Genome Size

A granulovirus (GV) isolated from Epinotia aporema (Lepidoptera: Tortricidae)—a major soybean pest—was studied in terms of its main morphological, biochemical, and biological properties. The ovoidal occlusion bodies were 466 by 296 nm in size, and their most prominent protein had an apparent molecular mass of 29 kDa. Its amino-terminal sequence was remarkably homologous to that of the granulins of other GVs. The DNA genome size was estimated to be 120 kbp. The high specificity and pathogenicity of this newly described granulovirus (EpapGV) indicate that it is indeed a good candidate for the biological control of this pest.

Background : The main goal of the work was to analyse intraspecific variation in Elettaria cardamomum Maton (cardamom) using genome size, cytological studies and molecular marker data. Nuclear DNA content and molecular marker details furnish data on genome size and genetic diversity respectively among the studied accessions and both complement each other for evolutionary and taxonomic studies.
Results: The relative 2C genome size and total number of base pairs of cardamom was determined through flow cytometric analysis using propidium iodide staining. The nuclear DNA content was estimated in various sections of the species representing individuals from wild and cultivar genotypes following Zea mays L. CE-777 (2C = 5.43 pg) as internal reference standard. Chromosome number from growing root tip was examined following standard protocols. Twenty-six ISSR primers that generated polymorphic bands were used for genetic diversity analysis of the thirty accessions of cardamom. Estimated nuclear 2C DNA content ranged from 2.57 to 3.22 pg demonstrating 1.25-fold variation. The mean amount of 2C nuclear DNA of the cardamom was calculated as 2.87 pg which is equivalent of 2806 Mbp as the diploid genome size. The chromosome number was found to be 2n = 48. Among the thirty accessions of carda-mom studied using ISSR markers, C53 (feral from Bonacaud) showed a very prominent level of genetic diversity and was lowest for C96 (Avinash-I, a released variety from Indian Institute of Spices Research, Kozhikode).
Conclusion: These analyses revealed the existence of genetic variability within the studied cardamom accessions. The plant specimens also differed significantly in their genome size. However, the genetic variability parameters did not show any correlation with genome size.

****The contents of Chapter 2, regarding Selfish DNA, is currently in prep for publication. Based on comments from my defense the eventual form of this paper will change a bit with some additional content added and a probable change in tone

Transposable elements (TEs), mobile pieces of self-replicating DNA, are one of the driving forces behind genomic evolution in eukaryotic organisms. Their contribution to genome size variation and as mutagens has led researchers to pursue their study in the hope of better understanding the evolution of genomic properties and organismal phenotypes But TEs can also be thought of in a multi-level evolutionary context, with TEs best understood as evolving populations residing within (and interacting with) the host genome. I argue, with empirical evidence from the literature, that the multi-level approach advocated by the classic “selfish DNA” papers of 1980 has become less commonly invoked over the past 35 years, in a favour of a strictly organism-centric view. I also make the case that an exploration of evolution at the level of TEs within genomes is required, one which articulates the similarities and differences between a TE population and a traditional population of organisms. A comprehensive analysis of sequenced eukaryote genomes outlines the landscape of how TE superfamilies are distributed, but also reveals that how TEs are reported needs to be addressed. A proper exploration of evolution at the TE level will require a dramatic change to how TE information is annotated, curated, and stored, and I make several specific recommendations in this regard.

Evidence for invertebrate feeding on glossopterid gymnosperms is documented from Middle Permian silicified peats of the Prince Charles Mountains, Antarctica, in the form of coprolites occurring both free in the peat matrix and clustered within excavations in roots, aerial wood and leaves. Observations of coprolites in thin-sections of the peats and from scanning electron microscopy of examples extracted via bulk maceration reveal nine morphotypes distinguished by size, shape, surface texture and contents. These include coprolites with coarse plant debris, spirally ornamented coprolites, coprolites containing spore/pollen remains and fern sporangia, coprolites within Glossopteris leaves, an ellipsoidal morphotype within a fern sporangium, large isolated coprolites between matted leaves, clustered forms filling galleries inside Vertebraria roots and Australoxylon wood, forms with coarse indeterminate constituents and others with fungal contents. Other faunal evidence is limited to indeterminate arthropod exoskeleton fragments. Collectively, the coprolites within the permineralised peat from the Prince Charles Mountains document the presence of diverse feeding behaviours including stem feeding, sporangial feeding, palynivory, root feeding and mycophagy. The first evidence of invertebrate feeding traces in Vertebraria (glossopterid) roots is identified. These findings indicate that herbivory by invertebrates in the high-latitude Permian forest-mire ecosystems of Antarctica was more intense and diverse than previous studies have reported, and affected all parts of the Glossopteris plant, together with components of associated herbaceous taxa.

