杨树全基因组微卫星序列的统计及其生物信息学分析

Statistics and Bioinformatics Analysis of Microsatellite Sequence in Poplar Whole Genomes

本文利用生物信息学方法搜索毛果杨全基因组中完整型SSRs序列,并对其进行生物信息学分析。结果表明,毛果杨全基因组共统计了143 810个SSRs序列,占其全基因组长度的比率为0.63%,其全基因组SSRs序列出现频率为331.26个/Mb。毛果杨基因组中SSRs数量最多的是第1条染色体,其次是第2、5、6条染色体,数量较少的是第9条染色体。毛果杨各条染色体上SSRs序列出现频率在310-360个/Mb,无明显差异。通过检验表明,毛果杨染色体长度与其所含SSRs频率和密度无相关性（Kendall＇s tau-b,P〉0.05;Spearman＇s rho,P〉0.05）,而其染色体长度与其所含SSRs数量具有高度正相关性（r〉0.85,P〈0.01）。毛果杨全基因组中单核苷酸SSRs序列数量最多（42.79%）,其次依次是二核苷酸〉三核苷酸〉四核苷酸〉五核苷酸〉六核苷酸重复类型。毛果杨全基因组SSRs各重复类型拷贝数分布范围为4-111次,主要集中在4-30次。

SSRs sequences in the complete genomos of black cottonwood （Populus trichocarpa） were searched by bioinformatios methods, and their number, frequency, density and distribution of microsatellites were comparatively analyzed in the study. The result showed that SSRs sequences in the black cottonwood were 143 810 loci, which accounted for 0. 63 % of its whole genome length. In the black cottonwood genome, total frequency of SSRs was 331.26 loci/Mb. The overall SSRs count was comparable in all chromosomes of black cottonwood, the largest SSRs count was found in chromosome 1 （ 17 472 loci）, followed by chromosome 2, 5 and 6 （ 8779, 8647, 9996 locis）, and the smaller SSRs number was in chromosome 9 （4613 loci）. Statistical analysis showed no correlation between chromosomes length and their containing SSRs frequency/density （P 〉 0.05）, and a significantly positive correlation between chromosome length and its containing SSRs numbers was observed in the black cottonwood genomes （r 〉 0.85, P 〈 0.01 ）. In the different SSRs repeat types of the black cottonwood genomos, mononuclcotide repeat type motifs was the most abundance, followed by dinucleetide, trinuclcotide, tetnmucleotide, pentanucleotide and hexanucleetide repeat types. The copy number distribution of all motif types in the black cottonwood genome was from 4 to 111 times and mainly concentrated in the range of 4 - 30 times.