Ishihara Shinya, Shiraishi Jun-Ichi, Shimamoto Saki, Ijiri Daichi
Department of Animal Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonancho, Musashino, Tokyo, 180-8602, Japan.
Department of Animal Science and Welfare, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima, 890-0065, Japan.
Sci Rep. 2025 Apr 10;15(1):12290. doi: 10.1038/s41598-025-96881-z.
When retroviruses infect germ cells and are transmitted to offspring, they become endogenous retroviruses (ERVs), whose insertions may influence the expression of nearby genes. In this study, we aimed to identify the genomic loci of ERVs in commercial broiler (Ross308), Tosa-Jidori, and Yakido chickens, as well as to elucidate their impact on neighboring gene expression. Whole-genome data were obtained using next-generation sequencing, and candidate ERV loci were identified using the RetroSeq software. The Integrative Genomics Viewer tool was used to confirm target site duplications (TSDs) as evidence of ERV insertions. All reads within 200 bp of these TSDs were extracted to create contigs, confirming the presence of ERV sequences in the contigs using BLASTN. Gene expression levels were estimated by focusing on genes located near the 172 identified ERV loci. Among these, 119 loci were detected in broiler chickens, 80 in Tosa-Jidori chickens, and 86 in Yakido chickens, with 28 loci shared among them. Moreover, of these 172 loci, 75 were located within or near genes. Significant differences in gene expression were observed for N-acetylated alpha-linked acidic dipeptidase 2 (NAALAD2) and phosphoribosylaminoimidazolesuccinocarboxamide synthase (PAICS) depending on the presence of ERV insertions. These results suggest that ERV insertions may influence the expression of NAALAD2 and PAICS, providing insights into the genetic diversity and evolutionary background of commercial and indigenous chickens. Understanding the effects of ERV insertions on gene expression can inform future genetic research and poultry breeding programs aimed at improving health and productivity.
当逆转录病毒感染生殖细胞并传递给后代时，它们就会成为内源性逆转录病毒（ERVs），其插入可能会影响附近基因的表达。在本研究中，我们旨在确定商品肉鸡（罗斯308）、土佐地鸡和八户鸡中ERVs的基因组位点，并阐明它们对邻近基因表达的影响。使用下一代测序获得全基因组数据，并使用RetroSeq软件识别候选ERV位点。使用综合基因组浏览器工具确认靶位点重复（TSDs）作为ERV插入的证据。提取这些TSD 200 bp内的所有读数以创建重叠群，使用BLASTN确认重叠群中ERV序列的存在。通过关注位于172个已识别的ERV位点附近的基因来估计基因表达水平。其中，在肉鸡中检测到119个位点，在土佐地鸡中检测到80个位点，在八户鸡中检测到86个位点，其中28个位点是共有的。此外，在这172个位点中，有75个位于基因内部或附近。根据ERV插入的存在情况，观察到N-乙酰化α-连接酸性二肽酶2（NAALAD2）和磷酸核糖氨基咪唑琥珀酰胺羧酰胺合酶（PAICS）的基因表达存在显著差异。这些结果表明，ERV插入可能会影响NAALAD2和PAICS的表达，为商品鸡和本地鸡的遗传多样性和进化背景提供了见解。了解ERV插入对基因表达的影响可为未来旨在改善健康和生产力的遗传研究及家禽育种计划提供参考。
