Genome-wide analysis of conservation and divergence of microsatellites in rice

被引:9
作者
Roorkiwal, Manish [1 ]
Grover, Atul [1 ]
Sharma, Prakash C. [1 ]
机构
[1] Guru Gobind Singh Indraprastha Univ, Univ Sch Biotechnol, Delhi 110403, India
关键词
Microsatellites; indica; japonica; Synteny; Genome alignment; SIMPLE SEQUENCE REPEATS; ORYZA-SATIVA L; TRANSPOSABLE ELEMENTS; GENETIC DIVERSITY; DRAFT SEQUENCE; CPG ISLANDS; EVOLUTION; DNA; COLINEARITY; LENGTH;
D O I
10.1007/s00438-009-0457-3
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Studies on microsatellite distribution and divergence in related genomes contribute towards understanding of genome evolution in eukaryotes. Despite the availability of whole genome sequences of four rice genomes, occurrence and significance of microsatellites in the rice genome has remained a relatively unexplored area of research. We have aligned genomes of two rice subspecies i.e. indica and japonica to understand the trends of microsatellite conservation and divergence in the rice genome. Nearly 62% of the indica microsatellites were also found in the japonica genome. Occurrence of microsatellites showed a negative association with that of retrotransposons. Microsatellites repeat unit length and sequence showed direct influence on the microsatellite locus length. Further, microsatellite allele length was also influenced by the sequence characteristics of the neighbouring regions. CCG repeats were most conserved microsatellite sequences across the different syntenic regions in the two rice genomes and often showed association with CpG islands. Our study suggested that microsatellite distribution is not only governed by a balance between replication slippage and point mutations as proposed earlier, but also by the microsatellite motif sequence and characteristics of microsatellite neighbouring regions in the genome. Thus, this study is likely to prove an important reference for understanding the process of microsatellite evolution and dynamics in the two rice subspecies.
引用
收藏
页码:205 / 215
页数:11
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