山羊和藏羚羊全基因组微卫星分布规律及其生物信息学分析
Distribution Regularities and Bioinformatics Analysis of Microsatellite in the Whole Genomes of goat and Tibetan antelope

微卫星（Microsatellite），又称简单重复序列（Simple sequences repeats，SSRs）是由1~6个核苷酸为基本重复单元构成的串联重复序列。本文利用生物信息学方法搜索和统计了山羊和藏羚羊全基因组中完整型SSRs序列，并对其生物信息学特征进行比较分析。山羊和藏羚羊全基因组中SSRs总数量分别为920 300 个和 913 059个，占其全基因组长度的比例分别为5.56‰和5.39‰。山羊和藏羚羊全基因组SSRs六种重复类型的数量、比例、丰度和密度分布模式如下：单核苷酸SSRs > 二核苷酸SSRs > 三核苷酸SSRs > 五核苷酸SSRs > 四核苷酸 SSRs > 六核苷酸SSRs，这六种重复类型SSRs特征相互比较有显著差异，而相同重复类型SSRs特征基本一致。山羊基因5′端非翻译区和外显子区均是三核苷酸SSR丰最丰富，其次依次是单核苷酸、二核苷酸、四核苷酸、五核苷酸和六核苷酸；而其3′端非翻译区和内含子区均是单核苷酸SSR最丰富，其次依次是二核苷酸、四核苷酸、三核苷酸、五核苷酸和六核苷酸。山羊第1条染色体上SSRs数量最多，其次依次是第2条、X染色体、第6条、第4条和第8条染色体，而较少的是第25、28条染色体，所有染色体上SSRs丰度不存在显著差异。山羊和藏羚羊全基因组各重复类型优势SSRs序列基本一致，并与牛、绵羊全基因组中不同重复类型SSRs优势序列相一致。
Microsatellites or simple sequence repeats (SSRs) are tandemly repeated tracts of DNA composed of 1？C6 base pair (bp) units. The perfect SRRs were searched and computed by using bioinformatics methods in the complete genomes of goat (Capra hircus) and Tibetan antelope (Pantholops hodgsonii), and their number, frequency, density and distribution of SSRs were comparative analyzed in the study. The total SSRs number detected in the goat and Tibetan antelope genomes were 920 300 and 913 059 loci respectively, which accounted for 5.56‰ and 5.39‰ of its whole genome length, respectively. The number, proportion, frequency and density of six SSRs repeat types were abided by the following pattern: mono- > di- > tri- > penta- > tetra- > hexa-nucleotide SSRs in the goat and Tibetan antelope genomes. There were significant differences compared among these characteristics of six SSRs repeat types, and no significant difference among these characteristics of the same SSRs repeat type. Tri- nucleotide SSRs was the most abundant type in the 5′-UTR (5′-Untranslated Regions) and exon area of goat genes, followed by the pattern: mono- > di- > tetra- > penta- > hexa-nucleotide SSRs; while mono- nucleotide SSRs was the most abundant type in its 3′-UTR (3′-Untranslated Regions) and intron area, followed by the pattern: di- > tetra- > tri- > penta- > hexa-nucleotide SSRs. The overall SSRs number was compared in all autosomes and X chromosome of goat, the largest SSRs number was found in chromosome 1 followed by chromosome 2, X, 6, 4 and 8, and the smaller SSRs number was in chromosome 25 and 28. There no significant difference in the SSRs frequency among all chromosomes in the goat (P > 0.05). The dominant SSRs motifs of all repeat type showed great similarity in the goat and Tibetan antelope genomes, which were consistent with the dominant SSRs motifs of different repeat type in the cattle and sheep genomes