ORIGINAL ARTICLE Chromosomal distribution and evolution of abundant retrotransposons in plants: gypsy elements in diploid and polyploid Brachiaria forage grasses Fabíola Carvalho Santos & Romain Guyot & Cacilda Borges do Valle & Lucimara Chiari & Vânia Helena Techio & Pat Heslop-Harrison & André Luís Laforga Vanzela Published online: 19 September 2015 # Springer Science+Business Media Dordrecht 2015 Abstract 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 thou- sands 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 var- ious families and domains. The genus Brachiaria in- cludes 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. Cytoge- netic studies and flow cytometry indicate a large varia- tion 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 ac- cesses 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 dis- persed signals, in addition to those proximal signals. These results show that the proximal region of Brachiaria chromosomes is a hotspot for retrotransposon insertion, Chromosome Res (2015) 23:571–582 DOI 10.1007/s10577-015-9492-6 Responsible Editors: Maria Assunta Biscotti and Ettore Olmo F. C. Santos : A. L. L. Vanzela (*) Department of General Biology, Center of Biological Sciences, State University of Londrina, Londrina 86057-970 Paraná State, Brazil e-mail: andrevanzela@uel.br R. Guyot Institut de Recherche pour le Développement (IRD), UMR IPME, BP 64501, 34394 Montpellier Cedex, France C. B. do Valle : L. Chiari Embrapa Gado de Corte, 79106-550 Campo Grande, Mato Grosso do Sul State, Brazil V. H. Techio Department of Biology, Federal University of Lavras, 37200-000, Lavras, Minas Gerais State, Brazil P. Heslop-Harrison (*) Department of Genetics, University of Leicester, Leicester LE1 7RH, UK e-mail: phh@molcyt.com