Kullman, Bellis (2014). Estimation of fungal genome size by flow cytometry.
Workshop flow cytometry as a tool in microbiology, Warsaw, Poland November 27-28.

Bellis Kullman “Estimation of fungal genome size by flow cytometry”

Abstract
Genome size is an important biodiversity character the study of which has both practical and theoretical uses in biology. Although variation in fungal genome sizes ranges from 2.5 Mbp  in Encephalitozoon cuniculi to 3050 Mbp in Neottiella sp., ca 90% of available values remain between 10 Mbp and 60 Mbp (http://www.zbi.ee/fungal-genomesize/).

A few flow cytometry methods have been developed for quantitative evaluation of the nuclear DNA content of fungal cells, spores, conidia and intact nuclei to estimate genome size (total DNA content of the unreplicated haploid nuclear genome, 1C-value, G1). Appropriate techniques and standards for estimation of the genome are presented.

Measurement by experimental series, performed with the use of one and the same standard, technique and fluorochrome, is suggested in estimation of ploidy levels as well as of slight differences between aneuploids.
Flow cytometric studies show improved resolution when complex fluorochromes are used. Staining with DAPI SR101 is essential in the study of aneuploidy and especially in genetic characterization of heteroploids derived by hybridisation.
This simple and precise method can prove highly promising in the analysis of DNA in the fundamental and applied cytogenetic research of the fungal cell as well as in the systematics of fungi. However, there are several important challenges that should be considered in the case of this method.

In order to understand the evolutionary significance of single triploids among the mostly diploid Poecilia formosa we have developed a simple, noninvasive technique for DNA content and ploidy determination. From dorsal fin clips of 14 different fish species single cell suspensions were obtained by chopping the material in 2.1% citric acid/0.5% Tween20, passing it through a 0. 6-gauge needle and incubating it for 20 min at room temperature (RT) with gentle agitation. After overnight fixation in 70% ethanol, the cells were treated with 1ml 0.5% pepsin/0.1 M HCl for 15 min at RT before adding DAPI to a final volume of 2 ml. The cells were stained for 1-3 h and then analyzed by flow cytometry. We obtained good measurements with CVs ranging from 1.23% to 3.36%. The poeciliid species measured contain from 1.6 to 2.0 pg/nucleus, Oryzias latipes (Medaka) exhibits a nuclear DNA content of 2.2 pg, Danio rerio (zebrafish) 4.6 pg, Tetraodon fluviatilis (freshwater fugu) 0.70 pg. All values exce...

Twenty-eight basil accessions including six Ocimum species and six botanical varieties or cultivars of O. basilicum were studied using molecular markers, nuclear DNA content, and chromosome counting. This is the first study reporting the nuclear DNA content in the genus Ocimum. The results supported the existence of more infrageneric groups within the genus. The section Ocimum was further divided into two separate clades. The first clade contained the accessions belonging to different botanical varieties and cultivars of O. basilicum as well as O. minimum, indicating that the separate species rank of O. minimum was not justified. The second clade, comprising O. americanum, O. africanum, and two O. basilicum var. purpurascens accessions, could represent a set of allopolyploid species sharing some common parental genomes. O. tenuiflorum was the most divergent species according to genetic distance; it had the smallest genome size, organized in small chromosomes, and the lowest chromosome number. Chromosome data obtained in our research could indicate that the basic chromosome number for species belonging to section Ocimum is x = 12. This suggestion implies that species belonging to O. basilicum clade are tetraploids, while species belonging to O. americanum clade are hexaploids. It seems that the basic chromosome number for O. gratissimum could be x = 10 and for O. tenuiflorum x = 9. The differences in genome size and chromosome number among Ocimum species indicate that evolution of their genomes was accompanied by both sequence deletion/amplification and chromosome rearrangements and polyploidization.

Flow cytometry was used to analyze the DNA content of nuclei isolated from four different shoot cultures growing in vitro, and from callus of Rubus chamaemorus. The protocol for isolation of the nuclei of this species was optimized. Flow cytometry proved to be a fast and accurate method for estimation of the genome size of R. chamaemorus, a species containing

Adult somatic nuclear DNA contents are reported for eleven cyclopoid species (Megacyclops latipes, Mesocyclops edax, M. longisetus, M. ruttneri, M. leuckarti, M. woutersi, Macrocyclops albidus, Cyclops strenuus, Acanthocyclops robustus, Diothona oculata, Thermocyclops crassus) and for the harpacticoid Tigriopus californicus and range from 0.50 to 4.1 pg DNA per nucleus. These diploid genome sizes are consistent with previously published values for