摘要
旨在对九疑山兔线粒体基因组进行组装,探究其系统进化和分类地位。本研究采用高通量测序技术对20只150日龄九疑山兔的耳组织进行了全基因组测序,利用生物信息学软件对线粒体基因组进行组装,并对获得的线粒体基因组进行序列分析、基因预测和注释,随后基于已发表的家兔、野兔、经济动物和模式动物的线粒体基因组序列进行多序列比对和系统进化分析,对研究群体的多态性位点进行鉴定。组装获得长度为17306 bp的九疑山兔线粒体基因组全序列,其碱基组成、基因分布与已发表的5个家兔品种的线粒体基因组基本一致。基于Dloop区的系统进化分析表明,九疑山兔与福建黄兔进化关系较近,而与欧洲穴兔、沂蒙毛兔、川白獭兔和新西兰白兔较远。通过其与14种野兔及11种经济/模式动物的种间系统进化分析表明,九疑山兔与欧洲野兔、海南兔和白靴兔亲缘关系较近,与其他野兔和经济/模式动物较远。研究群体的线粒体基因组保守区共鉴定到了12个突变位点,其中有3个突变的群体等位基因频率大于0.8,为多态性位点。本研究组装获得了首个九疑山兔的完整线粒体基因组序列,明确了九疑山兔与其它品种家兔、野兔和常见经济/模式动物的亲缘关系和分类地位,为九疑山兔的种质资源利用和品种选育等研究提供了基础数据。
The aim of the study was to assemble the mitochondrial genome of the Jiuyishan rabbit and to investigate its phylogenetic evolution and taxonomic position.High-throughput sequencing technology was employed to perform whole-genome sequencing on ear tissues from 20 Jiuyishan rabbits at 150 days of age.Bioinformatics software was employed for the assembly of the mitochondrial genome,followed by conducting sequence analysis,gene prediction and annotation of the obtained mitochondrial genome.Subsequently,multiple sequence alignment and phylogenetic analysis were conducted based on the published mitochondrial genome sequences of rabbits,hares,economically important animals and model animals.Polymorphic sites within the study population were identified.The complete mitochondrial genome sequence of the Jiuyishan rabbit was successfully obtained,the length was 17306 bp.The nucleotide composition and gene ar-rangement of the mitochondrial genome were found to be largely consistent with those reported for 5 previously published domestic rabbit breeds.Phylogenetic analysis based on the D-loop re-gion indicated a closer evolutionary relationship between the Jiuyishan rabbit and the Fujian Yellow rabbit,while Jiuyishan rabbit was more distantly related to the European rabbit,Yimeng Wool rabbit,Chuanbai Rex rabbit and New Zealand White rabbit.Interspecific phylogenetic analysis involving 14 wild rabbit species and 11 economic or model animal species demonstrated that the Jiuyishan rabbit shared a closer phylogenetic relationship with the European wild rabbit,Hainan rabbit,and the White-booted rabbit but was further with others.A total of 12 mutation sites were identified in the conserved regions of the mitochondrial genome of the study popula-tion,with 3 mutations having allele frequencies greater than 0.8,indicating polymorphism.This study has successfully assembled the first complete mitochondrial genome sequence of the Jiuyishan rabbit,clarifying its phylogenetic relationships and taxonomic status in comparison to other dome
作者
李聪聪
黄子珂
黄念旎
马诗语
刘晗
肖志标
宋果
蒋亮
彭为波
杨联熙
郭云涛
黄生强
LI Congcong;HUANG Zike;HUANG Nianni;MA Shiyu;LIU Han;XIAO Zhibiao;SONG Guo;JIANG Liang;PENG Weibo;YANG Lianxi;GUO Yuntao;HUANG Shengqiang(College of Animal Science and Technology,Hunan Agricultural University,Changsha 410128,China;Animal Husbandry and Fisheries Affairs Center of Ningyuan County,Yongzhou 425600,China;Hunan Hyplus Agricultural and Pastoral Technology Co.,Ltd.,Yongzhou 425600,China;The Medical Laboratory of Nantong ZhongKe Co.,Ltd.,Nantong 226000,China)
出处
《畜牧兽医学报》
CAS
CSCD
北大核心
2024年第10期4417-4427,共11页
ACTA VETERINARIA ET ZOOTECHNICA SINICA
基金
湖南省科技厅项目:九疑山兔选优提纯研究(2019NK4192)。
关键词
九疑山兔
线粒体基因组
高通量测序
系统进化
Jiuyishan rabbit
mitochondrial genome
high-throughput sequencing
phylogenetic evolution
