| Microsatellites are Short Tandem Repeats(STRs)or Simple Sequence Repeats(SSRs)which are widely distributed in plant genomes,and haves also been reported to be widespread in the rice genome.Microsatellites are mostly used in genetic marker-assisted breeding in plants.In this paper,the position-dependent differential calculator of microsatellite 2.0(DCM 2.0)was used to establish the microsatellite density feature map with a resolution of 1 Kbp in 50,000 base units in the rice reference genomes,namely the japonica genome and the Zhenshan 97 indica genome.Results found a large number of high-density microsatellites accumulation(HDMA)phenomenon in the maps,and constructed genome-based high density microsatellites accumulation maps.In this paper,the genomes of the two major cultivars of rice in Asia were selected as the research materials,the rice reference genome japonica genome and the fully sequenced Zhenshan 97 indica genome.Firstly,microsatellite density feature maps of7621 japonica rice genomes with 50,000 bases at 1 Kbp resolution was established based on the position-dependent microsatellite differential calculation algorithm,and microsatellite density feature maps of 7836 japonica rice genomes with 50,000 bases at1 Kbp resolution was established.These microsatellite density feature maps show the existence of a large number of HDMA peaks in the rice genome,with 213 HDMA peaks in the japonica genome and 405 HDMA peaks in the indica genome,found that the HDMA peaks are distributed on every chromosome in the rice genome.Finally,according to the position of the HDMA peak on the chromosome,HDMA peak distribution maps of 12 chromosomes in japonica and indica rice was constructed using Python code,it was found that most of the HDMA peaks were aggregates of(AT)_nrepeats by motif analysis.The whole genome sequence alignment analysis of japonica and indica found that the sequence similarity between the two subspecies of rice was as high as 95%,but it is found that there are only 77 highly similar HDMA peaks in the two subspecies of rice by comparing HDMA distribution maps,most of the HDMA peaks in the corresponding genomic positions of japonica and indica have large repeat unit and genome sequence variation,indicating that HDMA peaks have a relatively large contribution to the sequence differences of different rice cultivars.This high-density clustered distribution of microsatellites may imply important biological significance.This study discovered the HDMA peaks in the rice genome for the first time and established the HDMA peak distribution maps for the first time.It provides reference and help for scientific significance. |
