Plant Genome Size Research Articles

Evolution of Plant Genome Size and Composition.

The rapid development of sequencing technology has led to an explosion of plant genome data, opening up more opportunities for research in the field of comparative evolutionary analysis of plant genomes. In this review, we take changes in plant genome size and composition as a starting point and describe the effects of polyploidy, whole genome duplication and transposable elements changes on plant genome architecture and evolution, respectively. In addition, to address the lack of relevant information in some areas, we also collected and analyzed 234 representative plant genome data as a supplement. We aim to provide a global, up-to-date summary of information on plant genome architecture and evolution in this review.

Biotic and abiotic factors associated with genome size evolution in oaks.

The evolutionary processes that underlie variation in plant genome size have been much debated. Abiotic factors are thought to have played an important role, with negative and positive correlations between genome size and seasonal or stressful climatic conditions being reported in several systems. In turn, variation in genome size may influence plant traits which affect interactions with other organisms, such as herbivores. The mechanisms underlying evolutionary linkages between plant genome size and biotic and abiotic factors nonetheless remain poorly understod. To address this gap, we conducted phylogenetically controlled analyses testing for associations between genome size, climatic variables, plant traits (defenses and nutrients), and herbivory across 29 oak (Quercus) species. Genome size is significantly associated with both temperature and precipitation seasonality, whereby oak species growing in climates with lower and less variable temperatures but more variable rainfall had larger genomes. In addition, we found a negative association between genome size and leaf nutrient concentration (found to be the main predictor of herbivory), which in turn led to an indirect effect on herbivory. A follow-up test suggested that the association between genome size and leaf nutrients influencing herbivory was mediated by variation in plant growth, whereby species with larger genomes have slower growth rates, which in turn are correlated with lower nutrients. Collectively, these findings reveal novel associations between plant genome size and biotic and abiotic factors that may influence life history evolution and ecological dynamics in this widespread tree genus.

Centromere drive may propel the evolution of chromosome and genome size in plants.

Genome size is influenced by natural selection and genetic drift acting on variations from polyploidy and repetitive DNA sequences. We hypothesized that centromere drive, where centromeres compete for inclusion in the functional gamete during meiosis, may also affect genome and chromosome size. This competition occurs in asymmetric meiosis, where only one of the four meiotic products becomes a gamete. If centromere drive influences chromosome size evolution, it may also impact post-polyploid diploidization, where a polyploid genome is restructured to function more like a diploid through chromosomal rearrangements, including fusions. We tested if plant lineages with asymmetric meiosis exhibit faster chromosome size evolution compared to those with only symmetric meiosis, which lack centromere drive as all four meiotic products become gametes. We also examined if positive selection on centromeric histone H3 (CENH3), a protein that can suppress centromere drive, is more frequent in these asymmetric lineages. We analyzed plant groups with different meiotic modes: asymmetric in gymnosperms and angiosperms, and symmetric in bryophytes, lycophytes, and ferns. We selected species based on available CENH3 gene sequences and chromosome size data. Using Ornstein-Uhlenbeck evolutionary models and phylogenetic regressions, we assessed the rates of chromosome size evolution and the frequency of positive selection on CENH3 in these clades. Our analyses showed that clades with asymmetric meiosis have a higher frequency of positive selection on CENH3 and increased rates of chromosome size evolution compared to symmetric clades. Our findings support the hypothesis that centromere drive accelerates chromosome and genome size evolution, potenatially also influencing the process of post-polyploid diploidization. We propose a model which in a single famework helps explain the stability of chromosome size in symmetric lineages (bryophytes, lycophytes, and ferns) and its variability in asymmetric lineages (gymnosperms and angiosperms), providing a foundation for future research in plant genome evolution.

