Jakub Šmerda

Correlated evolution of LTR retrotransposons and genome size in the genus eleocharis

BackgroundTransposable elements (TEs) are considered to be an important source of genome size variation and genetic and phenotypic plasticity in eukaryotes. Most of our knowledge about TEs comes from large genomic projects and studies focused on model organisms. However, TE dynamics among related taxa from natural populations and the role of TEs at the species or supra-species level, where genome size and karyotype evolution are modulated in concert with polyploidy and chromosomal rearrangements, remain poorly understood. We focused on the holokinetic genus Eleocharis (Cyperaceae), which displays large variation in genome size and the occurrence of polyploidy and agmatoploidy/symploidy. We analyzed and quantified the long terminal repeat (LTR) retrotransposons Ty1-copia and Ty3-gypsy in relation to changes in both genome size and karyotype in Eleocharis. We also examined how this relationship is reflected in the phylogeny of Eleocharis.ResultsUsing flow cytometry, we measured the genome sizes of members of the genus Eleocharis (Cyperaceae). We found positive correlation between the independent phylogenetic contrasts of genome size and chromosome number in Eleocharis. We analyzed PCR-amplified sequences of various reverse transcriptases of the LTR retrotransposons Ty1-copia and Ty3-gypsy (762 sequences in total). Using real-time PCR and dot blot approaches, we quantified the densities of Ty1-copia and Ty3-gypsy within the genomes of the analyzed species. We detected an increasing density of Ty1-copia elements in evolutionarily younger Eleocharis species and found a positive correlation between Ty1-copia densities and C/n-values (an alternative measure of monoploid genome size) in the genus phylogeny. In addition, our analysis of Ty1-copia sequences identified a novel retrotransposon family named Helos1, which is responsible for the increasing density of Ty1-copia. The transition:transversion ratio of Helos1 sequences suggests that Helos1 recently transposed in later-diverging Eleocharis species.ConclusionsUsing several different approaches, we were able to distinguish between the roles of LTR retrotransposons, polyploidy and agmatoploidy/symploidy in shaping Eleocharis genomes and karyotypes. Our results confirm the occurrence of both polyploidy and agmatoploidy/symploidy in Eleocharis. Additionally, we introduce a new player in the process of genome evolution in holokinetic plants: LTR retrotransposons.

Measurements of genomic GC content in plant genomes with flow cytometry: a test for reliability

• Knowledge of the phylogenetic pattern and biological relevance of the base composition of large eukaryotic genomes (including those of plants) is poor. With the use of flow cytometry (FCM), the amount of available data on the guanine + cytosine (GC) content of plants has nearly doubled in the last decade. However, skepticism exists concerning the reliability of the method because of uncertainty in some input parameters. • Here, we tested the reliability of FCM for estimating GC content by comparison with the biochemical method of DNA temperature melting analysis (TMA). We conducted measurements in 14 plant species with a maximum currently known GC content range (33.6-47.5% as measured by FCM). We also compared the estimations of the GC content by FCM with genomic sequences in 11 Oryza species. • FCM and TMA data exhibited a high degree of correspondence which remained stable over the relatively wide range of binding lengths (3.39-4.09) assumed for the base-specific dye used. A high correlation was also observed between FCM results and the sequence data in Oryza, although the latter GC contents were consistently lower. • Reliable estimates of the genomic base composition in plants by FCM are comparable with estimates obtained using other methods, and so wider application of FCM in future plant genomic research, although it would pose a challenge, would be supported by these findings.

Revision of Central European taxa of Festuca ser. Psammophilae Pawlus: morphometrical, karyological and AFLP analysis

The taxonomic status of Central European taxa Festuca pallens s.l., F. psammophila, F. polesica, and F. vaginata was revised using the multivariate morphological analysis of well karyologically documented plants, and AFLP analysis. Six species were recognised: F. pallens Host (relict rocky habitats; diploid); F. csikhegyensis Simonk. (base-rich rocks; tetraploid); F. psammophila (Čelak.) Fritsch (acidic sands) with two subspecies, F. p. subsp. psammophila (E Germany, Poland, Bohemia) and F. p. subsp. dominii (Krajina) P. Šmarda (SW Moravia, NE Austria, SW Slovakia, C and E Poland); F. vaginata Willd. (base-rich sands mainly in the Pannonian Lowland); F. polesica Zapał. (seaside and inland sand dunes); and F. pseudovaginata Penksza (base-rich sands in the Pannonian Lowland). Identification key and distribution maps as well as informations about type specimens, exsiccata collections, synonyms, and hybrids are provided. Evolutionary relationships with the assumed putative ancestor F. pallens and the rather isolated position of F. polesica are discussed.

Polyploidy in a 'living fossil' Ginkgo biloba.

The ‘living fossil’ Ginkgo biloba L. is the only extant representative of Ginkgophyta, which is an ancient group of gymnosperms that constituted an important component of the Earth’s forests in the Mesozoic and early to mid-Cenozoic. The Ginkgo and its sister phylogenetic relatives, the cycads (Cycadophyta), are the last major lineages of green plants in which polyploidy (whole genome duplication) remains unknown. Surprisingly, however, Ginkgo has the potential to form spontaneous polyploid offspring. We found such a vital polyploid sapling of Ginkgo during a routine screening for genome size variation in plants used for cultivation experiments. This polyploid sapling (sex yet unknown) originated from the seeds collected from three female trees grown in the Botanical Garden of the Faculty of Science, Masaryk University in Brno (Czech Republic). Its genome size (2C = 37.4 0.2 Gbp) is approximately double that of the diploid Ginkgo biloba (2C = 18.4 0.1 Gbp, mean of all three possible mother trees), indicating that it is tetraploid. Compared with its diploid parental plants and same-age siblings, the leaves of the tetraploid had finely laciniate distal margins and enlarged stomata: 60 ± 6 µm in the tetraploid sapling vs. 39 ± 5 µm in its same-age diploid siblings or 34 ± 6 µm in putatively parental trees.

Evolution of genome size and genomic GC content in carnivorous holokinetics (Droseraceae)

Background and Aims Studies in the carnivorous family Lentibulariaceae in the last years resulted in the discovery of the smallest plant genomes and an unusual pattern of genomic GC content evolution. However, scarcity of genomic data in other carnivorous clades still prevents a generalization of the observed patterns. Here the aim was to fill this gap by mapping genome evolution in the second largest carnivorous family, Droseraceae, where this evolution may be affected by chromosomal holokinetism in Drosera. Methods The genome size and genomic GC content of 71 Droseraceae species were measured by flow cytometry. A dated phylogeny was constructed, and the evolution of both genomic parameters and their relationship to species climatic niches were tested using phylogeny-based statistics. Key Results The 2C genome size of Droseraceae varied between 488 and 10 927 Mbp, and the GC content ranged between 37·1 and 44·7 %. The genome sizes and genomic GC content of carnivorous and holocentric species did not differ from those of their non-carnivorous and monocentric relatives. The genomic GC content positively correlated with genome size and annual temperature fluctuations. The genome size and chromosome numbers were inversely correlated in the Australian clade of Drosera. Conclusions Our results indicate that neither carnivory (nutrient scarcity) nor the holokinetism have a prominent effect on size and DNA base composition of Droseraceae genomes. However, the holokinetic drive seems to affect karyotype evolution in one of the major clades of Drosera. Our survey confirmed that the evolution of GC content is tightly connected with the evolution of genome size and also with environmental conditions.