Genetika, Antropologia Fisikoa eta Animalien Fisiologia Saila, Zientzia eta Teknologia Fakultatea, Euskal Herriko Unibertsitatea, 644 Postakutxa, E-48080 Bilbao, Spain.
J Virol. 2010 Oct;84(20):10852-62. doi: 10.1128/JVI.00106-10. Epub 2010 Aug 4.
Endogenous retroviruses (ERVs) are the proviral phase of exogenous retroviruses that become integrated into a host germ line. They can play an important role in the host genome. Bioinformatic tools have been used to detect ERVs in several vertebrates, primarily primates and rodents. Less information is available regarding ERVs in other mammalian groups, and the source of this information is basically experimental. We analyzed the genome of the cow (Bos taurus) using three different methods. A BLAST-based method detected 928 possible ERVs, LTR_STRUC detected 4,487 elements flanked by long terminal repeats (LTRs), and Retrotector detected 9,698 ERVs. The ERVs were not homogeneously distributed across chromosomes; the number of ERVs was positively correlated with chromosomal size and negatively correlated with chromosomal GC content. The bovine ERVs (BoERVs) were classified into 24 putative families, with 20 of them not previously described. One of these new families, BoERV1, was the most abundant family and appeared to be specific to ruminants. An analysis of representatives of ERV families from rodents, primates, and ruminants showed a phylogenetic relationship following their hosts' relationships. This study demonstrates the importance of using multiple methods when trying to identify new ERVs and shows that the number of bovine ERV families is not as limited as previously thought.
内源性逆转录病毒 (ERVs) 是外源性逆转录病毒的前病毒阶段，它们整合到宿主的生殖系中。它们可以在宿主基因组中发挥重要作用。生物信息学工具已被用于检测几种脊椎动物（主要是灵长类动物和啮齿类动物）中的 ERVs。关于其他哺乳动物群体中的 ERVs 的信息较少，并且这些信息的来源基本上是实验性的。我们使用三种不同的方法分析了奶牛（Bos taurus）的基因组。基于 BLAST 的方法检测到 928 个可能的 ERVs，LTR_STRUC 检测到 4487 个侧翼有长末端重复序列 (LTR) 的元件，Retrotector 检测到 9698 个 ERVs。ERVs 在染色体上的分布不均匀；ERVs 的数量与染色体大小呈正相关，与染色体 GC 含量呈负相关。牛 ERVs（BoERVs）被分为 24 个假定家族，其中 20 个家族以前没有描述过。其中一个新家族 BoERV1 是最丰富的家族，似乎是反刍动物特有的。对来自啮齿动物、灵长类动物和反刍动物的 ERV 家族代表的分析表明，它们的进化关系与其宿主的进化关系一致。这项研究表明，在试图识别新的 ERVs 时，使用多种方法非常重要，并且表明牛 ERV 家族的数量并不像以前认为的那么有限。
