caa a22 4500 606190449 CHVBK 20210128100855.0 cr unu---uuuuu 210128e20150901xx s 000 0 eng 10.1007/s10577-015-9492-6 doi (NATIONALLICENCE)springer-10.1007/s10577-015-9492-6 Chromosomal distribution and evolution of abundant retrotransposons in plants: gypsy elements in diploid and polyploid Brachiaria forage grasses [Elektronische Daten] [Fabíola Santos, Romain Guyot, Cacilda do Valle, Lucimara Chiari, Vânia Techio, Pat Heslop-Harrison, André Vanzela] Like other eukaryotes, the nuclear genome of plants consists of DNA with a small proportion of low-copy DNA (genes and regulatory sequences) and very abundant DNA sequence motifs that are repeated thousands up to millions of times in the genomes including transposable elements (TEs) and satellite DNA. Retrotransposons, one class of TEs, are sequences that amplify via an RNA intermediate and reinsert into the genome, are often the major fraction of a genome. Here, we put research on retrotransposons into the larger context of plant repetitive DNA and genome behaviour, showing features of genome evolution in a grass genus, Brachiaria, in relation to other plant species. We show the contrasting amplification of different retroelement fractions across the genome with characteristics for various families and domains. The genus Brachiaria includes both diploid and polyploid species, with similar chromosome types and chromosome basic numbers x = 6, 7, 8 and 9. The polyploids reproduce asexually and are apomictic, but there are also sexual species. Cytogenetic studies and flow cytometry indicate a large variation in DNA content (C-value), chromosome sizes and genome organization. In order to evaluate the role of transposable elements in the genome and karyotype organization of species of Brachiaria, we searched for sequences similar to conserved regions of TEs in RNAseq reads library produced in Brachiaria decumbens. Of the 9649 TE-like contigs, 4454 corresponded to LTR-retrotransposons, and of these, 79.5% were similar to members of the gypsy superfamily. Sequences of conserved protein domains of gypsy were used to design primers for producing the probes. The probes were used in FISH against chromosomes of accesses of B. decumbens, Brachiaria brizantha, Brachiaria ruziziensis and Brachiaria humidicola. Probes showed hybridization signals predominantly in proximal regions, especially those for retrotransposons of the clades CRM and Athila, while elements of Del and Tat exhibited dispersed signals, in addition to those proximal signals. These results show that the proximal region of Brachiaria chromosomes is a hotspot for retrotransposon insertion, particularly for the gypsy family. The combination of high-throughput sequencing and a chromosome-centric cytogenetic approach allows the abundance, organization and nature of transposable elements to be characterized in unprecedented detail. By their amplification and dispersal, retrotransposons can affect gene expression; they can lead to rapid diversification of chromosomes between species and, hence, are useful for studies of genome evolution and speciation in the Brachiaria genus. Centromeric regions can be identified and mapped, and retrotransposon markers can also assisting breeders in the developing and exploiting interspecific hybrids. Springer Science+Business Media Dordrecht, 2015 centromeres nationallicence retrotransposons nationallicence FISH nationallicence in situ hybridization nationallicence metaviridae nationallicence grasses nationallicence genomics nationallicence genome organization nationallicence transposons nationallicence transposable elements nationallicence genetics nationallicence repetitive DNA nationallicence chromosomes nationallicence PBS : Primer binding site nationallicence PR : Protease nationallicence RT : Reverse transcriptase nationallicence RT- Athila : Reverse transcriptase of Athila lineage nationallicence RT- CRM : Reverse transcriptase of CRM lineage nationallicence RT- Tat : Reverse transcriptase of Tat lineage nationallicence RNAse H : Ribonuclease H nationallicence INT : Integrase nationallicence IRAP : Inter-retroelement amplified polymorphism nationallicence PPT : Polypurine tract nationallicence LTRs : Long terminal repeats nationallicence LTR-RTs : Retrotransposons with LTR nationallicence TEs : Transposable elements nationallicence POL : Polygenic string nationallicence FISH : Fluorescent in situ hybridization nationallicence CRM : Centromere-specific retrotransposons of Maize nationallicence Santos Fabíola Department of General Biology, Center of Biological Sciences, State University of Londrina, 86057-970, Londrina, Paraná State, Brazil aut Guyot Romain Institut de Recherche pour le Développement (IRD), UMR IPME, BP 64501, 34394, Montpellier Cedex, France aut do Valle Cacilda Embrapa Gado de Corte, 79106-550, Campo Grande, Mato Grosso do Sul State, Brazil aut Chiari Lucimara Embrapa Gado de Corte, 79106-550, Campo Grande, Mato Grosso do Sul State, Brazil aut Techio Vânia Department of Biology, Federal University of Lavras, 37200-000, Lavras, Minas Gerais State, Brazil aut Heslop-Harrison Pat Department of Genetics, University of Leicester, LE1 7RH, Leicester, UK aut Vanzela André Department of General Biology, Center of Biological Sciences, State University of Londrina, 86057-970, Londrina, Paraná State, Brazil aut Chromosome Research Springer Netherlands 23/3(2015-09-01), 571-582 0967-3849 23:3<571 2015 23 10577 https://doi.org/10.1007/s10577-015-9492-6 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s10577-015-9492-6 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Santos Fabíola Department of General Biology, Center of Biological Sciences, State University of Londrina, 86057-970, Londrina, Paraná State, Brazil aut NATIONALLICENCE 700 1- Guyot Romain Institut de Recherche pour le Développement (IRD), UMR IPME, BP 64501, 34394, Montpellier Cedex, France aut NATIONALLICENCE 700 1- do Valle Cacilda Embrapa Gado de Corte, 79106-550, Campo Grande, Mato Grosso do Sul State, Brazil aut NATIONALLICENCE 700 1- Chiari Lucimara Embrapa Gado de Corte, 79106-550, Campo Grande, Mato Grosso do Sul State, Brazil aut NATIONALLICENCE 700 1- Techio Vânia Department of Biology, Federal University of Lavras, 37200-000, Lavras, Minas Gerais State, Brazil aut NATIONALLICENCE 700 1- Heslop-Harrison Pat Department of Genetics, University of Leicester, LE1 7RH, Leicester, UK aut NATIONALLICENCE 700 1- Vanzela André Department of General Biology, Center of Biological Sciences, State University of Londrina, 86057-970, Londrina, Paraná State, Brazil aut NATIONALLICENCE 773 0- Chromosome Research Springer Netherlands 23/3(2015-09-01), 571-582 0967-3849 23:3<571 2015 23 10577