Comparitive Genomics and Analysis of Repetitive Sequence on Rice Chromosome 5
Date Issued
2005
Date
2005
Author(s)
Hour, Ai-Ling
DOI
zh-TW
Abstract
The IRGSP (The International Rice Genome Sequencing Program) completed a high quality sequence on schedule in December 2002. This result allows a large scale investigation on rice. We have done some detail analysis on rice chromosome 5, which sequenced by ASPGC（Academia Sinica Plant Genome Center）. This work accomplished basic characteristics of rice genome with some bioinformatics tools and combination with proper statistic approach.
This work fell into two parts. The first one was the comparison between genomic sequences of Japonica and Indica. The chromosome 5 sequences of Nipponbare were aligned with whole genome shotgun sequences of 93-11 Indica variety. The similarities between them were estimated by BLAST searching. The result revealed that the average similarity under the aligned region covered 80% of genome was 97%. After those alignments duplicated or over-dispersed were removed, 60% of genome could be aligned and the similarity was up to 98%.
The other one was the studying on repetitive sequences on rice chromosome 5. The distributions of different repetitive sequences on chromosome 5 were clarified. And details on centromere and telomere regions were featured. The differences between LTR sequences reflected the histories of insertion of retrotransposons. The completeness of centromere and telomere with highly repetitive sequences has been overcome by map-based approach.
These results are important for designing molecular markers. High density of molecular markers is the helpful tool on future breeding and genetic research of rice.
Subjects
重複序列
水稻
稉
基因組
稻
秈稻
rice
Oryza sativa
genome
repetitive sequence
Japonica
Indica
Type
thesis
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