SVA elements: A hominid-specific retroposon family
SVA elements: A hominid-specific retroposon family
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DOI：
10.1016/j.jmb.2005.09.085
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发表时间：
2005-12-09
影响因子：
5.6
通讯作者：
Batzer, MA
中科院分区：
文献类型：
--
作者：
Wang, H;Xing, J;Batzer, MA
SVA是一种复合重复元素，以其主要成分SINE、VNTR和Alu命名。我们已经从人类基因组草图序列中鉴定出2762个SVA元素。基因组分布分析表明，SVA元件在富含G+ c的区域富集，但对基因间和基因内区域没有偏好。对这些元素进行系统发育分析，恢复了6个亚家族，命名为SVA_A至SVA_F。研究了亚科的组成、年龄和基因组分布。基于核苷酸分化的亚家族年龄估计表明，SVA_A、SVA_B、SVA_C和SVA_D四个SVA亚家族的扩展早于人类、黑猩猩和大猩猩的分化，而SVA_E和SVA_F亚家族仅局限于人类谱系。与SVA_E和SVA_F亚家族成员相关的人类基因组多样性调查显示，插入多态性频率分别为37.5%和27.6%。此外，我们研究了整个灵长类目中SVA元素的扩增动态，并将其起源追溯到大约1800万至2500万年前的原始灵长类动物进化的开始。这使得SVA元件成为灵长类目中最年轻的逆转录子家族。(c) 2005 Elsevier Ltd版权所有。
SVA is a composite repetitive element named after its main components, SINE, VNTR and Alu. We have identified 2762 SVA elements from the human genome draft sequence. Genomic distribution analysis indicates that the SVA elements are enriched in G+C-rich regions but have no preferences for inter- or intragenic regions. A phylogenetic analysis of the elements resulted in the recovery of six subfamilies that were named SVA_A to SVA_F. The composition, age and genomic distribution of the subfamilies have been examined. Subfamily age estimates based upon nucleotide divergence indicate that the expansion of four SVA subfamilies (SVA_A, SVA_B, SVA_C and SVA_D) began before the divergence of human, chimpanzee and gorilla, while subfamilies SVA_E and SVA_F are restricted to the human lineage. A survey of human genomic diversity associated with SVA_E and SVA_F subfamily members showed insertion polymorphism frequencies of 37.5% and 27.6%, respectively. In addition, we examined the amplification dynamics of SVA elements throughout the primate order and traced their origin back to the beginnings of hominid primate evolution, approximately 18 to 25 million years ago. This makes SVA elements the youngest family of retroposons in the primate order. (c) 2005 Elsevier Ltd. All rights reserved.