Genome size and chromosome number variation in sugarcane (Saccharum spp.) families and phenotypically contrasting Saccharum genotypes

AbstractModern sugarcane (Saccharum spp.) cultivars originated from an intricate hybridization process, resulting in complex polyploid and aneuploid genomes. Flow cytometry (FCM), which has emerged as a precise and fast method for research on genome size in plants, has potential to unveil key aspects of sugarcane cytogenetics. In this study, FCM probes were conducted to estimate 2C DNA content in 175 Saccharum genotypes embracing phenotypically contrasting canes (commercial cultivars, energy‐cane hybrids, and a Saccharum spontaneum accession) and full‐sib sugarcane families. FCM‐mediated DNA content estimates exhibited high accuracy in predicting chromosome numbers, offering a time‐efficient alternative to classical cytogenetic procedure. Low‐magnitude correlations detected between DNA content and phenotypic traits suggest that indirect selection of agronomic traits using FCM‐mediated DNA content estimates may not be efficient. DNA content variation patterns in sugarcane families varied according to the crossing, and revealed transgressive variations associated with rampant aneuploidy. Altogether, the findings uncover that loss or gain of genetic material constitutes a source of high genetic variability that may substantially impact on crop breeding.

Genome size variation in Cape schoenoid sedges (Schoeneae) and its ecophysiological consequences.

Increases in genome size in plants-often associated with larger, low-density stomata and greater water-use efficiency (WUE)-could affect plant ecophysiological and hydraulic function. Variation in plant genome size is often due to polyploidy, having occurred repeatedly in the austral sedge genus Schoenus in the Cape Floristic Region (CFR), while species in the other major schoenoid genus in the region, Tetraria, have smaller genomes. Comparing these genera is useful as they co-occur at the landscape level, under broadly similar bioclimatic conditions. We hypothesized that CFR Schoenus have greater WUE, with lower maximum stomatal conductance (gwmax) imposed by larger, less-dense stomata. We investigated relationships between genome size and stomatal parameters in a phylogenetic context, reconstructing a phylogeny of CFR-occurring Schoeneae (Cyperaceae). Species' stomatal and functional traits were measured from field-collected and herbarium specimens. Carbon stable isotopes were used as an index of WUE. Genome size was derived from flow-cytometric measurements of leafy shoots. Evolutionary regressions demonstrated that stomatal size and density covary with genome size, positively and negatively, respectively, with genome size explaining 72-75% of the variation in stomatal size. Larger-genomed species had lower gwmax and C:N ratios, particularly in culms. We interpret differences in vegetative physiology between the genera as evidence of more-conservative strategies in CFR Schoenus compared to the more-acquisitive Tetraria. Because Schoenus have smaller, reduced leaves, they likely rely more on culm photosynthesis than Tetraria. Across the CFR Schoeneae, ecophysiology correlates with genome size, but confounding sources of trait variation limit inferences about causal relationships between traits.

Flow Cytometry for Estimating Plant Genome Size: Revisiting Assumptions, Sources of Variation, Reference Standards, and Best Practices

