With the expansion of molecular techniques, the historical collections have become widely used. The last boom started with using next- and second-generation sequencing in which massive parallel sequencing replaced targeted sequencing and third-generation technology involves single molecule technology. Studying plant DNA using these modern molecular techniques plays an important role in understanding evolutionary relationships, identification through DNA barcoding, conservation status, and many other aspects of plant biology. Enormous herbarium collections are an important source of material especially for taxonomic long-standing issues, specimens from areas difficult to access or from taxa that are now extinct. The ability to utilize these specimens greatly enhances the research. However, the process of extracting DNA from herbarium specimens is often fraught with difficulty related to such variables as plant chemistry, drying method of the specimen, and chemical treatment of the specimen. The result of these applications is often fragmented DNA. The reason new sequencing approaches have been so successful is that the template DNA needs to be fragmented for proper library building, and herbarium DNA is exactly that. Although many methods have been developed for extraction of DNA from herbarium specimens, the most frequently used are modified CTAB and DNeasy Plant Mini Kit protocols. Nine selected protocols in this chapter have been successfully used for high-quality DNA extraction from different kinds of plant herbarium tissues. These methods differ primarily with respect to their requirements for input material (from algae to vascular plants), type of the plant tissue (leaves with incrustations, sclerenchyma strands, mucilaginous tissues, needles, seeds), and further possible applications (PCR-based methods, microsatellites, AFLP or next-generation sequencing).

• Klíčová slova
• AFLP, DNA extraction, Difficult plant tissues, Herbarium specimens, Microsatellites, Next-generation sequencing, PCR,
• MeSH
• analýza polymorfismu délky amplifikovaných restrikčních fragmentů MeSH
• chemická frakcionace metody   MeSH
• DNA rostlinná genetika   izolace a purifikace   MeSH
• listy rostlin genetika   MeSH
• mikrosatelitní repetice MeSH
• orgánová specificita MeSH
• polymerázová řetězová reakce MeSH
• reagenční diagnostické soupravy MeSH
• rostliny klasifikace   genetika   MeSH
• sekvenční analýza DNA MeSH
• taxonomické DNA čárové kódování metody   MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH
• reagenční diagnostické soupravy MeSH

Food fraud has been and still is a problem in the food industry. It is detectable by several approaches, such as high performance liquid chromatography (HPLC), chemometric assays, or DNA-based techniques, each with its own drawbacks. This work addresses one major drawback of DNA-based methods, in particular their sensitivity to inhibitors contained in particular matrices from which DNA is isolated. We tested five commercial kits and one in-house method characterized by different ways of sample homogenization and DNA capture and purification. Using these methods, DNA was isolated from 10 different fruit species commonly used in plant-based foodstuffs. The quality of the DNA was evaluated by UV-VIS spectrophotometry. Two types of qPCR assays were used for DNA quality testing: (i) Method specific for plant ITS2 region, (ii) methods specific for individual fruit species. Based mainly on the results of real-time PCR assays, we were able to find two column-based kits and one magnetic carrier-based kit, which consistently provided fruit DNA isolates of sufficient quality for PCR-based assays useful for routine analysis and identification of individual fruit species in food products.

• Klíčová slova
• DNA isolation, Prunus, commercial kit, real-time PCR, red fruit, tropical fruit,
• MeSH
• DNA rostlinná analýza   izolace a purifikace   MeSH
• elektroforéza MeSH
• kvantitativní polymerázová řetězová reakce MeSH
• ovoce chemie   MeSH
• reagenční diagnostické soupravy MeSH
• rostlinné extrakty analýza   izolace a purifikace   MeSH
• slivoň chemie   MeSH
• spektrofotometrie MeSH
• Publikační typ
• časopisecké články MeSH
• srovnávací studie MeSH
• Názvy látek
• DNA rostlinná MeSH
• reagenční diagnostické soupravy MeSH
• rostlinné extrakty MeSH

Ancient DNA from historical and subfossil wood has a great potential to provide new insights into the history of tree populations. However, its extraction and analysis have not become routine, mainly because contamination of the wood with modern plant material can complicate the verification of genetic information. Here, we used sapwood tissue from 22 subfossil pines that were growing c. 13 000 yr bp in Zurich, Switzerland. We developed and evaluated protocols to eliminate surface contamination, and we tested ancient DNA authenticity based on plastid DNA metabarcoding and the assessment of post-mortem DNA damage. A novel approach using laser irradiation coupled with bleaching and surface removal was most efficient in eliminating contaminating DNA. DNA metabarcoding confirmed which ancient DNA samples repeatedly amplified pine DNA and were free of exogenous plant taxa. Pine DNA sequences of these samples showed a high degree of cytosine to thymine mismatches, typical of post-mortem damage. Stringent decontamination of wood surfaces combined with DNA metabarcoding and assessment of post-mortem DNA damage allowed us to authenticate ancient DNA retrieved from the oldest Late Glacial pine forest. These techniques can be applied to any subfossil wood and are likely to improve the accessibility of relict wood for genome-scale ancient DNA studies.

