基于最新参考序列UM_NZW_1.0绘制家兔基因组NUMTs图谱

doi:10.16431/j.cnki.1671-7236.2025.04.019

摘要/Abstract

摘要： 【目的】核内线粒体DNA序列(nuclear mitochondrial DNA segments,NUMTs)是线粒体DNA插入并整合到核基因组形成的。本研究基于家兔最新参考基因组序列UM_NZW_1.0绘制家兔基因组NUMTs图谱，分析NUMTs的分布特征、基因组环境偏好性并预测其生物学功能，从而解析家兔基因组中的NUMTs信息。【方法】将家兔最新版参考基因组UM_NZW_1.0的染色体DNA序列与线粒体DNA序列进行比对，获得NUMTs信息，并统计NUMTs序列长度及在染色体上的分布情况。将NUMTs片段整合为NUMTs区域分析插入事件，分析NUMTs插入核基因组位置的GC含量、重复序列比例，以及NUMTs插入基因组的环境偏好性；统计NUMTs同源序列在线粒体基因组的分布情况，对NUMTs覆盖的基因进行功能注释，并推测NUMTs生物功能。【结果】在兔基因组中共检测到237条NUMTs序列，其中3、5、6、8、10号染色体上不存在NUMTs，总长度311 549 bp，占参考基因组总大小的0.015512%，这些NUMTs可能由87个NUMTs插入事件形成。NUMTs在兔基因组中GC含量较低、重复序列较多的区域更易形成，表明家兔基因组NUMTs的形成不是随机性的。整个线粒体基因组序列都形成过NUMTs，其中COX1、COX2、ND2、tRNA-C、tRNA-A、tRNA-W、tRNA-V等基因覆盖次数≥20。通过功能注释NUMTs及其上、下游1 000 bp区域覆盖的基因，推测NUMTs可能与生殖和神经系统等功能有关。【结论】在家兔进化过程中，线粒体基因组序列都曾插入整合到染色体形成NUMTs，但并不是所有染色体都存在NUMTs，NUMTs倾向在基因组中GC含量较低、重复序列较多的区域形成，NUMTs可能与家兔生殖和神经系统等功能有关。本研究结果为家兔分子育种提供了遗传信息。

关键词: 核内线粒体DNA序列(NUMTs); 家兔; 核基因组

Abstract: 【Objective】 Nuclear mitochondrial DNA segments (NUMTs) are formed by the insertion and integration of mitochondrial DNA into the nuclear genome.This study was aimed to map NUMTs in rabbit genome based on the latest reference genome sequence UM_NZW_1.0,analyze the distribution characteristics and genomic environment preferences,and predict the biological function of NUMTs,so as to decipher the NUMTs information in rabbit genome.【Method】 The nuclear DNA sequence of the latest rabbit reference genome UM_NZW_1.0 was aligned with the mitochondrial genome to map the NUMTs,and the length and chromosomal distribution of NUMTs were analyzed.NUMTs fragments were integrated into NUMTs regions to study insertion events.GC content and repeat sequence ratio of NUMTs in nuclear genome were investigated to understand their insertion preferences in genomic context.The distribution of homologous mitochondrial sequences of NUMTs in mitochondrial genome was explored.Gene annotation was performed to predict the potential biological function of NUMTs.【Result】 Totally of 237 NUMTs sequences were detected in rabbit genome,there were no NUMTs on chromosomes 3,5,6,8 and 10,with a total length of 311 549 bp,accounting for 0.015512% of the total reference genome size.These NUMTs might be formed by 87 NUMTs insertion events.NUMTs were more likely to form in regions with lower GC content and more repetitive sequences in rabbit genome,indicating that the formation of NUMTs in rabbit genome was not random.The entire mitochondrial genome sequence had formed NUMTs,with genes such as COX1,COX2, ND2,tRNA-C,tRNA-A,tRNA-W and tRNA-V covering more than 20 times.By annotating the genes covered by NUMTs and their upstream and downstream 1 000 bp regions,it was speculated that NUMTs might be related to function such as reproduction and tnervous system.【Conclusion】 Segments of the mitochondrial genome had been inserted into chromosome to form NUMTs throughout the evolution process of rabbits,NUMTs were not uniformly distributed across all chromosomes.NUMTs tended to be found in genomic regions characterized by lower GC content and a higher density of repetitive sequences.NUMTs might play roles in crucial biological processes,such as reproduction and nervous system,which offered valuable genetic insights for the molecular breeding of rabbits.

Key words: nuclear mitochondrial DNA segments (NUMTs); rabbits; nuclear genome

中图分类号:

S829.1

周鑫, 杨铖, 朱桂名, 何黔蓉, 李岩, 樊新忠, 宁超, 王丹. 基于最新参考序列UM_NZW_1.0绘制家兔基因组NUMTs图谱[J]. 中国畜牧兽医, 2025, 52(4): 1660-1670.

ZHOU Xin, YANG Cheng, ZHU Guiming, HE Qianrong, LI Yan, FAN Xinzhong, NING Chao, WANG Dan. NUMTs Mapping of Rabbit Genome Based on the Latest Reference Sequence UM_NZW_1.0[J]. China Animal Husbandry and Veterinary Medicine, 2025, 52(4): 1660-1670.

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