Correlated evolution of LTR retrotransposons and genome size in the genus eleocharis

Zedek, František; Šmerda, Jakub; Šmarda, Petr; Bureš, Petr
January 2010
BMC Plant Biology;2010, Vol. 10, p265
Academic Journal
Background: Transposable elements (TEs) are considered to be an important source of genome size variation and genetic and phenotypic plasticity in eukaryotes. Most of our knowledge about TEs comes from large genomic projects and studies focused on model organisms. However, TE dynamics among related taxa from natural populations and the role of TEs at the species or supra-species level, where genome size and karyotype evolution are modulated in concert with polyploidy and chromosomal rearrangements, remain poorly understood. We focused on the holokinetic genus Eleocharis (Cyperaceae), which displays large variation in genome size and the occurrence of polyploidy and agmatoploidy/symploidy. We analyzed and quantified the long terminal repeat (LTR) retrotransposons Ty1-copia and Ty3-gypsy in relation to changes in both genome size and karyotype in Eleocharis. We also examined how this relationship is reflected in the phylogeny of Eleocharis. Results: Using flow cytometry, we measured the genome sizes of members of the genus Eleocharis (Cyperaceae). We found positive correlation between the independent phylogenetic contrasts of genome size and chromosome number in Eleocharis. We analyzed PCR-amplified sequences of various reverse transcriptases of the LTR retrotransposons Ty1-copia and Ty3-gypsy (762 sequences in total). Using real-time PCR and dot blot approaches, we quantified the densities of Ty1-copia and Ty3-gypsy within the genomes of the analyzed species. We detected an increasing density of Ty1-copia elements in evolutionarily younger Eleocharis species and found a positive correlation between Ty1-copia densities and C/n-values (an alternative measure of monoploid genome size) in the genus phylogeny. In addition, our analysis of Ty1-copia sequences identified a novel retrotransposon family named Helos1, which is responsible for the increasing density of Ty1-copia. The transition:transversion ratio of Helos1 sequences suggests that Helos1 recently transposed in later-diverging Eleocharis species. Conclusions: Using several different approaches, we were able to distinguish between the roles of LTR retrotransposons, polyploidy and agmatoploidy/symploidy in shaping Eleocharis genomes and karyotypes. Our results confirm the occurrence of both polyploidy and agmatoploidy/symploidy in Eleocharis. Additionally, we introduce a new player in the process of genome evolution in holokinetic plants: LTR retrotransposons.


Related Articles

  • DNA Underreplication in the Majority of Nuclei in the Drosophila Melanogaster Thorax: Evidence from Suur and Flow Cytometry. Johnston, J. Spencer; Schoener, Molly; McMahon, Dino P. // Journal of Molecular Biology Research;2013, Vol. 3 Issue 1, p47 

    The discovery of endoreduplication in the majority of cells of the thorax of Drosophila has implications for genomics, transcriptome levels, chromatin structure and life history of these model insects. The ratio of 2C/4C DNA amounts is 2.00 for nuclei from the head, yet is 1.75 and 1.83 for...

  • Plant DNA Flow Cytometry and Estimation of Nuclear Genome Size. DOLEŽEL, JAROSLAV; BARTOŠ, JAN // Annals of Botany;Jan2005, Vol. 95 Issue 1, p99 

    • Background DNA flow cytometry describes the use of flow cytometry for estimation of DNA quantity in cell nuclei. The method involves preparation of aqueous suspensions of intact nuclei whose DNA is stained using a DNA fluorochrome. The nuclei are classified according to their relative...

  • Multigenerational genomic responses to dietary phosphorus and temperature in Daphnia. Schwarzacher, T.; Jalal, Marwa; Shala, Nita K.; Wojewodzic, Marcin W.; Hessen, Dag O.; Andersen, Tom // Genome;2014, Vol. 57 Issue 8, p439 

    Temperature and nutrient availability are both hypothesized to affect organisms at the cellular and genomic levels. In this multigenerational study, Daphnia magna ( D. magna) and Daphnia pulex ( D. pulex) were maintained at high (20 °C) and low (10 °C) temperatures and nourished with...

