Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants

Abstract

Chromosome evolution is a fundamental aspect of evolutionary biology. The evolution of chromosome size, structure and shape, number, and the change in DNA composition suggest the high plasticity of nuclear genomes at the chromosomal level. Repetitive DNA sequences, which represent a conspicuous fraction of every eukaryotic genome, particularly in plants, are found to be tightly linked with plant chromosome evolution. Different classes of repetitive sequences have distinct distribution patterns on the chromosomes. Mounting evidence shows that repetitive sequences may play multiple generative roles in shaping the chromosome karyotypes in plants. Furthermore, recent development in our understanding of the repetitive sequences and plant chromosome evolution has elucidated the involvement of a spectrum of epigenetic modification. In this review, we focused on the recent evidence relating to the distribution pattern of repetitive sequences in plant chromosomes and highlighted their potential relevance to chromosome evolution in plants. We also discussed the possible connections between evolution and epigenetic alterations in chromosome structure and repatterning, such as heterochromatin formation, centromere function, and epigenetic-associated transposable element inactivation.

Keywords: epigenetic modification; plant chromosome evolution; repetitive sequences; transposable elements.

Figure 1

Distribution patterns of different transposable elements (TE) on chromosomes in Asparagus officinalis. The TE sequences were labeled with Texas Red (red signal), whereas 45S rDNA was labeled with Chroma Tide Alexa Fluor 488 (green signal), and the chromosomes were counterstained with DAPI (blue). (A) Ty1-copia; (B) Ty3-gypsy; (C) LINE-L1; (D) LINE-CR1; (E) hAT; (F) Helitron. The fluorescence in situ hybridization (FISH) images were captured with an ANDOR CCD camera under an Olympus BX63 fluorescence microscope. Bars = 10 μm.

Figure 2

Correlation analysis between genome size and gene numbers or quantities of different types of repetitive sequences in plants. (A) genome size versus genes; (B) genome size versus repetitive sequences; (C) genome size versus retrotransposons; (D) genome size versus transposons; (E) genome size versus Ty1-copia elements; (F) genome size versus Ty3-gypsy elements. This figure is drawn based on the data presented in Table S1. The black dots represent the analysis from data of higher plants, whereas the red dots indicate the analysis from data of lower algal plants.

Figure 3

A simple scheme summarizing the effect of repetitive sequences involved in individual processes on chromosome structure. See details in text.