Rapidly radiated groups are usually accompanied by unclear lineage and taxa delineation, which complicates their better understanding in terms of biodiversity, evolutionary processes, and taxonomic treatment. The most species-rich orchid subtribe, Pleurothallidinae, exemplifies an extremely diverse group with a complex evolutionary history associated with Andean orography. Here we combined multi-loci phylogeny reconstruction (HybSeq), genome-wide traits (inferred by flow cytometry), spatial analyses, and biogeography to investigate the evolutionary intricacy of one clade of Pleurothallidinae orchids. To achieve deep insights, we performed multiple species tree reconstruction approaches with the implementation of custom scripts to reveal sources of topological discrepancies and alternative evolutionary scenarios. The phylogeny clearly resolves the delimitation of the main evolutionary lineages corresponding to the accepted genera, with the exception of the genus Specklinia, which is divided into three distinct monophyletic lineages whose taxonomic treatment is proposed. Genome-wide characters (especially genome size) show an association with precipitation seasonality in a geographical context, and partial endoreplication, a unique character of orchids, is geographically restricted to the Andes, Central America, and the Caribbean. Specifically, the Andean region exemplifies the prevalence of bigger genome size and higher GC content, resulting from a higher proportion of species with partial endoreplication. The Andean origin of the clade was also revealed by biogeographic analysis. Our comprehensive approach has provided deep insights into the evolution of this clade and may be a useful tool for unraveling the intricate evolutionary history of similarly complex lineages.

• Keywords
• Andes, GC content, HybSeq, Pleurothallidinae, endoreplication, evolution, genome size, spatial analysis,
• MeSH
• Biological Evolution * MeSH
• Genome Size MeSH
• Phylogeny * MeSH
• Genome, Plant * genetics   MeSH
• Evolution, Molecular MeSH
• Orchidaceae * genetics   classification   MeSH
• Publication type
• Journal Article MeSH

BACKGROUND: 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. METHODS: We analysed 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. RESULTS: 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. CONCLUSIONS: Our findings support the hypothesis that centromere drive accelerates chromosome and genome size evolution, potentially also influencing the process of post-polyploid diploidization. We propose a model which in a single framework 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.

• Keywords
• Angiosperms, CENH3, asymmetric and symmetric meiosis, bryophytes, centromere drive, chromosome size, ferns, genome size, gymnosperms, lycophytes, post-polyploid diploidization,
• MeSH
• Biological Evolution MeSH
• Centromere * genetics   MeSH
• Chromosomes, Plant * genetics   MeSH
• Cycadopsida genetics   MeSH
• Genome Size * MeSH
• Phylogeny MeSH
• Genome, Plant * genetics   MeSH
• Histones genetics   metabolism   MeSH
• Ferns genetics   physiology   MeSH
• Magnoliopsida genetics   MeSH
• Meiosis * genetics   MeSH
• Evolution, Molecular * MeSH
• Polyploidy MeSH
• Plants genetics   MeSH
• Selection, Genetic MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Histones MeSH

BACKGROUND: Species of the carnivorous family Lentibulariaceae exhibit the smallest genomes in flowering plants. We explored the hypothesis that their minute genomes result from the unique mitochondrial cytochrome c oxidase (COX) mutation. The mutation may boost mitochondrial efficiency, which is especially useful for suction-bladder traps of Utricularia, but also increase DNA-damaging reactive oxygen species, leading to genome shrinkage through deletion-biased DNA repair. We aimed to explore the impact of this mutation on genome size, providing insights into genetic mutation roles in plant genome evolution under environmental pressures. METHODS: We compiled and measured genome and mean chromosome sizes for 127 and 67 species, respectively, representing all three genera (Genlisea, Pinguicula and Utricularia) of Lentibulariaceae. We also isolated and analysed COX sequences to detect the mutation. Through phylogenetic regressions and Ornstein-Uhlenbeck models of trait evolution, we assessed the impact of the COX mutation on the genome and chromosome sizes across the family. RESULTS: Our findings reveal significant correlations between the COX mutation and smaller genome and chromosome sizes. Specifically, species carrying the ancestral COX sequence exhibited larger genomes and chromosomes than those with the novel mutation. This evidence supports the notion that the COX mutation contributes to genome downsizing, with statistical analyses confirming a directional evolution towards smaller genomes in species harbouring these mutations. CONCLUSIONS: Our study confirms that the COX mutation in Lentibulariaceae is associated with genome downsizing, probably driven by increased reactive oxygen species production and subsequent DNA damage requiring deletion-biased repair mechanisms. While boosting mitochondrial energy output, this genetic mutation compromises genome integrity and may potentially affect recombination rates, illustrating a complex trade-off between evolutionary advantages and disadvantages. Our results highlight the intricate processes by which genetic mutations and environmental pressures shape genome size evolution in carnivorous plants.

