中国农业大学学报2024，Vol.29Issue(3)：134-142,9.DOI:10.11841/j.issn.1007-4333.2024.03.12
牦牛全基因组单纯型微卫星分布特征分析
Analysis on the distribution features of perfect microsatellite in the whole genome of yak
摘要
Abstract
To explore the distribution and feature of repetitive sequences in yak genome(BosGru3.1),the perfect SSRs were detected by bioinformatics methods in the yak genome,and its distribution characteristics were comprehensively analyzed.The results showed that:1)A total of 778 413 perfect SSRs were screened out in yak genome(2.83 Gb),with a total length of 14.42 Mb,accounting for 0.51％of the total length of the genome sequence.The relative frequency and relative density were 274.92 loci/Mb and 5 094.43 bp/Mb,respectively.2)Among the 31 chromosomes of yak,chromosome 1 contained the largest number of SSRs(48 592,6.24％),and chromosome 29 contained the lowest number of SSRs(11758,1.51％).The length of the chromosomal DNA sequence was significantly positively correlated with the number of SSRs contained.3)In yak genome,the distribution of six repeat types of perfect SSRs was uneven.Among them,the number of SSRs with mononucleotide repeat type was the highest(320 592,41.19％),followed by dinucleotide(197 824,25.41％),trinucleotide(130 441,16.76％),pentanucleotide(75 056,9.64％),tetranucleotide(52 523,6.75％),and hexanucleotide(1 977,0.25％).4)Repeat copy category of A,AC,AT,AGC,AAC,AAAT,AAAC,AACTG,AGATC,and AACCCT was predominate in six repeat types,showing a distinct A(T)base composition advantage.5)The repeat copy numbers of different type of perfect SSRs were concentrated at 12-25(mononucleotide),7-26(dinucleotide),5-13(trinucleotide),4-8(tetranucleotide),4-7(pentanucleotide),and 4-6(hexanucleotide).In conclusion,there are differences in the frequency,density,dominant base categories,and copy numbers among different types of SSRs,showing certain regularity.The results of this study can provide a reference for a deeper understanding of the composition and distribution features of repetitive sequences,especially perfect SSRs,and lay a foundation for subsequent studies on mining yak-specific SSR markers,constructing genetic maps,and carrying out marker-trait association analyses.关键词
牦牛/基因组/单纯型微卫星/丰度Key words
yak/genome/perfect microsatellite/abundance分类
农业科技引用本文复制引用
徐宇辉,马志杰,郭卫兴,莫延新,陈生梅..牦牛全基因组单纯型微卫星分布特征分析[J].中国农业大学学报,2024,29(3):134-142,9.基金项目
国家自然科学基金项目(31960656) （31960656）
青海省"昆仑英才·高端创新创业人才"计划项目(领军人才) （领军人才）
