Plant, animal and protist genomes often contain endogenous viral elements (EVEs), which correspond to partial and sometimes entire viral genomes that have been captured in the genome of their host organism through a variety of integration mechanisms. While the number of sequenced eukaryotic genomes is rapidly increasing, the annotation and characterization of EVEs remains largely overlooked. EVEs that derive from members of the family Caulimoviridae are widespread across tracheophyte plants, and sometimes they occur in very high copy numbers. However, existing programs for annotating repetitive DNA elements in plant genomes are poor at identifying and then classifying these EVEs. Other than accurately annotating plant genomes, there is intrinsic value in a tool that could identify caulimovirid EVEs as they testify to recent or ancient host-virus interactions and provide valuable insights into virus evolution. In response to this research need, we have developed CAULIFINDER, an automated and sensitive annotation software package. CAULIFINDER consists of two complementary workflows, one to reconstruct, annotate and group caulimovirid EVEs in a given plant genome and the second to classify these genetic elements into officially recognized or tentative genera in the Caulimoviridae. We have benchmarked the CAULIFINDER package using the Vitis vinifera reference genome, which contains a rich assortment of caulimovirid EVEs that have previously been characterized using manual methods. The CAULIFINDER package is distributed in the form of a Docker image.

中文翻译：

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CAULIFINDER：植物基因组中花椰菜病毒内源性病毒元件的自动检测和注释管道

植物、动物和原生生物基因组通常包含内源性病毒元件 (EVE)，这些元件对应于通过各种整合机制在宿主生物体基因组中捕获的部分甚至整个病毒基因组。虽然测序真核基因组的数量正在迅速增加，但 EVE 的注释和表征在很大程度上仍然被忽视。源自花椰菜科成员的 EVE 广泛存在于气管植物中，有时它们的拷贝数非常高。然而，用于注释植物基因组中重复 DNA 元素的现有程序在识别和分类这些 EVE 方面表现不佳。除了准确注释植物基因组，一种可以识别花椰菜 EVE 的工具具有内在价值，因为它们证明了最近或古代的宿主-病毒相互作用，并提供了对病毒进化的宝贵见解。为了响应这一研究需要，我们开发了 CAULIFINDER，一个自动化和敏感的注释软件包。CAULIFINDER 由两个互补的工作流程组成，一个用于重建、注释和分组给定植物基因组中的花椰菜 EVE，第二个用于将这些遗传元素分类为花椰菜科中官方认可或暂定的属。我们使用 Vitis vinifera 参考基因组对 CAULIFINDER 包进行了基准测试，该基因组包含丰富的花椰菜 EVE 分类，这些 EVE 以前使用手动方法进行过表征。CAULIFINDER 包以 Docker 镜像的形式分发。