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

Abstract

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