• Klíčová slova
• DNA metabarcoding, ancient DNA, experimental contamination, laser cleaning, post-mortem DNA damage, subfossil wood,
• MeSH
• borovice klasifikace   genetika   MeSH
• dekontaminace MeSH
• DNA rostlinná genetika   izolace a purifikace   MeSH
• dřevo genetika   MeSH
• druhová specificita MeSH
• lesy * MeSH
• smrk genetika   MeSH
• zkameněliny * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH

The carnivorous plant genus Utricularia L. (bladderwort) comprises about 240 species distributed worldwide and is traditionally classified into two subgenera (Polypompholyx and Utricularia) and 35 sections, based mainly on general and trap morphology. It is one out of the largest carnivorous genera, representing ca. 30% of all carnivorous plant species, and is also the most widely distributed. According to previous phylogenetic studies, most infrageneric sections are monophyletic, but there are several incongruences considering their relationships and also the dissenting position of some species as a result of a too few (mostly one or two) molecular markers analyzed. Thus, here we present a multilocus phylogeny for Utricularia species with a wide taxonomic sampling (78 species and 115 accessions) based on six plastid (rbcL, matK, rpl20-rps12, rps16, trnL-F) and nuclear DNA (ITS region) sequences. The aim is to reconstruct a well-resolved tree to propose evolutionary and biogeographic hypotheses for the radiation of lineages with inferences about the divergence times of clades using a molecular clock approach.

• Klíčová slova
• Bladderwort, Carnivorous plant, DNA sequencing, Multilocus phylogeny, Utricularia,
• MeSH
• Bayesova věta MeSH
• biologická evoluce MeSH
• buněčné jádro genetika   MeSH
• DNA rostlinná chemie   izolace a purifikace   metabolismus   MeSH
• fylogeneze MeSH
• hluchavkotvaré klasifikace   genetika   MeSH
• plastidy genetika   MeSH
• ribulosa-1,5-bisfosfát-karboxylasa klasifikace   genetika   metabolismus   MeSH
• rostlinné proteiny klasifikace   genetika   metabolismus   MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA MeSH
• sekvenční seřazení MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA rostlinná MeSH
• RbcL protein, plastid MeSH Prohlížeč
• ribulosa-1,5-bisfosfát-karboxylasa MeSH
• rostlinné proteiny MeSH

Frullania subgenus Microfrullania is a clade of ca. 15 liverwort species occurring in Australasia, Malesia, and southern South America. We used combined nuclear and chloroplast sequence data from 265 ingroup accessions to test species circumscriptions and estimate the biogeographic history of the subgenus. With dense infra-specific sampling, we document an important role of long-distance dispersal in establishing phylogeographic patterns of extant species. At deeper time scales, a combination of phylogenetic analyses, divergence time estimation and ancestral range estimation were used to reject vicariance and to document the role of long-distance dispersal in explaining the evolution and biogeography of the clade across the southern Hemisphere. A backbone phylogeny for the subgenus is proposed, providing insight into evolution of morphological patterns and establishing the basis for an improved sectional classification of species within Microfrullania. Several species complexes are identified, the presence of two undescribed but genetically and morphologically distinct species is noted, and previously neglected names are discussed.

• Klíčová slova
• Ancestral range reconstruction, Divergence time estimation, Diversification, Gondwanaland, Long distance dispersal, Species delimitation,
• MeSH
• biologická evoluce MeSH
• DNA rostlinná izolace a purifikace   metabolismus   MeSH
• Frullania anatomie a histologie   klasifikace   genetika   MeSH
• fylogeneze MeSH
• fylogeografie MeSH
• genetické lokusy MeSH
• sekvenční analýza DNA MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Australasie MeSH
• Jižní Amerika MeSH
• Názvy látek
• DNA rostlinná MeSH

