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Transposable Elements in the Organization and Diversification of the Genome of Aegilops speltoides Ta 时间:2018-09-29 10:06 来源:未知作者:admin 点击: 次 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.
1. Introduction
Repetitive DNA—specifically, transposable elements (TEs)—constitutes at least 45% of the human genome, wherein the fraction of long interspersed nucleotide element (LINE) retrotransposons is 17% [1]. In plants, 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]. Mobile elements move to new sites in the genome either through an RNA intermediate via a copy-and-paste mechanism (retrotransposons of Class I) or directly through a cut-and-paste mechanism (transposons of Class II) [1, 2, 6], generating the basis for genetic variability in somatic and generative tissues and resulting in intraspecific variations [7, 8]. TEs modify the host genome via insertional mutagenesis, affect both the expression of neighboring genes and translation, and contribute to new gene generation [9–12]. TE mobilization, especially under conditions of environmental stress and/or hybridization, causes prompt karyotype changes that accompany speciation [13–15].
Many epigenetically silent copies and fragments of TEs accumulate in the genome as an integral part of heterochromatin [10, 16], and the methylation and epigenetic remodeling of heterochromatin-specific repeats have been involved in the siRNA-mediated transcriptional silencing of full-length, transpositionally competent TEs [17, 18]. At the cytological level, heterochromatic DNA is traced as condensed chromatin blocks throughout the cell cycle, except during replication in the late S-phase [19]; the replication of euchromatic gene-rich DNA occurs earlier in the S-phase. 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]. Regardless of whether high polymorphism is present, the heterochromatin pattern is an integral chromosome- and species-specific characteristic. 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].