Flow cytometry has been widely used to estimate relative and absolute genome sizes (DNA contents) of plants for more than 50 years. However, the accuracy of these estimates can vary widely because of many factors, including errors in the genome size estimates of reference standards and various experimental methods. The objectives of this study were to reassess genome sizes of commonly used reference standards and quantify sources of variation and error in estimating plant genome sizes that arise from buffers, confounding plant tissues, tissue types, and plant reference standards using both 4′,6-diamidino-2-phenylindole (DAPI) and propidium iodide (PI) fluorochromes. Five separate studies were performed to elucidate these objectives. Revised estimates of genome sizes of commonly used plant reference standards were determined using human male leukocytes as a primary standard with an updated genome size (6.15 pg; 12.14% lower than that of earlier studies) using both DAPI and PI fluorochromes. Comparison of six different buffers (Galbraith’s, LB01, MB01, MgSO4, Otto’s, and Sysmex) resulted in variations in genome size estimates by as much as 18.1% for a given taxon, depending on the buffer–fluorochrome combination. The addition of different confounding plant tissues (representing 10 diverse taxa and associated secondary metabolites) resulted in variations in genome size estimates by as much as 10.3%, depending on the tissue–fluorochrome combination. Different plant tissue types (leaf color/exposure and roots) resulted in a variation in genome size estimates of 10.7%, independent of the fluorochrome. The selection of different internal reference standards introduced an additional variation in genome size estimates of 5.9%, depending on the standard–fluorochrome combination. The choice of fluorochrome (DAPI vs. PI) had one of the largest impacts on genome size estimates and differed by as much as 32.9% for Glycine max ‘Polanka’ when using human male leukocytes as an internal standard. A portion of this variation (∼10.0%) can be attributed to the base pair (bp) bias of DAPI and variations in Guanine-Cytosine (GC):Adenine-Thymine (AT) ratios between the sample and standard. However, as much as 22.9% of the variation in genome size estimates may result from how effectively these fluorochromes stain and report the genome. The combined variation/error from all these factors (excluding variation from bp bias for different fluorochromes, and assuming variations from confounding tissues and tissue types to both result from secondary metabolites) totaled 57.6%. Additional details of how selected factors impact accuracy, precision, and the interaction of these factors are presented. Overall, flow cytometry can be precise, repeatable, and extremely valuable for determining the relative genome size and ploidy of closely related plants when using consistent methods, regardless of fluorochrome. However, accurate determination of the absolute genome size by flow cytometry remains elusive, and estimates of genome size using flow cytometry should be considered gross approximations that may vary by ±29% or more as a function of experimental methods and plant environments. Additional recommendations of best practices are provided.

Apomixis and the paradox of sex in plants.

The predominance of sex in eukaryotes, despite the high costs of meiosis and mating, is still an evolutionary enigma. Many theories have been proposed, none of them being conclusive on its own, and they are partly not well applicable to land plants. Sexual reproduction is obligate in embryophytes for the great majority of species. This review will compare the main forms of sexual and asexual reproduction in ferns and angiosperms, based on the generation cycling of sporophyte and gametophyte (leaving vegetative propagation aside). The benefits of sexual reproduction for maintenance of genomic integrity compared to asexuality will be discussed in the light of developmental, evolutionary, genetic and phylogenetic studies. Asexual reproduction represents modifications of the sexual pathway, with various forms of facultative sexuality. For sexual land plants, meiosis provides direct DNA repair mechanisms of oxidative damage in reproductive tissues. The ploidy alternations of meiosis-syngamy cycles, and prolonged, multicellular stages in the haploid phase in the gametophytes provide a high efficiency of purifying selection against recessive deleterious mutations. Asexual lineages might buffer effects of such mutations via polyploidy, and can purge the mutational load via facultative sexuality. The role of organelle-nuclear genome compatibility for maintenance of genome integrity is still not well understood. The costs of mating are in plants in general low because of predominant hermaphroditism. Phylogenetic patterns in the Archaeplastid clade suggest that high frequencies of sexuality in land plants are concomitant with a stepwise increase of intrinsic and extrinsic stress factors. Furthermore, expansion of genome size in land plants would increase the potential mutational load. Sexual reproduction appears to be essential for keeping long term genomic integrity, and only rare combinations of extrinsic and intrinsic factors allow for shifts to asexuality.

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.

Phylogeny more than plant height and leaf area explains variance in seed mass.

