Endogenous retroviruses (ERVs) are the remnants of retroviral infections which can elicit prolonged genomic and immunological stress on their host organism. In chickens, endogenous Avian Leukosis Virus subgroup E (ALVE) expression has been associated with reductions in muscle growth rate and egg production, as well as providing the potential for novel recombinant viruses. However, ALVEs can remain in commercial stock due to their incomplete identification and association with desirable traits, such as ALVE21 and slow feathering. The availability of whole genome sequencing (WGS) data facilitates high-throughput identification and characterisation of these retroviral remnants. We have developed obsERVer, a new bioinformatic ERV identification pipeline which can identify ALVEs in WGS data without further sequencing. With this pipeline, 20 ALVEs were identified across eight elite layer lines from Hy-Line International, including four novel integrations and characterisation of a fast feathered phenotypic revertant that still contained ALVE21. These bioinformatically detected sites were subsequently validated using new high-throughput KASP assays, which showed that obsERVer was highly precise and exhibited a 0% false discovery rate. A further fifty-seven diverse chicken WGS datasets were analysed for their ALVE content, identifying a total of 322 integration sites, over 80% of which were novel. Like exogenous ALV, ALVEs show site preference for proximity to protein-coding genes, but also exhibit signs of selection against deleterious integrations within genes. obsERVer is a highly precise and broadly applicable pipeline for identifying retroviral integrations in WGS data. ALVE identification in commercial layers has aided development of high-throughput diagnostic assays which will aid ALVE management, with the aim to eventually eradicate ALVEs from high performance lines. Analysis of non-commercial chicken datasets with obsERVer has revealed broad ALVE diversity and facilitates the study of the biological effects of these ERVs in wild and domesticated populations.

中文翻译：

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鸡全基因组测序数据中内源性禽白血病病毒 E 亚组 (ALVE) 插入的鉴定和表征。

内源性逆转录病毒 (ERV) 是逆转录病毒感染的残余物，可对其宿主生物体造成长期的基因组和免疫应激。在鸡中，内源性禽白血病病毒 E 亚组 (ALVE) 的表达与肌肉生长速度和产蛋量的降低有关，并为新型重组病毒提供了潜力。然而，由于 ALVE 的不完整识别和与理想性状（如 ALVE21 和缓慢羽化）的关联，它们可以保留在商业库存中。全基因组测序 (WGS) 数据的可用性有助于对这些逆转录病毒残留物进行高通量鉴定和表征。我们开发了 obSERVer，一种新的生物信息学 ERV 识别管道，无需进一步测序即可识别 WGS 数据中的 ALVE。有了这条管道，从 Hy-Line International 的八个精英层系中鉴定了 20 个 ALVE，包括四个新的整合和仍然包含 ALVE21 的快速羽毛表型回复体的表征。随后使用新的高通量 KASP 测定对这些生物信息检测位点进行了验证，这表明 obSERVer 具有高度精确性，并且具有 0% 的错误发现率。进一步分析了 57 个不同的鸡 WGS 数据集的 ALVE 内容，确定了总共 322 个集成站点，其中超过 80% 是新的。与外源性 ALV 一样，ALVE 表现出对接近蛋白质编码基因的位点偏好，但也表现出针对基因内有害整合的选择迹象。obSERVer 是一种高度精确且广泛适用的管道，用于识别 WGS 数据中的逆转录病毒整合。商业层中的 ALVE 识别有助于开发高通量诊断分析，这将有助于 ALVE 管理，旨在最终从高性能生产线中根除 ALVE。使用 obSERVer 对非商业鸡数据集的分析揭示了广泛的 ALVE 多样性，并有助于研究这些 ERV 在野生和驯养种群中的生物学效应。