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The Phytophthora cactorum species complex in Europe is composed of P. cactorum, Phytophthora hedraiandra, and a hybrid species Phytophthora × serendipita. Evolutionary analyses using the amplified fragment length polymorphism (AFLP) method were carried out on 133 isolates from 19 countries. The AFLP data were complemented by sequence analysis of three genes (ITS region of ribosomal RNA gene, phenolic acid decarboxylase – Pheca I, and Cytochrome oxidase – Cox I), morphometric analysis and cardinal temperature data. The high proportion of clonal genotypes, low gene flow among groups, which was defined by the structure analysis, and low Nei's gene diversity confirms the homothallic life cycle of the groups. On the other hand, the ITS, Cox I and Pheca I sequence data support occasional hybridization between species. The structure K = 5 grouping revealed two groups of hybrid origin (C2 and F). While the C2 group resembles P. × serendipita, the F group includes Finnish isolates characterized by high oogonial abortion rates and slow growth. The morphological characters routinely used in identification of Phytophthora species are not useful for delimitation of species from the P. cactorum complex. Therefore, we discuss the status of P. hedraiandra as a separate species. The epitypification of P. cactorum is proposed.

Here, we present an improved amplified fragment length polymorphism (AFLP) protocol using restriction enzymes (AscI and SbfI) that recognize 8-base pair sequences to provide alternative optimization suitable for species with a genome size over 70 Gb. This cost-effective optimization massively reduces the number of amplified fragments using only +3 selective bases per primer during selective amplification. We demonstrate the effects of the number of fragments and genome size on the appearance of nonidentical comigrating fragments (size homoplasy), which has a negative impact on the informative value of AFLP genotypes. We also present various reaction conditions and their effects on reproducibility and the band intensity of the extremely large genome of Viscum album. The reproducibility of this octo-cutter protocol was calculated using several species with genome sizes ranging from 1 Gb (Carex panicea) to 76 Gb (V. album). The improved protocol also succeeded in detecting high intraspecific variability in species with large genomes (V. album, Galanthus nivalis and Pinus pumila).

Wild river gravel banks (RGB) represent an extremely fragile biotope that is significantly endangered by human activities due to its fragmentation over the past century. The consequences of such processes were studied using the endangered violet willow (Salix daphnoides) at the westernmost foothills of the Carpathian Mountains. We quantified population genetic characteristics for 14 ecologically and demographically characterised populations using simple sequence repeats (SSR) and amplified fragment length polymorphism (AFLP) markers. We found a significant correlation between the biotope, sex, age and genetic structure of the populations. The natural RGB populations revealed high genotypic variability when using SSR markers, in contrast to low genotypic variability of the populations of other biotopes of Cirsium wet meadows (CWM) and Ash-alder forests (AAF) that consisted of one to two clones at each site. High heterozygosity (H obs = 0.428–0.532) was similar across all natural (RGB) populations; however, these populations were deficient in heterozygotes (F IS/ρ IS > 0). All RGB populations exhibited moderate to very significant genetic differentiation for microsatellites, despite the fact that the AFLP data showed strong differentiation only between CWM and AAF populations. Division into clusters by Structure confirmed consistent geographic groups for the RGB populations. According to our results, the strong decrease in previously continuous and large natural habitats for the violet willow is slightly counterbalanced by among-population gene flow. However, the survival of natural populations is tightly linked to the presence of river gravel banks and bars. Strict protection of this habitat is therefore essential for the conservation of the species.

Coevolution of cellular genetic compartments is a fundamental aspect in eukaryotic genome evolution that becomes apparent in serious developmental disturbances after interspecific organelle exchanges. The genus Oenothera represents a unique, at present the only available, resource to study the role of the compartmentalized plant genome in diversification of populations and speciation processes. An integrated approach involving cDNA cloning, EST sequencing, and bioinformatic data mining was chosen using Oenothera elata with the genetic constitution nuclear genome AA with plastome type I. The Gene Ontology system grouped 1621 unique gene products into 17 different functional categories. Application of arrays generated from a selected fraction of ESTs revealed significantly differing expression profiles among closely related Oenothera species possessing the potential to generate fertile and incompatible plastid/nuclear hybrids (hybrid bleaching). Furthermore, the EST library provides a valuable source of PCR-based polymorphic molecular markers that are instrumental for genotyping and molecular mapping approaches.