Although variation in seed mass can be attributed to other plant functional traits such as plant height, leaf size, genome size, growth form, leaf N and phylogeny, until now, there has been little information on the relative contributions of these factors to variation in seed mass. We compiled data consisting of 1071 vascular plant species from the literature to quantify the relationships between seed mass, explanatory variables and phylogeny. Strong phylogenetic signals of these explanatory variables reflected inherited ancestral traits of the plant species. Without controlling phylogeny, growth form and leaf N are associated with seed mass. However, this association disappeared when accounting for phylogeny. Plant height, leaf area, and genome size showed consistent positive relationship with seed mass irrespective of phylogeny. Using phylogenetic partial R2s model, phylogeny explained 50.89% of the variance in seed mass, much more than plant height, leaf area, genome size, leaf N, and growth form explaining only 7.39%, 0.58%, 1.85%, 0.06% and 0.09%, respectively. Therefore, future ecological work investigating the evolution of seed size should be cautious given that phylogeny is the best overall predictor for seed mass. Our study provides a novel avenue for clarifying variation in functional traits across plant species, improving our better understanding of global patterns in plant traits.

Best practices for instrument settings and raw data analysis in plant flow cytometry.

Flow cytometry (FCM) is now the most widely used method to determine ploidy levels and genome size of plants. To get reliable estimates and allow reproducibility of measurements, the methodology should be standardized and follow the best practices in the field. In this article, we discuss instrument calibration and quality control and various instrument and acquisition settings (parameters, flow rate, number of events, scales, use of discriminators, peak positions). These settings must be decided before measurements because they determine the amount and quality of the data and thus influence all downstream analyses. We describe the two main approaches to raw data analysis (gating and histogram modeling), and we discuss their advantages and disadvantages. Finally, we provide a summary of best practice recommendations for data acquisition and raw data analysis in plant FCM.

The Plant DNA C-Values Database: A One-Stop Shop for Plant Genome Size Data.

Genome size is a plant character with far-reaching implications, ranging from impacts on the financial and computing feasibility of sequencing and assembling genomes all the way to influencing the very ecology and evolution of species. The increasing recognition of the role of genome size in plant science has led to a rising demand for comprehensive and easily accessible sources of genome size data. The Plant DNA C-values database has established itself as a trusted and widely used central hub for users needing to access available plant genome size data, complemented with related cytogenetic (ploidy level) and karyological (chromosome number) information where available. Since its inception in 2001, the database has undergone six major updates to incorporate newly available genome size information, leading to the most recent release (Release 7.1), which comprises data for 12,273 species across all the major land plant and some algal lineages. Here we describe how to use the database efficiently, making use of its different query and filtering settings.

Fern Spores-"Ready-to-Use" Standards for Plant Genome Size Estimation Using a Flow Cytometric Approach.

Spores and pollen of plants were used as flow cytometric materials to efficiently infer genome sizes. Given this advantage, they hold great potential for various flow cytometric applications, particularly as plant genome size standards. To develop such novel standards, we investigated conditions of pretreatment (bead vortex), buffer, and reliable genome sizes of three fern spore collections-Cibotium taiwanense "Kuo4395", Sphaeropteris lepifera "Tang0001", and Alsophila metteniana "Lee s.n.". Additionally, up to 30 year-old spore collections were obtained from herbarium specimens and from samples stored at 4 °C; their spore nuclei were extracted, and the quality and quantity of these nucleus extractions through storage ages were examined. Nuclear extractions with a longer bead vortex duration or lower spore/bead ratio generally resulted in a higher recovered quantity but a lower quality or purity. For each spore standard, the protocol optimization was determined by their performance in bead vortex conditions, and a 1C genome size was further inferred by linear regression (C. taiwanense "Kuo4395" = 5.058 pg; S. lepifera "Tang0001" = 7.117 pg; and A. metteniana "Lee s.n." = 19.379 pg). Spore nucleus quality and quantity are significantly negatively correlated with storage ages. Nuclear extractions of 10-year-old refrigerated spores remained qualified as a genome size standard; however, none of the herbarium spore collections fit such criteria. Our study is the first to develop and apply dried and refrigerated spores for genome size standards. These standards are ready to use, easy to manipulate, and feature long-term storage in comparison with traditionally used standards of fresh leaves.

Plant genome size modulates grassland community responses to multi-nutrient additions.

