Nijman Isaäc J, van Tessel Patrick, Lenstra Johannes A
Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands.
J Mol Evol. 2002 Jan;54(1):9-16. doi: 10.1007/s00239-001-0012-2.
SINE retrotransposition events have proven their value as phylogenetic markers in several eukaryotic taxa at different taxonomic levels. The genomes of ruminants contain three related SINE elements, Bov-tA, Bov-A2, and Bov-B. To estimate the time points of retrotransposition of individual copies of these SINEs, we designed PCR primers on database sequences containing SINE insertions in cattle, sheep, or goat genomes and tested for the presence of these copies in the genomes of other ruminants. It was checked by sequencing whether length variation of the PCR products reflected a SINE retrotransposition. One Bov-B and nine Bov-tA insertions were shared by cattle, sheep, goat, and giraffe, indicating an early retrotransposition event before the radiation of the Pecora, while three other Bov-tA and two Bov-B elements were apparently inserted later. The ruminant alpha-lactalbumine gene contains a hotspot of early and more recent Bov-tA insertions, a Bov-tA replacement as well as a recent Bov-B insertion. Three Bov-A2 insertions were found to be shared only by the Bovidae, the Bovini, and the Bos and Bison species, respectively, indicating that most Bov-A2 insertions are relatively recent. The time elapsed since the retrotransposition was also reflected in the degeneration of the direct repeats that flank SINE inserts. We suggest that retrotransposition of SINEs may serve as phylogenetic markers in the ruminant families, subfamilies, and even tribes. In addition, sequencing of SINE insertions revealed several other unique deletions/insertions that also may be informative for phylogenetic reconstructions of ruminants.
短散在核元件（SINE）反转录转座事件已在不同分类水平的几个真核生物类群中证明了其作为系统发育标记的价值。反刍动物的基因组包含三种相关的SINE元件，即牛tA、牛A2和牛B。为了估计这些SINE单个拷贝的反转录转座时间点，我们根据牛、绵羊或山羊基因组中含有SINE插入的数据库序列设计了PCR引物，并检测这些拷贝在其他反刍动物基因组中的存在情况。通过测序检查PCR产物的长度变异是否反映了SINE反转录转座。一个牛B和九个牛tA插入在牛、绵羊、山羊和长颈鹿中共享，表明在鹿总科辐射之前发生了早期反转录转座事件，而另外三个牛tA和两个牛B元件显然是后来插入的。反刍动物α-乳白蛋白基因包含早期和近期牛tA插入的热点、一个牛tA替代以及一个近期牛B插入。分别发现三个牛A2插入仅在牛科、牛亚科以及牛属和野牛属物种中共享，这表明大多数牛A2插入相对较新。自反转录转座以来经过的时间也反映在SINE插入侧翼的正向重复序列的退化中。我们认为，SINE的反转录转座可能作为反刍动物科、亚科甚至族的系统发育标记。此外，SINE插入的测序揭示了其他几个独特的缺失/插入，这也可能为反刍动物的系统发育重建提供信息。