• Keywords
• Genlisea, Pinguicula, Utricularia, Carnivory, Lentibulariaceae, chromosome size, cytochrome oxidase, genome size, recombination rate, smallest genomes,
• MeSH
• Genome Size * MeSH
• Phylogeny MeSH
• Genome, Plant * MeSH
• Magnoliopsida genetics   MeSH
• Evolution, Molecular MeSH
• Mutation MeSH
• Electron Transport Complex IV genetics   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Electron Transport Complex IV MeSH

BACKGROUND AND AIMS: It is unclear how widespread polyploidy is throughout the largest holocentric plant family - the Cyperaceae. Because of the prevalence of chromosomal fusions and fissions, which affect chromosome number but not genome size, it can be impossible to distinguish if individual plants are polyploids in holocentric lineages based on chromosome count data alone. Furthermore, it is unclear how differences in genome size and ploidy levels relate to environmental correlates within holocentric lineages, such as the Cyperaceae. METHODS: We focus our analyses on tribe Schoeneae, and more specifically the southern African clade of Schoenus. We examine broad-scale patterns of genome size evolution in tribe Schoeneae and focus more intensely on determining the prevalence of polyploidy across the southern African Schoenus by inferring ploidy level with the program ChromEvol, as well as interpreting chromosome number and genome size data. We further investigate whether there are relationships between genome size/ploidy level and environmental variables across the nutrient-poor and summer-arid Cape biodiversity hotspot. KEY RESULTS: Our results show a large increase in genome size, but not chromosome number, within Schoenus compared to other species in tribe Schoeneae. Across Schoenus, there is a positive relationship between chromosome number and genome size, and our results suggest that polyploidy is a relatively common process throughout the southern African Schoenus. At the regional scale of the Cape, we show that polyploids are more often associated with drier locations that have more variation in precipitation between dry and wet months, but these results are sensitive to the classification of ploidy level. CONCLUSIONS: Polyploidy is relatively common in the southern African Schoenus, where a positive relationship is observed between chromosome number and genome size. Thus, there may be a high incidence of polyploidy in holocentric plants, whose cell division properties differ from monocentrics.

• Keywords
• Schoenus, Aneuploidy, Cape Floristic Region, Cyperaceae, Schoeneae, chromosome fission, chromosome fusion, climate, genome size, holocentric chromosomes, polyploidy, soil chemistry,
• MeSH
• Biodiversity MeSH
• Chromosomes, Plant MeSH
• Phylogeny MeSH
• Genome, Plant MeSH
• Ploidies MeSH
• Polyploidy MeSH
• Cyperaceae * genetics   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

BACKGROUND AND AIMS: While variation in genome size and chromosome numbers and their consequences are often investigated in plants, the biological relevance of variation in chromosome size remains poorly known. Here, we examine genome and mean chromosome size in the cyperid clade (families Cyperaceae, Juncaceae and Thurniaceae), which is the largest vascular plant lineage with predominantly holocentric chromosomes. METHODS: We measured genome size in 436 species of cyperids using flow cytometry, and augment these data with previously published datasets. We then separately compared genome and mean chromosome sizes (2C/2n) amongst the major lineages of cyperids and analysed how these two genomic traits are associated with various environmental factors using phylogenetically informed methods. KEY RESULTS: We show that cyperids have the smallest mean chromosome sizes recorded in seed plants, with a large divergence between the smallest and largest values. We found that cyperid species with smaller chromosomes have larger geographical distributions and that there is a strong inverse association between mean chromosome size and number across this lineage. CONCLUSIONS: The distinct patterns in genome size and mean chromosome size across the cyperids might be explained by holokinetic drive. The numerous small chromosomes might function to increase genetic diversity in this lineage where crossovers are limited during meiosis.