BACKGROUND AND AIMS: Dessert and cooking bananas are vegetatively propagated crops of great importance for both the subsistence and the livelihood of people in developing countries. A wide diversity of diploid and triploid cultivars including AA, AB, AS, AT, AAA, AAB, ABB, AAS and AAT genomic constitutions exists. Within each of this genome groups, cultivars are classified into subgroups that are reported to correspond to varieties clonally derived from each other after a single sexual event. The number of those founding events at the basis of the diversity of bananas is a matter of debate. METHODS: We analysed a large panel of 575 accessions, 94 wild relatives and 481 cultivated accessions belonging to the section Musa with a set of 498 DArT markers previously developed. KEY RESULTS: DArT appeared successful and accurate to describe Musa diversity and help in the resolution of cultivated banana genome constitution and taxonomy, and highlighted discrepancies in the acknowledged classification of some accessions. This study also argues for at least two centres of domestication corresponding to South-East Asia and New Guinea, respectively. Banana domestication in New Guinea probably followed different schemes that those previously reported where hybridization underpins the emergence of edible banana. In addition, our results suggest that not all wild ancestors of bananas are known, especially in M. acuminata subspecies. We also estimate the extent of the two consecutive bottlenecks in edible bananas by evaluating the number of sexual founding events underlying our sets of edible diploids and triploids, respectively. CONCLUSIONS: The attribution of clone identity to each sample of the sets allowed the detection of subgroups represented by several sets of clones. Although morphological characterization of some of the accessions is needed to correct potentially erroneous classifications, some of the subgroups seem polyclonal.

• Klíčová slova
• DArT, Musa acuminata, Musa balbisiana, Musa spp., banana, classification, domestication, taxonomy,
• MeSH
• banánovník klasifikace   genetika   MeSH
• biodiverzita MeSH
• biologická evoluce MeSH
• DNA rostlinná genetika   izolace a purifikace   MeSH
• genetické markery genetika   MeSH
• genom rostlinný genetika   MeSH
• sekvenční analýza DNA MeSH
• sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů MeSH
• šlechtění rostlin MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH
• genetické markery MeSH

There is relatively little information concerning long-term alterations in DNA methylation following exposure of plants to environmental stress. As little is known about the ratio of non-heritable changes in DNA methylation and mitotically-inherited methylation changes, dynamics and reversibility of the DNA methylation states were investigated in grapevine plants (Vitis vinifera) stressed by in vitro cultivation. It was observed that significant part of induced epigenetic changes could be repeatedly established by exposure to particular planting and stress conditions. However, once stress conditions were discontinued, many methylation changes gradually reverted and plants returned to epigenetic states similar to those of maternal plants. In fact, in the period of one to three years after in vitro cultivation it was difficult to distinguish the epigenetic states of somaclones and maternal plants. Forty percent of the observed epigenetic changes disappeared within a year subsequent to termination of stress conditions ending and these probably reflect changes caused by transient and reversible stress-responsive acclimation mechanisms. However, sixty percent of DNA methylation diversity remained after 1 year and probably represents mitotically-inherited epimutations. Sequencing of regions remaining variable between maternal and regenerant plants revealed that 29.3% of sequences corresponded to non-coding regions of grapevine genome. Eight sequences (19.5%) corresponded to previously identified genes and the remaining ones (51.2%) were annotated as "hypothetical proteins" based on their similarity to genes described in other species, including genes likely to undergo methylation changes following exposure to stress (V. vinifera gypsy-type retrotransposon Gret1, auxin-responsive transcription factor 6-like, SAM-dependent carboxyl methyltransferase).

• MeSH
• DNA rostlinná analýza   izolace a purifikace   MeSH
• elektroforéza kapilární MeSH
• epigeneze genetická MeSH
• fyziologický stres * MeSH
• metylace DNA * MeSH
• rostlinné buňky metabolismus   MeSH
• sekvenční analýza DNA MeSH
• teplota MeSH
• Vitis genetika   růst a vývoj   MeSH
• vysokoúčinná kapalinová chromatografie MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH

Mitogen-activated protein kinases (MAPK) are key regulatory elements in many processes. They are highly conserved throughout eukaryotes. In plants, MAPKs are involved in biotic and abiotic stress responses; they regulate cell division, cell growth, and also programmed cell death. In vivo visualization of MAPKs is crucial for understanding of their spatiotemporal organization. Cloning of MAPK-fluorescent protein fusions might present difficulties related to the preservation of protein-protein interactions essential for MAPK localization, interactions with upstream and downstream regulators, and finally substrate targeting. In this chapter we describe cloning of MAPKs in the flexible MultiSite Gateway(®) cloning system followed by easy and quick testing of binary vectors by transient assays in Arabidopsis thaliana and Nicotiana benthamiana.

