Chromosome Research

, Volume 23, Issue 3, pp 571–582 | Cite as

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
Original Article


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.


centromeres retrotransposons FISH in situ hybridization metaviridae grasses genomics genome organization transposons transposable elements genetics repetitive DNA chromosomes 



Primer binding site




Reverse transcriptase


Reverse transcriptase of Athila lineage


Reverse transcriptase of CRM lineage


Reverse transcriptase of Tat lineage


Ribonuclease H




Inter-retroelement amplified polymorphism


Polypurine tract


Long terminal repeats


Retrotransposons with LTR


Transposable elements


Polygenic string


Fluorescent in situ hybridization


Centromere-specific retrotransposons of Maize



The authors thank the Brazilian agencies Fundação Araucária, CNPq and CAPES for financial support. JSHH thanks IAEA-FAO for support via Cooperative Research Programme D23029 Climate Proofing of Food Crops: Genetic Improvement for Adaptation to High Temperatures in Drought Prone Areas and Beyond.


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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Fabíola Carvalho Santos
    • 1
  • Romain Guyot
    • 2
  • Cacilda Borges do Valle
    • 3
  • Lucimara Chiari
    • 3
  • Vânia Helena Techio
    • 4
  • Pat Heslop-Harrison
    • 5
  • André Luís Laforga Vanzela
    • 1
  1. 1.Department of General Biology, Center of Biological SciencesState University of LondrinaLondrinaBrazil
  2. 2.Institut de Recherche pour le Développement (IRD), UMR IPMEMontpellier CedexFrance
  3. 3.Embrapa Gado de CorteCampo GrandeBrazil
  4. 4.Department of BiologyFederal University of LavrasLavrasBrazil
  5. 5.Department of GeneticsUniversity of LeicesterLeicesterUK

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