Satellite DNA and Transposable Elements in Seabuckthorn (Hippophae rhamnoides), a Dioecious Plant with Small Y and Large X Chromosomes

Abstract

Seabuckthorn (Hippophae rhamnoides) is a dioecious shrub commonly used in the pharmaceutical, cosmetic, and environmental industry as a source of oil, minerals and vitamins. In this study, we analyzed the transposable elements and satellites in its genome. We carried out Illumina DNA sequencing and reconstructed the main repetitive DNA sequences. For data analysis, we developed a new bioinformatics approach for advanced satellite DNA analysis and showed that about 25% of the genome consists of satellite DNA and about 24% is formed of transposable elements, dominated by Ty3/Gypsy and Ty1/Copia LTR retrotransposons. FISH mapping revealed X chromosome-accumulated, Y chromosome-specific or both sex chromosomes-accumulated satellites but most satellites were found on autosomes. Transposable elements were located mostly in the subtelomeres of all chromosomes. The 5S rDNA and 45S rDNA were localized on one autosomal locus each. Although we demonstrated the small size of the Y chromosome of the seabuckthorn and accumulated satellite DNA there, we were unable to estimate the age and extent of the Y chromosome degeneration. Analysis of dioecious relatives such as Shepherdia would shed more light on the evolution of these sex chromosomes.

Keywords: chromosomal localization; genome composition; repetitive DNA; sex chromosomes.

Fig. 1.—

Repeat composition of clusters and their genomic proportions. Each column corresponds to one cluster and repeat types are distinguished by colors. The height of columns represents number of reads in each cluster, the width of column indicate genomic proportion of cluster.

Fig. 2.—

Phylogenetic trees of Hippophae rhamnoides Ty3/Gypsy (A) and Ty1/Copia (B) retrotransposons based on reverse transcriptase sequences. RT domains of retrotransposons reconstructed from Illumina reads in this study are in red, representative RT domains of retrotransposons from other plant species (from TREP and GyDB) are in black. Individual families are highlighted by different colors.

Fig. 3.—

Comparison of structure of selected retrotransposon families in Hippophae rhamnoides. Graphs of coverage by male (in blue) and female (in red) genomic reads are showed under the structure of Ty3/Gypsy (A, B) and Ty1/Copia (C–F) elements shown in phylogenetic tree (fig. 2). Graph layouts on the right are visualized by SeqGrapheR program (http://cran.rproject.org/web/packages/SeqGrapheR/index.html). Protein domains and possible LTRs are distinguished by colors, found possible different three ORFs are marked by grey rectangles and orange line represents sequence for probes used for FISH.

Fig. 4.—

Comparison of repeats in male and female of Hippophae rhamnoides. Number of male versus female reads corresponding to individual clusters. Each circle in plot represents one cluster. Repeat types are marked by different color. Clusters in left upper part of graph are enriched (or specific) for males and thus potentially located on the Y chromosome while clusters in the right bottom part are enriched in female and thus potentially located on the X chromosome.

Fig. 5.—

Visualization of male/female reads homogeneity in satellite families. Graph nodes correspond to sequenced reads and edges connect overlapping reads with more than 70% of sequence identity over at least 55% read length. Distances between reads are inversely proportional to their sequence similarity. Male reads are labeled by blue and female reads by red color. Individual families are highlighted by different colors. Please note HRTR12 family that is composed of male reads only assuming to be Y-specific.

Fig. 6.—

Localization of main satellite families on metaphase chromosomes of Hippophae rhamnoides using fluorescence in situ hybridization. The name of satellite family and sex of individual are indicated inside each figure. Blue are DAPI stained chromosomes, red and green signals show chromosomal localization of satellite families. Bar indicates 5 µm.

Fig. 7.—

FISH and scheme of four satellites on sex chromosomes. The HRTR1, Y-specific HRTR12, X-accumulated HRTR8, sex chromosome-accumulated HRTR2.

Fig. 8.—

Localization of transposable elements and rDNA on metaphase chromosomes of Hippophae rhamnoides using fluorescence in situ hybridization. The name of transposable element family (together with the number of corresponding cluster) or type of rDNA cluster is inside each figure. Blue are DAPI stained chromosomes, red signal shows chromosomal localization of selected transposable elements and 45S and 5S rDNA. Bar indicates 5 µm.