Construction Of Polymorphic Microsatellites Database And Analysis Of Pseudogenes For Rice Genomes

Tri-nucleotide repeats (TNRs) are extremely abundant in rice genome, of which CCG/CGG repeats have an advantage over other repeats, with approximate half of all the TNRs in the genome. Our results show that rice genome has relatively abundant TNRs with high GC content, and containing only purines or pyrimidines under the same GC content. The highest frequency of TNRs occurs in 5-UTR regions, followed by in coding and 5.-flanking regions. Purines-rich TNRs prefer to the coding regions, but pyrimidines-rich TNRs exhibit a stronger bias to upstream regions, suggesting that they might be considered as the regulatory elements in gene expression. As if TNRs located predominantly near the start of coding regions do not significantly influence on the protein function. In coding regions, GC3 (GC content of the third base) of the codon repeats is up to 90%, and codon repeats coding for (Ala)n and (Gly)n were most abundant. We speculate that TNRs in coding regions might be predominantly located near the start of coding regions. As if TNRs located predominantly near these regions do not significantly influence on the protein function. Those Genes involved in transcription regulator activity prefer to containing more TNRs, especially in coding regions, suggesting TNRs could have an important role in gene expression and evolution.On the basis of numbers, distributions, and polymorphisms of microsatellites from both subspecies, Indica cv. 9311 and Japonica cv. Nipponbare, We have first found a total of 45,220 polymorphic microsatellites flanked by specific sequence, or approximately one polymorphic microsatellite every 8.3Kb and 7.8Kb for indica and japonica, respectively. It was also found that the polymorphism rate in intronic regions is the highest, followed in order by UTR, intergenic and coding regions. DNRs and TNRs except for the GC-rich repeats prefer to being polymorphic in general. To develop their polymorphic microsatellites for both subspecies Indica and Japonica, we also mapped the microsatellite markers from Gramene and genetic markers from JRGP onto the two public genomes sequences, therefore significantly facilitating their applications to genetic researches and molecular breeding. 100primer pairs of randomly selected microsatellites were also amplified by PCR using genomic DNA of 9311 and Nipponbare as templates and sequenced. The results indicate that more than 90% appeare to be polymorphic, therefore validating the polymorphisms of these microsatellites, and providing markers for molecular breeding and gene mapping. This data set could be downloaded freely from our website.A total of 4607 processed, 2153 duplicated and 6720 fragmental pseudogenes were identified in indica genome using homology searches. The numbers are 4320, 2025 and 5989 for Syngenta japonica genome, and 4034, 1117 and 9304 for IRGSP japonica genome. Pseudogenes in rice appear to be more abundant near centromeric areas, especially for processed pseudogenes. And there is no significant correlation between the density of pseudogenes and the GC content like genes. By calculating the Ka/Ks ratios we confirmed their un-functionality. The majority of pseudogenes create after Oryza branched off from the genera of Oryzeae 20 million years ago, and most processed pseudogenes are older than non-processed pseudogenes. In addition, the distribution of sequence divergence for processed pseudogenes closely resembles that of LTR, suggesting they might be generated at the same time generally. Most pseudogenes generate from those genes with binding and enzyme activity, another two important resources are cytochrome and ribosomal proteins, indicating the preference of genesis for pseudogenes...