Eukaryotic genome size databases

Three independent databases of eukaryotic genome size information have been launched or re-released in updated form since 2005: the Plant DNA C-values Database (), the Animal Genome Size Database () and the Fungal Genome Size Database (). In total, these databases provide freely accessible genome size data for >10 000 species of eukaryotes assembled from more than 50 years' worth of literature. Such data are of significant importance to the genomics and broader scientific community as fundamental features of genome structure, for genomics-based comparative biodiversity studies, and as direct estimators of the cost of complete sequencing programs

Feulgen densitometry: some observations relevant to best practice in quantitative nuclear DNA content determination

Despite of a huge amount of literature on the Feulgen reaction for DNA relatively few investigations deal with the special needs of plant scientists. As a consequence various modifications of the method are practised in different laboratories, which may in part be responsible for contradictory results. In the present work tests are conducted to find out, which steps of the procedure must be stringently controlled and in which steps such a control is less critical. Test material were mainly root tip meristems of Pisum sativum, which were hydrolysed and further processed in toto. Some tests involved also Zea mays. Glycine max, and Hordeum vulgare. Fixations may be stored at -20 °C in ethanol for at least 5 years without loss of quality. Nothing is known about permitted conditions of storing fixations at temperatures higher than -20 °C, except that at room temperature a security limit for acetic alcohol fixed material is about 3 days. Staining intensity after fixation with formaldehyde is dependent on concentration, time, and temperature of the fixative. Therefore, co-fixation of test and standard material, if to be included, is strongly recommended, while with acetic alcoholic fixation this point is less critical. Hydrolysis is the most critical step of the procedure. Precise control of HC1 molarity, temperature, and optimum time is essential. This is often given not due attention in contemporary publications on plant DNA amounts and Feulgen staining. Hydrolysis curves for methanol acetic acid fixed material with 5 M HC1 at 20 °C, 10 °C, and 0 °C show staining optima after 60 min, 220 min, and 20 h, and a plateau of optimum staining about 5 h long in the latter. Hydrolysis optimum (5 M HC1) for formaldehyde fixed material at 20 °C is at 90 min. Washing time after hydrolysis is a surprisingly sensitive step of the procedure and should be kept as short as possible. Time of staining and of all further steps of the procedure, if conducted longer than necessary, lead to a gradual decrease of nuclear dye content. It is suggested to keep these steps as short as possible, because the gradual decay of staining intensity is assumed to proceed not in a stoichiometric fashion. Relatively insensitive steps of the procedure are a final wash in ethanol before drying the slides and storing the slides in the dark

2C or not 2C: a closer look at cell nuclei and their DNA content

Abstract The life cycle of animals and plants involves changes in chromosome number (nuclear phase) and sometimes even the karyotype, and consequently the DNA content of a nuclear genome is not static in time. Thus, in order to interpret DNA content data, it is important that the status of the materials from which DNA content is estimated be precisely defined. The previously proposed distinction between "holoploid" (C) and "monoploid" (Cx) genome size covers the most frequent states of plant and animal nuclear genomes. However, restricting nomenclature to just C and Cx still leaves a number of unresolved problems. Here, we propose an extension of the C-value terminology to handle a range of cytogenetic conditions, life cycle segments, and nuclear phases. A set of superscripts and subscripts are used in a formal way to identify life cycle segments and to express the quantitative relationship between these segments. A revision of the current usage of the holoploid chromosome number n was necessary to maintain the intimate link between n and Cvalue and between the monoploid chromosome number x and Cx-value. In this revision, haplophase individuals (i.e., "haploid" animals and "haploid" spontaneous or experimentally induced land plant sporophytes) have chromosome number n (not 2n, as is the current tradition) and thus nuclear DNA contents based on 1C. However, to avoid an unlimited progression of n levels due to generative polyploidy, zygotic individuals are assigned as 2n starting from the zygote, whatever their ploidy level. Their ploidy is indicated by multiples of the basic chromosome number x. The extended terminology for genome size should eliminate ambiguities in reporting DNA contents in both plants and animals

Franz Speta (1941–2015) zum Gedenken

Der österreichische Botaniker W. Hofrat Univ.-Doz. Dr. Franz Speta verstarb am 5. 12. 2015 in Linz nach längerem schwerem Leiden. Er wurde am 22. 12. 1941 in Linz-Urfahr in bescheidenen Verhältnissen geboren, erlernte den Beruf des Spediteurs und maturierte im Zweiten Bildungsweg. Er studierte Botanik und Zoologie ab 1964, dissertierte am Botanischen Institut der Universität Wien bei Lothar Geitler und Elisabeth Woess, promovierte 1972, hatte aber schon 1970 eine Stelle als Wissenschaftler am OÖ Landesmuseum in Linz angenommen. Er profilierte sich durch wissenschaftliche Arbeiten (Schwerpunkt Systematik der Hyacinthaceae), historisch-biographische Studien, Gründung wissenschaftlicher Schriftenreihen, engagierte Ausstellungstätigkeit und kontinuierlichen Aufbau der Sammlungen. Er erreichte die Errichtung des Biologiezentrums in Linz-Dornach (Eröffnung 1993) und war dessen Leiter bis zu seiner Pensionierung 2003. An der Universität Salzburg war er für Systematische Botanik habilitiert. Eine Laudatio zu seinem 70. Geburtstag findet sich bei Greilhuber (2012). Er hatte mannigfache Beziehungen zum Botanischen Institut der Universität Wien (heute das Department für Botanik und Biodiversitätsforschung) und zum Verein zur Erforschung der Flora Österreichs. Die Verfasser des vorliegenden Nachrufs standen seit ihrer Studienzeit in enger Beziehung zu Franz Speta, sei es als guter Freund und Koautor (J. G.) oder als Ehefrau (E. S.). Dieser Nachruf enthält außerdem als Anhänge folgende Auflistungen: gewidmete Taxa (Dedikationen) und Publikationen, die nicht in Greilhuber (2012) erwähnt werden, eine vollständige Liste von Franz Speta beschriebenen Taxa und eine Zusammenstellung seiner Sammelreisen

Plant Genome Diversity Volume 1Plant Genomes, their Residents, and their Evolutionary Dynamics /

X, 282 p.online resource