Understanding the proximate and ultimate causes of genome size variation has been the focus of considerable research. However, the extent and cause of intraspecific variation in genome size are debated and poorly understood. This study aimed to test the role of genome size in adaptation through variations in intraspecific genome size. Genome size was measured in 53 Roscoea tibetica populations from the Hengduan Mountains using flow cytometry. Stomatal size and density data were collected from wild and common garden populations. Associations among genome size, environmental factors, and stomatal traits were explored. We found that high genome size variability was positively correlated with most environmental factors but negatively correlated with solar radiation during the growing season. The environment, rather than geography, significantly influenced variations in genome size. Stomatal traits measured in the wild were significantly correlated with genome size, but no such correlations were detected in the common garden. Populations in the common garden had larger stomatal sizes and lower stomatal densities. Populations with smaller genome size presented a larger degree of stomatal trait variation from the wild to the common garden. Our findings suggest that intraspecific genome size has undergone adaptive evolution driven by environmental stress. A smaller genome size is more advantageous for the alpine ginger to adapt to and thrive in changing alpine habitats.

• Klíčová slova
• Roscoea tibetica, adaptation, common garden, environmental factors, intraspecific genome size, stomatal traits,
• Publikační typ
• časopisecké články MeSH

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.

• Klíčová slova
• Andes, GC content, HybSeq, Pleurothallidinae, endoreplication, evolution, genome size, spatial analysis,
• MeSH
• biologická evoluce * MeSH
• délka genomu MeSH
• fylogeneze * MeSH
• genom rostlinný * genetika   MeSH
• molekulární evoluce MeSH
• Orchidaceae * genetika   klasifikace   MeSH
• Publikační typ
• časopisecké články MeSH

Knowledge of population variation across species' ranges is a prerequisite for correctly assessing the overall variability of any group of organisms and provides an invaluable basis for unraveling evolutionary history, optimizing taxonomy and devising effective conservation strategies. Here, we examine the genus Neotinea, which represents a relatively recently delimited monophyletic genus of orchids, for which a detailed study of its overall variability was lacking. We applied a suite of biosystematic methods, consisting of flow cytometry, multivariate and geometric morphometrics, and analysis of genomic SNP data, to identify phylogenetic lineages within the genus, to delineate phenotypic variation relevant to these lineages, and to identify potential cryptic taxa within lineages. We found clear differentiation into four major lineages corresponding to the groups usually recognized within the genus: Neotinea maculata as a distinct and separate taxon, the Neotinea lactea group comprising two Mediterranean taxa N. lactea and Neotinea conica, the Neotinea ustulata group comprising two phenologically distinct varieties, and the rather complex Neotinea tridentata group comprising two major lineages and various minor lineages of unclear taxonomic value. N. conica constitutes both a monophyletic group within N. lactea and a distinct phenotype within the genus and merits its proposed subspecies-level recognition. By contrast, the spring and summer flowering forms of N. ustulata (var. ustulata and var. aestivalis) were confirmed to be distinct only morphologically, not phylogenetically. The most complex pattern emerged in the N. tridentata group, which splits into two main clades, one containing lineages from the Balkans and eastern Mediterranean and the other consisting of plants from Central Europe and the central Mediterranean. These individual lineages differ in genome size and show moderate degrees of morphological divergence. The tetraploid Neotinea commutata is closely related to the N. tridentata group, but our evidence points to an auto- rather than an allopolyploid origin. Our broad methodological approach proved effective in recognizing cryptic lineages among the orchids, and we propose the joint analysis of flow cytometric data on genome size and endopolyploidy as a useful and beneficial marker for delineating orchid species with partial endoreplication.

• Klíčová slova
• RADseq, cryptic diversity, genome size, geometric morphometric, multivariate morphometric, orchids (Orchidaceae), partial endoreplication,
• Publikační typ
• časopisecké články MeSH

Polyploidy has played a crucial role in the evolution of many plant taxa, namely in higher latitudinal zones. Surprisingly, after several decades of an intensive research on polyploids, there are still common polyploid species whose evolutionary history is virtually unknown. Here, we addressed the origin of sweet vernal grass (Anthoxanthum odoratum) using flow cytometry, DNA sequencing, and in situ hybridization-based cytogenetic techniques. An allotetraploid and polytopic origin of the species has been verified. The chromosome study reveals an extensive variation between the European populations. In contrast, an autopolyploid origin of the rarer tetraploid vernal grass species, A. alpinum, has been corroborated. Diploid A. alpinum played an essential role in the polyploidization of both European tetraploids studied.

• Klíčová slova
• FISH, GBSSI, GISH, Poaceae, flow cytometry, genome size, polyploidy,
• MeSH
• biologická evoluce * MeSH
• chromozomy rostlin genetika   MeSH
• diploidie MeSH
• fylogeneze MeSH
• hybridizace genetická * MeSH
• hybridizace in situ MeSH
• lipnicovité cytologie   genetika   MeSH
• molekulární evoluce * MeSH
• polyploidie MeSH
• sekvence nukleotidů MeSH
• tetraploidie MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

