Chromosomal distribution and evolution of abundant retrotransposons in plants: gypsy elements in diploid and polyploid Brachiaria forage grasses

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 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.

Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis

“…Coffee unigenes were compared against transposable elements sequences available at Repbase protein transposable elements database [36] using a strategy similar to that reported by Santos et al [37] and Marcon et al [38]. Unigenes were considered related to TEs when there was a minimum alignment of 200 bp, a score greater than 200 and a 1e-10 evalue in BlastN.…”

Physical Map of Repetitive DNA Sites in Brachiaria spp.: Intravarietal and Interspecific Polymorphisms

“…It must be emphasized that these authors have also indicated the occurrence of differences between accessions, which has been attributed to structural changes or possible hybridization between different accessions of the species. Repetitive CRM sequences have also been studied in chromosomes of Brachiaria species by Santos et al (2015). This class of retrotransposons is typical of centromeres in grass species, however, there are several CR derivations already identified in species such as barley, wheat, rye, and rice (Presting et al, 1998).…”

“…B. brizantha and B. decumbens probably have a more abundant, distinct CR responsible for the organization of the centromere. Repetitive CRM sequences have also been studied in chromosomes of Brachiaria species by Santos et al (2015). Discrete signals have been found in the pericentromeric-interstitial region in diploids of B. ruziziensis and B. brizantha.…”

“…Unlike other families of retrotransposons that diverge rapidly during evolution, the CR family was found in centromeres of all grass species studied so far (Miller et al, 1998). Maize CR subtypes 1 and 2 (CRM1 and CRM2) are frequently used to determine the centromere position in maize (Kato et al, 2004) and other species including Brachiaria (Santos et al, 2015); discrete CR in maize signals were found in the pericentromericinterstitial region of the chromosomes in B. ruziziensis and B. brizantha and proximal-interstitial signals in B. decumbens.…”

Chromosomal distribution of H3K4me2, H3K9me2 and 5-methylcytosine: variations associated with polyploidy and hybridization in Brachiaria (Poaceae)

“…Sometimes this mark extended up to the chromosomal arms in the species and hybrids assessed in the current study. According to study of Santos et al (2015) the chromosomal distribution and evolution of gypsy elements (retrotransposons) in diploid and polyploid Brachiaria species are preferably integrated into proximal chromosome regions.…”