• Keywords
• Chromosome number, Cyperaceae, Juncaceae, Thurniaceae, chromosome size, distribution range size, genome size, holocentric chromosomes, holokinetic drive,
• MeSH
• Chromosomes, Plant * genetics   MeSH
• Genome Size MeSH
• Phylogeny MeSH
• Genome, Plant genetics   MeSH
• Evolution, Molecular * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

The estimation of nuclear DNA content has been by far the most popular application of flow cytometry in plants. Because flow cytometry measures relative fluorescence intensities of nuclei stained by a DNA fluorochrome, ploidy determination, and estimation of the nuclear DNA content in absolute units both require comparison to a reference standard of known DNA content. This implies that the quality of the results obtained depends on the standard selection and use. Internal standardization, when the nuclei of an unknown sample and the reference standard are isolated, stained, and measured simultaneously, is mandatory for precise measurements. As DNA peaks representing G1 /G0 nuclei of the sample and standard appear on the same histogram of fluorescence intensity, the quotient of their position on the fluorescence intensity axis provides the quotient of DNA amounts. For the estimation of DNA amounts in absolute units, a number of well-established standards are now available to cover the range of known plant genome sizes. Since there are different standards in use, the standard and the genome size assigned to it has always to be reported. When none of the established standards fits, the introduction of a new standard species is needed. For this purpose, the regression line approach or simultaneous analysis of the candidate standard with several established standards should be prioritized. Moreover, the newly selected standard organism has to fulfill a number of requirements: it should be easy to identify and maintain, taxonomically unambiguous, globally available, with known genome size stability, lacking problematic metabolites, suitable for isolation of sufficient amounts of nuclei, and enabling measurements with low coefficients of variation of DNA peaks, hence suitable for the preparation of high quality samples.

• Keywords
• C-value, GC content, best practices, flow cytometry, genome size, plant sciences, plant standard species, standardization,
• MeSH
• DNA, Plant genetics   MeSH
• Genome, Plant * MeSH
• Ploidies * MeSH
• Flow Cytometry methods   MeSH
• Reference Standards MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Names of Substances
• DNA, Plant MeSH

BACKGROUND: Carnivorous plants are an ecological group of approx. 810 vascular species which capture and digest animal prey, absorb prey-derived nutrients and utilize them to enhance their growth and development. Extant carnivorous plants have evolved in at least ten independent lineages, and their adaptive traits represent an example of structural and functional convergence. Plant carnivory is a result of complex adaptations to mostly nutrient-poor, wet and sunny habitats when the benefits of carnivory exceed the costs. With a boost in interest and extensive research in recent years, many aspects of these adaptations have been clarified (at least partly), but many remain unknown. SCOPE: We provide some of the most recent insights into substantial ecophysiological, biochemical and evolutional particulars of plant carnivory from the functional viewpoint. We focus on those processes and traits in carnivorous plants associated with their ecological characterization, mineral nutrition, cost-benefit relationships, functioning of digestive enzymes and regulation of the hunting cycle in traps. We elucidate mechanisms by which uptake of prey-derived nutrients leads to stimulation of photosynthesis and root nutrient uptake. CONCLUSIONS: Utilization of prey-derived mineral (mainly N and P) and organic nutrients is highly beneficial for plants and increases the photosynthetic rate in leaves as a prerequisite for faster plant growth. Whole-genome and tandem gene duplications brought gene material for diversification into carnivorous functions and enabled recruitment of defence-related genes. Possible mechanisms for the evolution of digestive enzymes are summarized, and a comprehensive picture on the biochemistry and regulation of prey decomposition and prey-derived nutrient uptake is provided.