BACKGROUND AND AIMS: The idea that genome (size) evolution in eukaryotes could be driven by environmental factors is still vigorously debated. In extant plants, genome size correlates positively with stomatal size, leading to the idea that conditions enabling the existence of large stomata in fossil plants also supported growth of their genome size. We test this inductive assumption in drought-adapted, prostrate-leaved Cape (South Africa) geophytes where, compared with their upright-leaved geophytic ancestors, stomata develop in a favourably humid microclimate formed underneath their leaves. METHODS: Stomatal parameters (leaf cuticle imprints) and genome size (flow cytometry) were measured in 16 closely related geophytic species pairs from seven plant families. In each pair, representing a different genus, we contrasted a prostrate-leaved species with its upright-leaved phylogenetic relative, the latter whose stomata are exposed to the ambient arid climate. KEY RESULTS: Except for one, all prostrate-leaves species had larger stomata, and in 13 of 16 pairs they also had larger genomes than their upright-leaved relatives. Stomatal density and theoretical maximum conductance were less in prostrate-leaved species with small guard cells (<1 pL) but showed no systematic difference in species pairs with larger guard cells (>1 pL). Giant stomata were observed in the prostrate-leaved Satyrium bicorne (89-137 µm long), despite its relatively small genome (2C = 9 Gbp). CONCLUSIONS: Our results imply that climate, through selection on stomatal size, might be able to drive genome size evolution in plants. The data support the idea that plants from 'greenhouse' geological periods with large stomata might have generally had larger genome sizes when compared with extant plants, though this might not have been solely due to higher atmospheric CO2 in these periods but could also have been due to humid conditions prevailing at fossil deposit sites.

• Klíčová slova
• Cape Floristic Region, South Africa, carbon dioxide, flow cytometry, fossil plants, genome size evolution, geophyte, paleoclimate, stomatal size,
• MeSH
• délka genomu MeSH
• fylogeneze MeSH
• genom rostlinný genetika   MeSH
• listy rostlin MeSH
• průduchy rostlin genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Jihoafrická republika MeSH

BACKGROUND AND AIMS: Most crucifer species (Brassicaceae) have small nuclear genomes (mean 1C-value 617 Mb). The species with the largest genomes occur within the monophyletic Hesperis clade (Mandáková et al., Plant Physiology174: 2062-2071; also known as Clade E or Lineage III). Whereas most chromosome numbers in the clade are 6 or 7, monoploid genome sizes vary 16-fold (256-4264 Mb). To get an insight into genome size evolution in the Hesperis clade (~350 species in ~48 genera), we aimed to identify, quantify and localize in situ the repeats from which these genomes are built. We analysed nuclear repeatomes in seven species, covering the phylogenetic and genome size breadth of the clade, by low-pass whole-genome sequencing. METHODS: Genome size was estimated by flow cytometry. Genomic DNA was sequenced on an Illumina sequencer and DNA repeats were identified and quantified using RepeatExplorer; the most abundant repeats were localized on chromosomes by fluorescence in situ hybridization. To evaluate the feasibility of bacterial artificial chromosome (BAC)-based comparative chromosome painting in Hesperis-clade species, BACs of arabidopsis were used as painting probes. KEY RESULTS: Most biennial and perennial species of the Hesperis clade possess unusually large nuclear genomes due to the proliferation of long terminal repeat retrotransposons. The prevalent genome expansion was rarely, but repeatedly, counteracted by purging of transposable elements in ephemeral and annual species. CONCLUSIONS: The most common ancestor of the Hesperis clade has experienced genome upsizing due to transposable element amplification. Further genome size increases, dominating diversification of all Hesperis-clade tribes, contrast with the overall stability of chromosome numbers. In some subclades and species genome downsizing occurred, presumably as an adaptive transition to an annual life cycle. The amplification versus purging of transposable elements and tandem repeats impacted the chromosomal architecture of the Hesperis-clade species.

• Klíčová slova
• Bunias, Hesperis, Matthiola, Brassicaceae, Genome size evolution, Lineage III, chromosome organization, interstitial telomeric repeats (ITRs), repetitive DNA, retrotransposons, tandem repeats,
• MeSH
• Brassicaceae * MeSH
• délka genomu MeSH
• fylogeneze MeSH
• genom rostlinný * MeSH
• hybridizace in situ fluorescenční MeSH
• molekulární evoluce MeSH
• proliferace buněk MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

In many plant species, somatic cell differentiation is accompanied by endoreduplication, a process during which cells undergo one or more rounds of DNA replication cycles in the absence of mitosis, resulting in nuclei with multiples of 2C DNA amounts (4C, 8C, 16C, etc.). In some orchids, a disproportionate increase in nuclear DNA contents has been observed, where successive endoreduplication cycles result in DNA amounts 2C + P, 2C + 3P, 2C + 7P, etc., where P is the DNA content of the replicated part of the 2C nuclear genome. This unique phenomenon was termed "progressively partial endoreplication" (PPE). We investigated processes behind the PPE in Ludisia discolor using flow cytometry (FCM) and Illumina sequencing. In particular, we wanted to determine whether chromatin elimination or incomplete genome duplication was involved, and to identify types of DNA sequences that were affected. Cell cycle analysis of root tip cell nuclei pulse-labeled with EdU revealed two cell cycles, one ending above the population of nuclei with 2C + P content, and the other with a typical "horseshoe" pattern of S-phase nuclei ranging from 2C to 4C DNA contents. The process leading to nuclei with 2C + P amounts therefore involves incomplete genome replication. Subsequent Illumina sequencing of flow-sorted 2C and 2C + P nuclei showed that all types of repetitive DNA sequences were affected during PPE; a complete elimination of any specific type of repetitive DNA was not observed. We hypothesize that PPE is part of a highly controlled transition mechanism from proliferation phase to differentiation phase of plant tissue development.

• Klíčová slova
• DNA replication, EdU, Ludisia discolor, cell cycle, endoreduplication, orchids,
• MeSH
• buněčné jádro genetika   MeSH
• endoreduplikace genetika   MeSH
• genom rostlinný MeSH
• listy rostlin genetika   MeSH
• mitóza genetika   MeSH
• Orchidaceae genetika   MeSH
• polyploidie MeSH
• průtoková cytometrie metody   MeSH
• replikace DNA genetika   MeSH
• vysoce účinné nukleotidové sekvenování metody   MeSH
• Publikační typ
• časopisecké články MeSH