Chicken (Gallus gallus) endogenous retrovirus generates genomic variations in the chicken genome.
Chicken (Gallus gallus) endogenous retrovirus generates genomic variations in the chicken genome.
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鸡肉（Gallus Gallus）内源性逆转录病毒在鸡基因组中产生基因组变异。
DOI：
10.1186/s13100-016-0085-5
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发表时间：
2017
期刊：
影响因子：
4.9
通讯作者：
Han K
中科院分区：
文献类型：
--
作者：
Lee J;Mun S;Kim DH;Cho CS;Oh DY;Han K
转座因子（te）占鸡（Gallus Gallus）基因组的10%。te的含量远低于哺乳动物基因组的含量，在哺乳动物基因组中，te约占基因组的一半。内源性逆转录病毒占鸡基因组的约1.3%。其中，Gallus Gallus内源性逆转录病毒10 （GGERV10）是最年轻的内源性逆转录病毒家族之一，大约在300万年前出现在鸡基因组中。我们利用UCSC基因组数据库和RepeatMasker在鸡参考基因组中共鉴定出593个GGERV10元件。虽然大部分的GGERV10元素被截断，但49个GGERV10元素是全长保留5 ‘和3 ’ ltr。我们详细研究了它们的结构特征、染色体分布、基因组环境和系统发育关系。我们比较了5个不同GGERV10亚家族的LTR序列，发现LTR序列之间存在差异。使用传统的PCR方法，我们检测了49个GGERV10全长基因在韩国家鸡、来角鸡和阿鲁卡那鸡三个不同种群中的多态性率。结果在韩国家鸡中发现了一个品种特异性的GGERV10B插入位点，可以作为韩国家鸡特异性标记。GGERV10家族是最年轻的ERV家族，因此可能在不同的鸡种群中导致最近的基因组变异。本研究结果表明，在韩国家鸡与其他近缘鸡种群分化后，GGERV10的一个元件被整合到鸡基因组中，提示GGERV10可以作为鸡品种鉴定的分子标记。本文的在线版本（doi:10.1186/s13100-016-0085-5）包含补充材料，可供授权用户使用。
Transposable elements (TEs) comprise ~10% of the chicken (Gallus gallus) genome. The content of TEs is much lower than that of mammalian genomes, where TEs comprise around half of the genome. Endogenous retroviruses are responsible for ~1.3% of the chicken genome. Among them is Gallus gallus endogenous retrovirus 10 (GGERV10), one of the youngest endogenous retrovirus families, which emerged in the chicken genome around 3 million years ago. We identified a total of 593 GGERV10 elements in the chicken reference genome using UCSC genome database and RepeatMasker. While most of the elements were truncated, 49 GGERV10 elements were full-length retaining 5′ and 3′ LTRs. We examined in detail their structural features, chromosomal distribution, genomic environment, and phylogenetic relationships. We compared LTR sequence among five different GGERV10 subfamilies and found sequence variations among the LTRs. Using a traditional PCR assay, we examined a polymorphism rate of the 49 full-length GGERV10 elements in three different chicken populations of the Korean domestic chicken, Leghorn, and Araucana. The result found a breed-specific GGERV10B insertion locus in the Korean domestic chicken, which could be used as a Korean domestic chicken-specific marker. GGERV10 family is the youngest ERV family and thus might have contributed to recent genomic variations in different chicken populations. The result of this study showed that one of GGERV10 elements integrated into the chicken genome after the divergence of Korean domestic chicken from other closely related chicken populations, suggesting that GGERV10 could be served as a molecular marker for chicken breed identification. The online version of this article (doi:10.1186/s13100-016-0085-5) contains supplementary material, which is available to authorized users.