• Keywords
• Dionaea, Drosera, Nepenthes, Carnivorous plant, co-option, cost–benefit relationships, digestive enzymes, evolution of carnivory, hunting cycle, mineral nutrient economy, regulation of enzyme secretion, terrestrial and aquatic species,
• MeSH
• Photosynthesis MeSH
• Plant Leaves MeSH
• Carnivory * MeSH
• Plants * genetics   MeSH
• Nutrients MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

BACKGROUND AND AIMS: While nuclear DNA content variation and its phenotypic consequences have been well described for animals, vascular plants and macroalgae, much less about this topic is known regarding unicellular algae and protists in general. The dearth of data is especially pronounced when it comes to intraspecific genome size variation. This study attempts to investigate the extent of intraspecific variability in genome size and its adaptive consequences in a microalgal species. METHODS: Propidium iodide flow cytometry was used to estimate the absolute genome size of 131 strains (isolates) of the golden-brown alga Synura petersenii (Chrysophyceae, Stramenopiles), identified by identical internal transcribed spacer (ITS) rDNA barcodes. Cell size, growth rate and genomic GC content were further assessed on a sub-set of strains. Geographic location of 67 sampling sites across the Northern hemisphere was used to extract climatic database data and to evaluate the ecogeographical distribution of genome size diversity. KEY RESULTS: Genome size ranged continuously from 0.97 to 2.02 pg of DNA across the investigated strains. The genome size was positively associated with cell size and negatively associated with growth rate. Bioclim variables were not correlated with genome size variation. No clear trends in the geographical distribution of strains of a particular genome size were detected, and strains of different genome size occasionally coexisted at the same locality. Genomic GC content was significantly associated only with genome size via a quadratic relationship. CONCLUSIONS: Genome size variability in S. petersenii was probably triggered by an evolutionary mechanism operating via gradual changes in genome size accompanied by changes in genomic GC content, such as, for example, proliferation of transposable elements. The variation was reflected in cell size and relative growth rate, possibly with adaptive consequences.

• Keywords
• Synura petersenii, GC content, ITS, Intraspecific DNA content variation, biovolume, environmental conditions, flow cytometry, genome size, golden-brown algae, growth rate,
• MeSH
• Biological Evolution MeSH
• Chrysophyta * MeSH
• Genome Size MeSH
• Genome, Plant * genetics   MeSH
• Ploidies MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Centromeres are essential for proper chromosome segregation to the daughter cells during mitosis and meiosis. Chromosomes of most eukaryotes studied so far have regional centromeres that form primary constrictions on metaphase chromosomes. These monocentric chromosomes vary from point centromeres to so-called "meta-polycentromeres", with multiple centromere domains in an extended primary constriction, as identified in Pisum and Lathyrus species. However, in various animal and plant lineages centromeres are distributed along almost the entire chromosome length. Therefore, they are called holocentromeres. In holocentric plants, centromere-specific proteins, at which spindle fibers usually attach, are arranged contiguously (line-like), in clusters along the chromosomes or in bands. Here, we summarize findings of ultrastructural investigations using immunolabeling with centromere-specific antibodies and super-resolution microscopy to demonstrate the structural diversity of plant centromeres. A classification of the different centromere types has been suggested based on the distribution of spindle attachment sites. Based on these findings we discuss the possible evolution and advantages of holocentricity, and potential strategies to segregate holocentric chromosomes correctly.

• Keywords
• CENH3, CENP-A, Cuscuta, Lathyrus, Luzula, Pisum, Rhynchospora, clustered centromere, holocentromere, microtubule, monocentromere, structured illumination microscopy,
• MeSH
• Cell Cycle MeSH
• Centromere metabolism   MeSH
• Chromosomes, Plant metabolism   MeSH
• Microscopy * MeSH
• Evolution, Molecular MeSH
• Plants metabolism   MeSH
• Publication type
• Journal Article MeSH
• Review MeSH