@article{fdi:010065489,
  title = {{C}hromosomal distribution and evolution of abundant retrotransposons in plants : gypsy elements in diploid and polyploid {B}rachiaria forage grasses},
  author = {{S}antos, {F}. {C}. and {G}uyot, {R}omain and do {V}alle, {C}. {B}. and {C}hiari, {L}. and {T}echio, {V}. {H}. and {H}eslop-{H}arrison, {P}. and {V}anzela, {A}. {L}. {L}.},
  editor = {},
  language = {{ENG}},
  abstract = {{L}ike 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 ({TE}s) and satellite {DNA}. {R}etrotransposons, one class of {TE}s, are sequences that amplify via an {RNA} intermediate and reinsert into the genome, are often the major fraction of a genome. {H}ere, 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, {B}rachiaria, in relation to other plant species. {W}e show the contrasting amplification of different retroelement fractions across the genome with characteristics for various families and domains. {T}he genus {B}rachiaria includes both diploid and polyploid species, with similar chromosome types and chromosome basic numbers x = 6, 7, 8 and 9. {T}he polyploids reproduce asexually and are apomictic, but there are also sexual species. {C}ytogenetic studies and flow cytometry indicate a large variation in {DNA} content ({C}-value), chromosome sizes and genome organization. {I}n order to evaluate the role of transposable elements in the genome and karyotype organization of species of {B}rachiaria, we searched for sequences similar to conserved regions of {TE}s in {RNA}seq reads library produced in {B}rachiaria decumbens. {O}f the 9649 {TE}-like contigs, 4454 corresponded to {LTR}-retrotransposons, and of these, 79.5 % were similar to members of the gypsy superfamily. {S}equences of conserved protein domains of gypsy were used to design primers for producing the probes. {T}he probes were used in {FISH} against chromosomes of accesses of {B}. decumbens, {B}rachiaria brizantha, {B}rachiaria ruziziensis and {B}rachiaria humidicola. {P}robes showed hybridization signals predominantly in proximal regions, especially those for retrotransposons of the clades {CRM} and {A}thila, while elements of {D}el and {T}at exhibited dispersed signals, in addition to those proximal signals. {T}hese results show that the proximal region of {B}rachiaria chromosomes is a hotspot for retrotransposon insertion, particularly for the gypsy family. {T}he 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. {B}y 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 {B}rachiaria genus. {C}entromeric regions can be identified and mapped, and retrotransposon markers can also assisting breeders in the developing and exploiting interspecific hybrids.},
  keywords = {centromeres ; retrotransposons ; {FISH} ; in situ hybridization ; metaviridae ; grasses ; genomics ; genome organization ; transposons ; transposable ; elements ; genetics ; repetitive {DNA} ; chromosomes},
  booktitle = {},
  journal = {{C}hromosome {R}esearch},
  volume = {23},
  numero = {3},
  pages = {571--582},
  ISSN = {0967-3849},
  year = {2015},
  DOI = {10.1007/s10577-015-9492-6},
  URL = {https://www.documentation.ird.fr/hor/fdi:010065489},
}