鸭 3 个参考基因组中内源性逆转录病毒的全基因组特征分析与比较。

Genome-wide characterization and comparison of endogenous retroviruses among 3 duck reference genomes.

机构信息

State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China.

出版信息

Poult Sci. 2024 May;103(5):103543. doi: 10.1016/j.psj.2024.103543. Epub 2024 Feb 9.

DOI:10.1016/j.psj.2024.103543

PMID:38447307

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11067759/

Abstract

Endogenous retroviruses (ERV) are viral genomes integrated into the host genome and can be stably inherited. Although ERV sequences have been reported in some avian species' genome, the duck endogenous retroviruses (DERV) genome has yet to be quantified. This study aimed to identify ERV sequences and characterize genes near ERVs in the duck genome by utilizing LTRhavest and LTRdigest tools to forecast the duck genome and analyze the distribution of ERV copies. The results revealed 1,607, 2,031, and 1,908 full-length ERV copies in the Pekin duck (ZJU1.0), Mallard (CAU_wild_1.0), and Shaoxing duck (CAU_laying_1.0) genomes, respectively, with average lengths of 7,046, 7,027, and 6,945 bp. ERVs are mainly distributed on the 1, 2, and sex chromosomes. Phylogenetic analysis demonstrated the presence of Betaretrovirus in 3 duck genomes, whereas Alpharetrovirus was exclusively identified in the Shaoxing duck genome. Through screening, 596, 315, and 343 genes adjacent to ERV were identified in 3 duck genomes, respectively, and their functions of ERV neighboring genes were predicted. Functional enrichment analysis of ERV-adjacent genes revealed enrichment for Focal adhesion, Calcium signaling pathway, and Adherens junction in 3 duck genomes. The overlapped genes were highly expressed in 8 tissues (brain, fat, heart, kidney, liver, lung, skin, and spleen) of 8-wk-old Mallard, revealing their important expression in different tissues. Our study provides a new perspective for understanding the quantity and function of DERVs, and may also provide important clues for regulating nearby genes and affecting the traits of organisms.

摘要

内源性逆转录病毒 (ERV) 是整合到宿主基因组中的病毒基因组，可以稳定遗传。尽管已经在一些禽类物种的基因组中报告了 ERV 序列，但鸭内源性逆转录病毒 (DERV) 基因组尚未被量化。本研究旨在通过利用 LTRhavest 和 LTRdigest 工具预测鸭基因组并分析 ERV 拷贝的分布，鉴定 ERV 序列并分析鸭基因组中 ERV 附近的基因。结果表明，在 Pekin 鸭 (ZJU1.0)、Mallard (CAU_wild_1.0) 和 Shaoxing 鸭 (CAU_laying_1.0) 基因组中分别有 1607、2031 和 1908 个全长 ERV 拷贝，平均长度分别为 7046、7027 和 6945bp。ERV 主要分布在 1、2 和性染色体上。系统发育分析表明，在 3 个鸭基因组中存在 Betaretrovirus，而 Alpharetrovirus 仅在 Shaoxing 鸭基因组中被鉴定。通过筛选，在 3 个鸭基因组中分别鉴定到 596、315 和 343 个 ERV 附近的基因，预测了它们的功能。对 ERV 附近基因的功能富集分析表明，在 3 个鸭基因组中，Focal adhesion、Calcium signaling pathway 和 Adherens junction 富集。8 周龄 Mallard 的 8 种组织（脑、脂肪、心脏、肾脏、肝脏、肺、皮肤和脾脏）中重叠基因的表达水平较高，表明它们在不同组织中的重要表达。本研究为理解 DERV 的数量和功能提供了新的视角，也可能为调节附近基因和影响生物体特性提供重要线索。