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

Seabuckthorn (Hippophae rhamnoides) is a dioecious shrub traditionally used in the pharmaceutical, cosmetic and environmental industry as a source of oil, minerals and vitamins. The first cytogenetic studies on the seabuckthorn demonstrated either a small or large Y chromosome and information on the seabuckthorn genome is lacking. We performed Illumina DNA sequencing and reconstructed the main repetitive DNA sequences. For data analysis, we have developed a new bioinformatic approach for advanced satellite DNA analysis. We showed that about 25% of genome is represented by satellite DNA and about 24% is formed of transposable elements, dominated by Ty3/Gypsy and Ty1/Copia LTR retrotransposons. Our FISH mapping revealed X chromosome-specific, Y chromosome-specific or both sex chromosomes-specific satellites but most satellites were present on autosomes. Transposable elements were present mostly in the subtelomeres of all chromosomes. The 5S rDNA and 45S rDNA were localized on one autosomal locus each. The small size of the Y chromosome and gathering of satellite DNA there, indicate that the Y chromosome of H. rhamnoides is in a later stage of evolution but an analysis of dioecious relatives like Shepherdia would shed more light on the age of these sex chromosomes.

沙棘（Hippophae rhamnoides）是一种雌雄异株灌木，传统上作为油脂、矿物质与维生素的来源，应用于制药、化妆品及环保产业。此前针对沙棘的首批细胞遗传学研究仅报道了存在小型或大型Y染色体（Y chromosome），而目前关于沙棘基因组（genome）的相关信息仍较为匮乏。本研究开展了Illumina DNA测序（Illumina DNA sequencing），并重构了主要的重复DNA序列（repetitive DNA sequences）；在数据分析环节，我们开发了一种全新的高级卫星DNA（satellite DNA）分析生物信息学方法（bioinformatic approach）。研究结果显示，沙棘基因组约25%的组分为卫星DNA，约24%由转座因子（transposable elements）构成，其中优势类群为Ty3/Gypsy型与Ty1/Copia型LTR逆转录转座子（Ty3/Gypsy、Ty1/Copia LTR逆转录转座子）。通过荧光原位杂交（FISH）定位（FISH mapping）实验，我们鉴定出三类卫星DNA：分别特异性结合X染色体、Y染色体，或同时靶向两条性染色体的卫星序列；但绝大多数卫星DNA均分布于常染色体（autosomes）之上。转座因子则主要富集于所有染色体的亚端粒区域（subtelomeres）。5S核糖体DNA（5S rDNA）与45S核糖体DNA（45S rDNA）各自仅定位于一个常染色体位点（locus）。沙棘Y染色体体积小巧且富集卫星DNA的特征，提示该物种的Y染色体已处于进化后期；而对Shepherdia属这类雌雄异株近缘物种的分析，将为进一步阐明此类性染色体的演化年代提供更多关键线索。