Grassland ecosystems cover c. 40% of global land area and contain c. 40% of soil organic carbon. Understanding the effects of adding nutrients to grasslands is essential because they provide much of our food, support diverse ecosystem services and harbor rich biodiversity. Using the meadow steppe (grassland) study site of Inner Mongolia, we manipulated seven key nutrients and a cocktail of micronutrients to examine their effects on grassland biomass productivity and diversity. The results, explained in structural equation models, link two previously disparate hypotheses in grassland ecology: (1) the light asymmetry competition hypothesis and (2) the genome size-nutrient interaction hypothesis. We show that aboveground net primary productivity increases predominantly from species with large genome sizes with the addition of nitrogen, and nitrogen plus phosphorus. This drives an asymmetric competition for light, causing a decline in species richness mainly in species with small genome sizes. This dynamic is likely to be caused by the nutrient demands of the nucleus and/or the scaling effects of nuclear size on cell size which impact water use efficiency. The model will help inform the best management approaches to reverse the rapid and unprecedented degradation of grasslands globally.

Genome size and gas chromatography-mass spectrometry (GC-MS) analysis of field-grown and in vitro regenerated Pluchea lanceolata plants.

Pluchea lanceolata is a threatened pharmacologically important plant from the family Asteraceae. It is a source of immunologically active compounds; large-scale propagation may offer compounds with medicinal benefits. Traditional propagation method is ineffective as the seeds are not viable; and root sprout propagation is a slow process and produces less numbers of plants. Plant tissue culture technique is an alternative, efficient method for increasing mass propagation and it also facilitate genetic improvement. The present study investigated a three-way regeneration system in P. lanceolata using indirect shoot regeneration (ISR), direct shoot regeneration (DSR), and somatic embryo mediated regeneration (SER). Aseptic leaf and nodal explants were inoculated on Murashige and Skoog (MS) medium amended with plant growth regulators (PGRs), 2,4-dichlorophenoxy acetic acid (2,4-D), 1-naphthalene acetic acid (NAA), and 6-benzyl amino purine (BAP) either singly or in combinations. Compact, yellowish green callus was obtained from leaf explants in 1.0 mg/l BAP (89.10%) added medium; ISR percentage was high, i.e., 69.33% in 2.0 mg/l BAP + 0.5 mg/l NAA enriched MS with 4.02 mean number of shoots per callus mass. Highest DSR frequency (67.15%) with an average of 5.62 shoot numbers per explant was noted in 0.5 mg/l BAP added MS medium. Somatic embryos were produced in 1.0 mg/l NAA fortified medium with 4.1 mean numbers of somatic embryos per culture. On BAP (1.0 mg/l) + 0.5 mg/l gibberellic acid (GA3) amended medium, improved somatic embryo germination frequency (68.14%) was noted showing 12.18 mean numbers of shoots per culture. Histological and scanning electron microscopic (SEM) observation revealed different stages of embryos, confirming somatic embryogenesis in P. lanceolata. Best rooting frequency (83.95%) of in vitro raised shootlets was obtained in 1.0 mg/l IBA supplemented half MS medium with a maximum of 7.83 roots per shoot. The regenerated plantlets were transferred to the field with 87% survival rate. The 2C genome size of ISR, DSR, and SER plants was measured and noted to be 2.24, 2.25, and 2.22 pg respectively, which are similar to field-grown mother plant (2C = 2.26 pg). Oxidative and physiological events suggested upregulation of enzymatic activities in tissue culture regenerated plants compared to mother plants, so were photosynthetic pigments. Implementation of gas chromatography-mass spectrometry (GC–MS) technique on in vivo and in vitro raised plants revealed the presence of diverse phyto-chemicals. The yields of alpha amyrin and lupeol (medicinally important triterpenoids) were quantified using high-performance thin-layer chromatography (HPTLC) method and enhanced level of alpha amyrin (2.129 µg g−1 dry wt) and lupeol (1.232 µg g−1 dry wt) was noted in in vitro grown leaf tissues, suggesting in vitro conditions act as a potential trigger for augmenting secondary metabolite synthesis. The present protocol represents a reliable mass propagation technique in producing true-to-type plants of P. lanceolata, conserving 2C DNA and ploidy successfully without affecting genetic homogeneity.Supplementary InformationThe online version contains supplementary material available at 10.1007/s13353-022-00727-7.

