Transposable Elements in the Organization and Diversification of the Genome of Aegilops speltoides Tausch (Poaceae, Triticeae).

Olga Raskina

doi:10.1155/2018/4373089

Abstract

Repetitive DNA—specifically, transposable elements (TEs)—is a prevailing genomic fraction in cereals that underlies extensive genome reshuffling and intraspecific diversification in the wild. Although large amounts of data have been accumulated, the effect of TEs on the genome architecture and functioning is not fully understood. Here, plant genome organization was addressed by means of cloning and sequencing TE fragments of different types, which compose the largest portion of the Aegilops speltoides genome. Individual genotypes were analyzed cytogenetically using the cloned TE fragments as the DNA probes for fluorescence in situ hybridization (FISH). The obtained TE sequences of the Ty1-copia, Ty3-gypsy, LINE, and CACTA superfamilies showed the relatedness of the Ae. speltoides genome to the Triticeae tribe and similarities to evolutionarily distant species. A significant number of clones consisted of intercalated fragments of TEs of various types, in which Fatima (Ty3-gypsy) sequences predominated. At the chromosomal level, different TE clones demonstrated sequence-specific patterning, emphasizing the effect of the TE fraction on the Ae. speltoides genome architecture and intraspecific diversification. Altogether, the obtained data highlight the current species-specific organization and patterning of the mobile element fraction and point to ancient evolutionary events in the genome of Ae. speltoides.

Highlights

Repetitive DNA—transposable elements (TEs)— constitutes at least 45% of the human genome, wherein the fraction of long interspersed nucleotide element (LINE) retrotransposons is 17% [1]
Three sets of nucleotide sequences were obtained via the cloning and sequencing of Polymerase Chain Reaction (PCR) products amplified using degenerate primers for Reverse Transcriptase (RT) of Ty1-copia (10 sequences, clones Aesp1 to Aesp10), Ty3gypsy (13 sequences, clones Aesp11 to Aesp23), and LINE (11 sequences, clones Aesp24 to Aesp34) retrotransposons (Supplementary Table S1)
PCR with degenerate primers for RT of Ty1-copia amplified a mix of approximately 280 bp fragments (Supplementary Figure S1)

Summary

Introduction

Repetitive DNA—transposable elements (TEs)— constitutes at least 45% of the human genome, wherein the fraction of long interspersed nucleotide element (LINE) retrotransposons is 17% [1]. TEs comprise up to 80% of the genomes, with prevailing long terminal repeat (LTR) families of Ty1-copia and Ty3-gypsy retrotransposons [2, 3], which vary extensively in their sequence motifs and abundances, even between closely related species [4, 5]. Nuclear chromatin organization and dynamics are associated with genome functioning; during cell differentiation, gene replication and expression timing can change due to repositioning in the nuclei and chromatin remodeling [20]. In the wild, ongoing chromosomal rearrangements lead to considerable changes in the numbers, sizes, and positions of highly repetitive DNA clusters and underlie the divergence of natural populations [21]

Methods

Results

Discussion

Conclusion