• MeSH
• Agrobacterium genetika   MeSH
• Arabidopsis enzymologie   genetika   MeSH
• cetrimoniové sloučeniny chemie   MeSH
• cetrimonium MeSH
• DNA primery genetika   MeSH
• DNA rostlinná genetika   izolace a purifikace   MeSH
• Escherichia coli genetika   MeSH
• genetické inženýrství metody   MeSH
• genetické vektory genetika   MeSH
• genom rostlinný genetika   MeSH
• klonování DNA MeSH
• listy rostlin genetika   MeSH
• mitogenem aktivované proteinkinasy genetika   metabolismus   MeSH
• polymerázová řetězová reakce MeSH
• promotorové oblasti (genetika) genetika   MeSH
• proteiny huseníčku genetika   metabolismus   MeSH
• rekombinantní fúzní proteiny genetika   metabolismus   MeSH
• tabák genetika   MeSH
• transformace genetická MeSH
• transport proteinů MeSH
• zelené fluorescenční proteiny genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• cetrimoniové sloučeniny MeSH
• cetrimonium MeSH
• DNA primery MeSH
• DNA rostlinná MeSH
• mitogenem aktivované proteinkinasy MeSH
• MPK6 protein, Arabidopsis MeSH Prohlížeč
• proteiny huseníčku MeSH
• rekombinantní fúzní proteiny MeSH
• zelené fluorescenční proteiny MeSH

With the expansion of molecular techniques, the historical collections have become widely used. Studying plant DNA using modern molecular techniques such as DNA sequencing plays an important role in understanding evolutionary relationships, identification through DNA barcoding, conservation status, and many other aspects of plant biology. Enormous herbarium collections are an important source of material especially for specimens from areas difficult to access or from taxa that are now extinct. The ability to utilize these specimens greatly enhances the research. However, the process of extracting DNA from herbarium specimens is often fraught with difficulty related to such variables as plant chemistry, drying method of the specimen, and chemical treatment of the specimen. Although many methods have been developed for extraction of DNA from herbarium specimens, the most frequently used are modified CTAB and DNeasy Plant Mini Kit protocols. Nine selected protocols in this chapter have been successfully used for high-quality DNA extraction from different kinds of plant herbarium tissues. These methods differ primarily with respect to their requirements for input material (from algae to vascular plants), type of the plant tissue (leaves with incrustations, sclerenchyma strands, mucilaginous tissues, needles, seeds), and further possible applications (PCR-based methods or microsatellites, AFLP).

• MeSH
• cetrimoniové sloučeniny chemie   MeSH
• cetrimonium MeSH
• chemická frakcionace metody   MeSH
• DNA rostlinná chemie   genetika   izolace a purifikace   MeSH
• druhová specificita MeSH
• filtrace MeSH
• kyselina dusičná chemie   MeSH
• listy rostlin chemie   MeSH
• mikrosatelitní repetice MeSH
• rostliny chemie   MeSH
• semena rostlinná chemie   MeSH
• uchovávání tkání * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• cetrimoniové sloučeniny MeSH
• cetrimonium MeSH
• DNA rostlinná MeSH
• kyselina dusičná MeSH

Here, we describe a method for the combined metabolomic, proteomic, transcriptomic and genomic analysis from one single sample as a major step for multilevel data integration strategies in systems biology. While extracting proteins and DNA, this protocol also allows the separation of metabolites into polar and lipid fractions, as well as RNA fractionation into long and small RNAs, thus allowing a broad range of transcriptional studies. The isolated biomolecules are suitable for analysis with different methods that range from electrophoresis and blotting to state-of-the-art procedures based on mass spectrometry (accurate metabolite profiling, shot-gun proteomics) or massive sequencing technologies (transcript analysis). The low amount of starting tissue, its cost-efficiency compared with the utilization of commercial kits, and its performance over a wide range of plant, microbial, and algal species such as Chlamydomonas, Arabidopsis, Populus, or Pinus, makes this method a universal alternative for multiple molecular isolation from plant tissues.

• Klíčová slova
• Arabidopsis thaliana, Chlamydomonas reinhardtii, Pinus sp., Populus sp., RNA, combined isolation, metabolites, proteins, small RNA, systems biology, technical advance,
• MeSH
• Arabidopsis genetika   metabolismus   MeSH
• borovice genetika   metabolismus   MeSH
• Chlamydomonas reinhardtii genetika   metabolismus   MeSH
• DNA rostlinná izolace a purifikace   MeSH
• genomika metody   MeSH
• metabolomika metody   MeSH
• Populus genetika   metabolismus   MeSH
• proteomika metody   MeSH
• reprodukovatelnost výsledků MeSH
• RNA rostlin izolace a purifikace   MeSH
• rostlinné proteiny izolace a purifikace   MeSH
• rostliny * genetika   metabolismus   MeSH
• systémová biologie metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH
• RNA rostlin MeSH
• rostlinné proteiny MeSH