Research Progress of AP2/ERF Transcription Factor Family in Important Crops

Plants have the ability to show responses against various environmental stresses. It is one of the necessities to understand stress response mechanisms to improve crops productivity and quality, under the stressed condition. The AP2/ERF transcription factors are one of the putative candidates that are involved in the regulation of biotic and abiotic stress. Most of the research has been conducted on functional analysis of AP2/ERF genes in many plants; however, a comprehensive review is required to show a broad picture of functionally characterized AP2/ERF in different plants. In this study, a comprehensive review is carried on genome-wide studies of AP2/ERF gene family and their evolutionary divergence in plant species including mustard (Arabidopsis, brassica), cereal (rice, wheat, maize, sorghum), and fiber (upland cotton and island cotton). Review exhibited that AP2/ERF superfamily is classified into four sub-families e.g. AP2, DREB, ERF, RAV and solicit, in which the ERF was the largest sub-family of AP2/ERF superfamily. Each subfamily was further divided into multiple groups and sub-groups. Furthermore, each plant species showed different number of paralogs showing correspondence to the plant genome size .e.g. higher genome possess higher gene copy number. The change in copy number may be due to either tandem gene duplication or whole genome duplication during evolutionary adaptation that developed special feature in plant species under environmental stresses. Moreover, current study also surveyed on the expression of AP/ERF genes with the conclusion that expression of AP2/ERF produced tolerance against biotic and abiotic stresses. However further studies are required to improve crops resistance by studying the same variables and gene families in different plants.

Genome Size Variation Assessment in Vitis vinifera L. Landraces in Ibiza and Formentera (Balearic Islands).

Plant genome size has many applications in different biological fields including ecology and plant breeding. The 2C value for Vitis vinifera L. has not been widely studied; furthermore, to date, no data from local landraces in the Pityusic Islands (the two smaller inhabited Balearic Islands, Ibiza, and Formentera) have been reported. This research aims to contribute to this knowledge and investigate whether there are variations between different grape landraces cultivated in Ibiza and Formentera and also among the same landraces on each island. To this end, 36 accessions of 15 cultivars and 6 landraces, identified with SSR markers, were assessed using flow cytometry. The results revealed that 2C values ranged from 1.09 pg to 1.28 pg. There were statistically significant differences in ‘AG1’ and ‘AG2’ landraces and ‘Santa Magdalena’, ‘Garnatxa’, ‘Danugue’, and ‘Valencí tinto/Grumier’ cultivars. No statistically significant differences were found in terms of the genome size content between islands. Statistically significant differences were found in accessions within ‘AG2’ landrace group and ‘Beba’ cultivar. The results presented here constitute the first-ever reported information on genome size in the genus Vitis vinifera in Pityusic, Balearic, and, in general, Spanish accessions, and they are one of the largest prospections in this field for this species anywhere. Further research should be conducted to explain the differences in nuclear DNA content found between landraces and cultivars studied here with others cultivated in different islands or countries to understand whether genome size varies in modern cultivars compared with local landraces. Additionally, it would be interesting to investigate whether there is a relationship between genome size and adaptations to diverse climatology conditions, crop management, and ripening characteristics.

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 0.49pg to 25.8pg 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.

