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Eukaryotic genome size databases

Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
Nucleic Acids Research (Impact Factor: 9.11). 02/2007; 35(Database issue):D332-8. DOI: 10.1093/nar/gkl828
Source: PubMed

ABSTRACT 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 (www.kew.org/genomesize/homepage.html), the Animal Genome Size Database (www.genomesize.com) and the Fungal Genome Size Database (www.zbi.ee/fungal-genomesize/). 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.

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    • "Dennis (Ascomycota, Pezizales; Kullman, 2002) and Scutellospora castanea Walker (Glomeromycota, Diversisporales; Zeze et al., 1996; Hijri and Sanders, 2005), with 750 and 795 Mbp/1C, respectively . Variations in chromosome number and size are far from being an exception and ploidy levels ranging from 1x to 50x have already been found (Gregory et al., 2007). Nevertheless, Basidiomycota cells are more frequently dikaryotic with haploid nuclei for most of their life cycles. "
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    ABSTRACT: Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.
    Frontiers in Plant Science 08/2014; 5(422). DOI:10.3389/fpls.2014.00422 · 3.95 Impact Factor
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    • "Because the stem salmonid underwent WGD, unchanged chromosome numbers would result in extant salmonids with around 50 chromosomes, a number twice that of their closest relatives. In contrast, although cells of salmonid fishes consistently have double the DNA content (Gregory et al. 2007) and chromosome arms (Phillips et al. 2009) as compared to their closest relatives, their chromosome numbers vary extensively between 26 and 51. Most of the species have a lower chromosome number than the original number after duplication (Supp. "
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    ABSTRACT: Whole-genome duplication (WGD) events have shaped the history of many evolutionary lineages. One such duplication has been implicated in the evolution of teleost fishes, by far the most species-rich vertebrate clade. After initial controversy, there is now solid evidence that such event took place in the common ancestor of all extant teleosts. It is termed teleost-specific (TS) WGD. After WGD, duplicate genes have different fates. The most likely outcome is non-functionalization of one duplicate gene due to the lack of selective constraint on preserving both. Mechanisms that act on preservation of duplicates are subfunctionalization (partitioning of ancestral gene functions on the duplicates), neofunctionalization (assigning a novel function to one of the duplicates) and dosage selection (preserving genes to maintain dosage balance between interconnected components). Since the frequency of these mechanisms is influenced by the genes' properties, there are over-retained classes of genes, such as highly expressed ones and genes involved in neural function. The consequences of the TS-WGD, especially its impact on the massive radiation of teleosts, have been matter of controversial debate. It is evident that gene duplications are crucial for generating complexity and that WGDs provide large amounts of raw material for evolutionary adaptation and innovation. However, it is less clear whether the TS-WGD is directly linked to the evolutionary success of teleosts and their radiation. Recent studies let us conclude that TS-WGD has been important in generating teleost complexity, but that more recent ecological adaptations only marginally related to TS-WGD might have even contributed more to diversification. It is likely, however, that TS-WGD provided teleosts with diversification potential that can become effective much later, such as during phases of environmental change.
    Molecular Genetics and Genomics 08/2014; 289(6). DOI:10.1007/s00438-014-0889-2 · 2.83 Impact Factor
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    • "Glomeromycota genome size estimations showed great variations according to species, ranging from 0.18 to 1.08 pg of DNA per nucleus (Bianciotto & Bonfante, 1992; Hosny, Gianinazzi-Pearson, & Dulieu, 1998), that is, 176 Mb to over 1 Gb using the conversion formula of Doležel, Bartoš, Voglmayr, and Greilhuber (2003). Glomeromycota hence present the largest genome sizes among fungi (37 Mb on average—Gregory et al., 2007). Flow cytometry assays performed on isolate DAOM197198 first led to a genome size estimation of around 15 Mb (Hijri & Sanders, 2004), but later measurements using different standards indicated that the genome size could be in fact 10 times higher (154.8 "
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    ABSTRACT: Arbuscular mycorrhizal (AM) symbiosis is the most widespread mutualistic association. It concerns 80% of land plants and involves fungi belonging to the phylum Glomeromycota. Benefits to the host plants due to this symbiosis range from nutrient supply to protection against pathogens. AM fungi are important components of the soil microbiome and are of great interest for managing sustainable agriculture, provided that their life cycle is better understood. Recently, major advances in the genomics of the model AM fungus Rhizophagus irregularis DAOM197198 have been published, offering new tools to investigate the biology of this symbiosis. In this chapter, we provide an overview of the efforts that were necessary to reach these results, from the discovery of these fungi and the description of their mutualistic incidence to their in vitro cultivation and on to genomics. The genome of DAOM197198 is estimated at ca. 150 Mb. It is haploid and less polymorphic than expected. Although it is an obligate biotrophic fungus, very little gene loss was observed. We put the Rhizophagus gene repertoire in perspective with previous investigations performed on the physiology of AM fungi: germination, early signalling with host plants, plant invasion, metabolism (phosphorous, carbon and nitrogen) and sexuality. Clearly, the publication of the genome of R. irregularis DAOM197198 is a turning point in the study of AM fungi, and large areas of their biology that still remain to be elucidated will now become accessible for investigation.
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