論文

筆頭著者 責任著者
2024年8月7日

Endogenous Retrovirus Loci and Induced Changes in Gene Expression in Japanese Indigenous Chickens

BioRxiv
  • Shinya Ishihara
  • ,
  • Jun-ichi Shiraishi
  • ,
  • Saki Shimamoto
  • ,
  • Daichi Ijiri

記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1101/2024.08.05.606564
出版者・発行元
Cold Spring Harbor Laboratory

Summary

When retroviruses infect germ cells and are transmitted to offspring, they become endogenous retroviruses (ERVs), whose insertions influence the expression of nearby genes. This study 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, glypican 6, and phospholipid scramblase family member 5 depending on the presence of ERV insertions. These results suggest that ERV insertions may influence the expression of certain genes, 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.

Author Summary

Recently, endogenous retroviruses (ERVs) have gained significant attention as valuable markers for understanding genetic relationships and evolutionary processes among species. In this study, we investigated the loci and characteristics of ERVs in commercial and traditional Japanese chickens. ERVs are genetic remnants of ancient viral infections that can provide insights into avian evolution. We identified a total of 172 ERV loci in broiler, Tosa-Jidori, and Yakido chickens. Each chicken breed exhibited unique ERV insertion patterns. Notably, we found that ERV insertions near certain genes may influence gene expression. Our research enhances the understanding of how chickens have acquired traits, particularly through genetic mechanisms influenced by ERVs. These insights significantly contribute to our knowledge of biological evolution and the overall biodiversity of birds.

リンク情報
DOI
https://doi.org/10.1101/2024.08.05.606564
共同研究・競争的資金等の研究課題
ニワトリの多様化と内在性レトロウイルスの関連性の解明
URL
https://syndication.highwire.org/content/doi/10.1101/2024.08.05.606564
ID情報
  • DOI : 10.1101/2024.08.05.606564

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