Correlated evolution of seed mass and genome size varies among life forms in flowering plants

AbstractSeeds show important variation as plant regenerative units among species, but their evolutionary co-variations with other plant characteristics are still poorly understood. Whilst a positive association of seed mass with genome size (GS) and life forms has already been documented, a broad-scale quantification of their evolutionary correlation and adaptive selection has never been conducted. Here, we tested for correlated evolution of seed mass and GS towards distinct selective regimes related to life form in angiosperms. In particular, we tested the hypothesis that the selection toward lighter seeds and smaller genomes is stronger for annual plants, ensuring high regenerative potential. Using multivariate evolutionary models over a dataset containing 3242 species, we showed an overall positive correlated evolution of seed mass and GS deviating from a pure drift process. Instead, evolutionary changes in seed and genome sizes were driven by adaptive selection towards optimal values differing among life forms. Specifically, the evolutionary optima towards which the seed and genome sizes evolve show a covariation toward small values in annuals, intermediate values in perennial herbs and a trade-off between seed mass and GS in woody plants. Moreover, the evolutionary correlation between seed mass and GS is strongest in annuals as an adaption to complete their life cycle in a short time window, when environmental conditions are favourable for regeneration and development to maturity. The asymmetry in the correlated evolution acting on seed and genome sizes due to life form could explain how life-history traits interplay with functional traits and how plants have evolved diverse successful life-history strategies.

Green plant genomes: What we know in an era of rapidly expanding opportunities

Green plants play a fundamental role in ecosystems, human health, and agriculture. As de novo genomes are being generated for all known eukaryotic species as advocated by the Earth BioGenome Project, increasing genomic information on green land plants is essential. However, setting standards for the generation and storage of the complex set of genomes that characterize the green lineage of life is a major challenge for plant scientists. Such standards will need to accommodate the immense variation in green plant genome size, transposable element content, and structural complexity while enabling research into the molecular and evolutionary processes that have resulted in this enormous genomic variation. Here we provide an overview and assessment of the current state of knowledge of green plant genomes. To date fewer than 300 complete chromosome-scale genome assemblies representing fewer than 900 species have been generated across the estimated 450,000 to 500,000 species in the green plant clade. These genomes range in size from 12 Mb to 27.6 Gb and are biased toward agricultural crops with large branches of the green tree of life untouched by genomic-scale sequencing. Locating suitable tissue samples of most species of plants, especially those taxa from extreme environments, remains one of the biggest hurdles to increasing our genomic inventory. Furthermore, the annotation of plant genomes is at present undergoing intensive improvement. It is our hope that this fresh overview will help in the development of genomic quality standards for a cohesive and meaningful synthesis of green plant genomes as we scale up for the future.

Genome size variation in Deschampsia cespitosa sensu lato (Poaceae) in Eurasia

The grass Deschampsia cespitosa is a variable taxon out of which many varieties, subspecies and endemic species have been separated. In this paper, the variation in genome size (GS) and ploidy of this grass including several of its subspecies and two related species in Eurasia was investigated by flow cytometric (FCM) measurements. GS and ploidy data were also related to specific environments and reproduction mode. Ploidy levels found by FCM were confirmed by chromosome counts of diploid (2n = 26) and tetraploid (2n = 52) samples. Seminiferous (seed bearing) D. cespitosa was mainly diploid (GS between 3.754 and 5.438 pg/1C). GS variation in diploids showed a geographic pattern with a significant difference (H = 41,441, P < 0.001) between European (median = 4.377 pg) and Asian (median = 4.881 pg) accessions. Genome size (1C) in tetraploids ranged from 7.9426 to 9.0399 pg. Tetraploid seminiferous D. cespitosa was found mostly in disturbed habitats in western and southern Europe, while tetraploids in Asia were registered in wet Arctic habitats. Genome size (1C between 8.3278 and 8.8603 pg) of the pseudoviviparous plants (spikelets produce plantlets asexually) of wet habitats in central and northern Europe indicated tetraploidy. A putative triploid (GS 6.6817 pg) was detected in Iceland. Summing up, we found a high variation in GS on the geographic scale with significant regional differences in diploid D. cespitosa. Among the tetraploids, the asexually reproducing plants were bound to specific habitats, while the seminiferous plants showed a habitat preference similar to the diploids.