毛果杨(Populus trichocarpa)全基因组SSR位点分布规律

以毛果杨全基因组数据为试验材料,探究其SSR位点的分布模式及规律,通过分析可知,毛果杨全基因组全长307840768 bp,共存在726种SSR重复单元,213634个SSR位点,平均每1441 bp出现一个SSR位点。1号染色体SSR位点和种类最多,17号染色体SSR位点最少。单核苷酸到六核苷酸的数量呈降低趋势,其中单核苷酸~四核苷酸在不同染色体中的比例相对稳定,比例接近61.5:16.5:7.3:1。毛果杨SSR序列长度范围在10~216 bp间变化,平均长度为14.48 bp,主要是以10~30 bp长度的序列为主,达到95%。研究发现SSR重复单元都随着重复长度的递增,微卫星丰度呈递减趋势,即SSR重复次数越多,微卫星出现频率越低。所有类型SSR中序列显示出显著的碱基偏好性,均以A/T的重复类型占主导地位。毛果杨全基因组共存在383种稀有SSR单元,不同染色体上存在的SSR稀有单元数存在较大差异。通过SSR分布矩阵可将所有染色体分为3大类,第1类的2号、3号、4号、9号、15号、16号共6对染色体与其他染色体间相对独立,没有或很少与其他染色体间发生交流;在第2、3大类中,各染色体间的关系相对比较紧密,这些染色体存在频繁的交流,进而存在相近的SSR位点分布模式。

Distribution Rule of SSR Loci in Whole Genome of Populus trichocarpa

The whole genome data of Populus trichocarpa was as material to explore the distribution pattern of the SSR locus and its regularity.Through the analysis,we can know that the whole genome of Populus trichocarpa were 307840768 bp length and there were 213634 SSR sites with 726 SSR repeat units,an average of 1441 bp appear a SSR site.The number and type of SSR in chromosome 1 were the most,whereas the chromosome 17 were the least.The number of mono-nucleotide to hexa-nucleotide showed a decreasing trend.The proportion from mono-nucleotide to tetra-nucleotide in different chromosomes is relatively stable,the ratio of close to 61.5:16.5:7.3:1.The length of SSR sequence of Populus trichocarpa ranged from 10 to 216 bp,with an average length of14.48 bp,and 10~30 bp length were the main sequence which reaching 95%.The study found that with the increasing of the length of the repeat the SSR repeat units showed a decreasing trend,that is,the more the number of SSR repeat,the lower the frequency of the microsatellite.The sequence of all types of SSR showed a significant base preference,and A/T occupy the leading position.There were 383 kinds of rare SSR units in the whole genome of Populus trichocarpa,whereas there are significant differences in different chromosomes.All chromosomes can be divided into 3 categories by SSR distribution matrix,and 2,3,4,9,15,16 chromosome were relatively independent and there is no or very little communication with other chromosomes.The relation of each chromosome is relatively close in the second and third categories.These chromosomes have frequent exchanges,and there are similar distribution patterns of SSR sites.