  • Reproduction and cytogenetic characterization of interspecific hybrids derived from Cucumis hystrix Chakr. × Cucumis sativus L. Chen, J.; Staub, J.; Qian, Ch.; Jiang, J.; Luo, X.; Zhuang, F. // Theoretical & Applied Genetics;Feb2003, Vol. 106 Issue 4, p688 

    Interspecific hybrids between Cucumis hystrix Chakr. (2n = 2x = 24) and Cucumis sativus L. (2n = 2x = 14) were produced by means of F1 (2n = 19) embryo rescue and subsequent chromosome doubling. The hybridity was confirmed by genomic in situ hybridization (GISH) and chromosome analysis. The...

  • New insights into the karyotypic relationships of Chinese muntjac (Muntiacus reevesi), forest musk deer (Moschus berezovskii) and gayal (Bos frontalis). Chi, J.; Fu, D. B.; Nie, W.; J. Wang; Graphodatsky, A. S.; F. Yang // Cytogenetic & Genome Research;2005, Vol. 108 Issue 4, p310 

    To investigate the karyotypic relationships between Chinese muntjac (Muntiacus reevesi), forest musk deer (Moschus berezovskii) and gayal (Bos frontalis), a complete set of Chinese muntjac chromosome-specific painting probes has been assigned to G-banded chromosomes of these three species....

  • Chromatin and the genome integrity network. Papamichos-Chronakis, Manolis; Peterson, Craig L. // Nature Reviews Genetics;Jan2013, Vol. 14 Issue 1, p62 

    The maintenance of genome integrity is essential for organism survival and for the inheritance of traits to offspring. Genomic instability is caused by DNA damage, aberrant DNA replication or uncoordinated cell division, which can lead to chromosomal aberrations and gene mutations. Recently,...

  • Plant Genome Size Estimation by Flow Cytometry: Inter-laboratory Comparison. Doležel, J.; Greilhuber, J.; Lucretti, S.; Meister, A.; Lysák, M. A.; Nardi, L.; Obermayer, R. // Annals of Botany;1998, Vol. 82 Issue suppl_1, p17 

    Flow cytometry is a convenient and rapid method that has been used extensively for estimation of nuclear genome size in plants. In contrast to general expectations, results obtained in different laboratories showed some striking discrepancies. The aim of this joint experiment was to test the...

  • New cytogenetically visible copy number variant in region 8q21.2. Manvelyan, Marina; Cremer, Friedrich W.; Lancé, Jeannette; Kläs, Rüdiger; Kelbova, Christina; Ramel, Christian; Reichenbach, Herbert; Schmidt, Catharina; Ewers, Elisabeth; Kreskowski, Katharina; Ziegler, Monika; Kosyakova, Nadezda; Liehr, Thomas // Molecular Cytogenetics (17558166);2011, Vol. 4 Issue 1, p1 

    Background: Cytogenetically visible unbalanced chromosomal abnormalities (UBCA), reported for >50 euchromatic regions of almost all human autosomes, are comprised of a few megabases of DNA, and carriers are in many cases clinically healthy. It may be speculated, that some of the UBCA may be...

  • Comparative analysis of copy number detection by whole-genome BAC and oligonucleotide array CHG. Neill, Nicholas J.; Torchia, Beth S.; Bejjani, Bassem A.; Shaffer, Lisa G.; Ballif, Blake C. // Molecular Cytogenetics (17558166);2010, Vol. 3, p11 

    Background: Microarray-based comparative genomic hybridization (aCGH) is a powerful diagnostic tool for the detection of DNA copy number gains and losses associated with chromosome abnormalities, many of which are below the resolution of conventional chromosome analysis. It has been presumed...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics