摘要
微卫星广泛存在于真核生物和原核生物基因组中,是较为理想的分子标记。食蟹猴是生物医学研究领域中重要的灵长类动物模型,而食蟹猴基因组微卫星研究有助于筛选和开发更多的微卫星标记。利用生物信息学软件对食蟹猴全基因组微卫星进行了搜索,共搜索到微卫星总数为1284929个,微卫星序列长度为26044651 bp,占全基因组的0.890%。整个基因组微卫星平均丰度是451.3个/Mb,平均密度9118.7 bp/Mb。不同重复类型微卫星表现为单碱基(56.74%)>四碱基(16.72%)>二碱基(16.67%)>三碱基(5.96%)>五碱基(3.35%)>六碱基(0.56%)。不同染色体上微卫星数量上,以1号最多,其次是3号,最少的是18号。染色体上微卫星丰度、密度与染色体GC含量呈显著线性正相关(P<0.01),而与微卫星GC含量呈显著线性负相关(P<0.01)。食蟹猴基因组微卫星数量排名前5位的拷贝类别依次是A、AC、AAAT、AG、AT,数量优势单碱基、二碱基、三碱基、四碱基、五碱基和六碱基分别是A、AC、AAT、AAAT、AAACA和AAACAA。
Microsatellites(short tandem repeats(STRs))are potent molecular markers that are widely distributed in the genomes of eucaryotic and procaryotic organisms.Crab-eating macaque is an important animal model of non-human primates in biomedical studies.We investigated the distribution of STRs across the entire genome of crab-eating macaque to contribute to the selection and exploration of more STR markers.We searched for STRs by using bioinformatics software.A total of 1284929 STRs were obtained with a sequence of 26044651 bp length,accounting for 0.890%of the entire genome.The frequency and density of STRs in the entire genome were 451.3 loci/Mb and 9118.7 bp/Mb,respectively.The dominant repeat type motifs were mononucleotide(56.7%),followed by tetranucleotide(16.7%),dinucleotide(16.7%),trinucleotide(6.0%),pentanucleotide(3.4%),and hexanucleotide(0.6%).The largest STR count was found in chromosome 1,followed by chromosome 3.The smallest STR count was observed in chromosome 18.The frequency and density of STRs in all chromosomes were significantly positively correlated with guanine-cytosine(GC)content of the chromosome(P<0.01)and significantly negatively correlated with GC content of the STRs(P<0.01).The top five STR repeat type motifs occurred most frequently as A,AC,AAAT,AG and AT.The dominant STRs of mononucleotide,dinucleotide,trinucleotide,tetranucleotide,pentanucleotide and hexanucleotide were A,AC,AAT,AAAT,AAACA and AAACAA,respectively.
作者
涂飞云
刘俊
韩卫杰
黄挺
黄晓凤
Tu Feiyun;Liu Jun;Han Weijie;Huang Ting;Huang Xiaofeng(Jiangxi Academy of Forestry,Nanchang,330013,China;Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife,College of Life Sciences,Sichuan University,Chengdu,610064,China)
出处
《野生动物学报》
北大核心
2018年第2期400-404,共5页
CHINESE JOURNAL OF WILDLIFE
基金
江西省主要学科学术和技术带头人项目(20153BCB22007)
江西省科研院所基础设施配套项目(20151BBA13037)
江西省林业科学院青年科技人才培养项目(2018521602)
关键词
食蟹猴
微卫星分布
基因组
Crab-eating macaque
Microsatellites distribution
Genome
