplifications, deletions, or rearrangements. Further knowledge of genome size will provide crucial information needed for planning of whole genome sequencing and accurate annotations. We studied the genome size of Cocos nucifera and its variation among cultivars, and compared it to values for related palms from the Attaleinae subtribe.

METHODS

Flow cytometric analysis of isolated nuclei from young palm leaves was used to estimate genome sizes of 23 coconut cultivars (Talls, Dwarfs, and hybrids) worldwide and 17 Cocoseae species. Ancestral genome size was reconstructed on a maximum likelihood phylogeny of Attaleinae from seven WRKY loci.

KEY RESULTS

The coconut genome is large-averaging 5.966 pg-and shows intraspecific variation associated with domestication. Variation among Tall coconuts was significantly greater than among Dwarfs. Attaleinae genomes showed moderate size variation across genera, except polyploids Jubaeopsis caffra, Voanioala gerardii, Beccariophoenix alfredii, and Allagoptera caudescens, which had larger genomes.

CONCLUSIONS

Our results contribute to the understanding of the relationship between domestication and genome size in long-lived tree crops and provide a basis for whole-genome sequencing of the coconut and other domesticated plants. Polyploidy evolved independently in two clades within Attaleinae.

Cytogenetic description of the earthworm Drawida ghilarovi Gates, 1969 (Oligochaeta, Moniligastridae) from the southern Russian Far East

Sixty-six specimens of the earthworm Drawida ghilarovi Gates, 1969 (Oligochaeta, Moniligastridae) from 15 localities of the southern Russian Far East were studied cytogenetically. We examined chromosome sets during mitosis and diakinesis as well as DNA content in the spermatogenous and somatic cell nuclei. The populations and morphs displayed no differences in karyotype and ploidy levels estimated in terms of both chromosome number and DNA mass index: n = 10, 2n = 20; c = 1.1 pg, 2c = 2.2 pg. We conclude that polyploidy as a species- or race-forming factor is not typical of these earthworms.

Flow cytometry and K-mer analysis estimates of the genome sizes of Bemisia tabaci B and Q (Hemiptera: Aleyrodidae)

The genome sizes of the B- and Q-types of the whitefly Bemisia tabaci (Gennnadius) were estimated using flow cytometry (Drosophila melanogaster as the DNA reference standard and propidium iodide (PI) as the fluorochrome) and k-mer analysis. For flow cytometry, the mean nuclear DNA content was 0.686 pg for B-type males, 1.392 pg for B-type females, 0.680 pg for Q-type males, and 1.306 pg for Q-type females. Based on the relationship between DNA content and genome size (1 pg DNA = 980 Mbp), the haploid genome size of B. tabaci ranged from 640 to 682 Mbp. For k-mer analysis, genome size of B-type by two methods were consistent highly, but the k-mer depth distribution graph of Q-type was not enough perfect and the genome size was estimated about 60 M larger than its flow cytometry result. These results corroborate previous reports of genome size based on karyotype analysis and chromosome counting. However, these estimates differ from previous flow cytometry estimates, probably because of differences in the DNA reference standard and dyeing time, which were superior in the current study. For Q-type genome size difference by two method, some discussion were also stated, and all these results represent a useful foundation for B. tabaci genomics research.

A universe of dwarfs and giants: genome size and chromosome evolution in the monocot family Melanthiaceae

• Since the occurrence of giant genomes in angiosperms is restricted to just a few lineages, identifying where shifts towards genome obesity have occurred is essential for understanding the evolutionary mechanisms triggering this process. • Genome sizes were assessed using flow cytometry in 79 species and new chromosome numbers were obtained. Phylogenetically based statistical methods were applied to infer ancestral character reconstructions of chromosome numbers and nuclear DNA contents. • Melanthiaceae are the most diverse family in terms of genome size, with C-values ranging more than 230-fold. Our data confirmed that giant genomes are restricted to tribe Parideae, with most extant species in the family characterized by small genomes. Ancestral genome size reconstruction revealed that the most recent common ancestor (MRCA) for the family had a relatively small genome (1C = 5.37 pg). Chromosome losses and polyploidy are recovered as the main evolutionary mechanisms generating chromosome number change. • Genome evolution in Melanthiaceae has been characterized by a trend towards genome size reduction, with just one episode of dramatic DNA accumulation in Parideae. Such extreme contrasting profiles of genome size evolution illustrate the key role of transposable elements and chromosome rearrangements in driving the evolution of plant genomes.

Genome size analyses of Pucciniales reveal the largest fungal genomes

Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.