Comparative Analysis Of Plant Genome Essay

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Comparative Analysis of Plant Genome – An Overview
Introduction
Comparative genomics is used to study the similarities and differences in the structure and function of genome in living organisms. In the medical field, this information can help scientist to better understand the human genome. This allows them to develop new strategies to combat human disease. Comparative genomics is also a powerful tool to study the evolutionary relationship among organisms. We are able to identify genes that are conserved among the species. We can also identify genes that give organisms their unique and complex characteristics (Comparative Genomics Fact Sheet). This allows us to make inferences regarding the rate of evolution of particular genes, duplication
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One of the traditional approaches is using molecular markers such as Restriction Fragment Length Polymorphism (RFLP). This allows the mapping of genome of two species from a common set of marker. The differences in homologous DNA sequences are able to be detected after a digestion procedure with specific restriction endonucleases. Comparative genomics using RFLP is pioneered by Tanksley et al by using tomato RFLP probes to map tomato, chili papers and potato genome for comparison.
A slightly modern approach would be to use computational tools that allow us to access the large amount of genomic data available today for comparison. Among the tools that are usually used for plant genomic comparison are PlantGDB, VISTA, PLAZA and BLAST. The availability of these tools allows more efficient research work to be done. Furthermore, these software and databases are constantly being developed and updated. However, there are some limitations of these methods. A major limitation is the lack of plant genome sequenced to completion. To date, there is only around 55 plant genome sequenced to completion (Broad Institute). This limits the data available on these tools to allow a wide range of
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Multiple gene marker similarities and conserved region is a result of late divergence event in the point of time. Genome comparison of different species between families is proven to be quite difficult. Lack of gene similarities provides a challenge to use DNA probe based analysis such as RFLP (Ku, Hsin-Mei, et al). However, a research done by Paterson et al suggested that there are region of linked genes that is conserved across higher plant families by using comparative genome data between Arabidopsis and rice. Ku, Hsin-Meti et al then compared sequenced segments of tomato and Arabidopsis genome to further understand the role of these linked genes in higher plants. They chose bacterial artificial chromosome (BAC19) from the ovate-containing region of the tomato chromosome II. At the time when this research is conducted, the tomato genome is not yet sequenced to completion. Therefore the ovate-region is used since several ORFs near the ovate¬ locus have been shown to possess homologous matches in Arabidopsis. The Tomato II sequence is then subjected to shotgun sequencing and assembled. The assembled sequence is then analyzed for open reading frames (ORFs) using GENSCAN and BLAST under Arabidopsis setting. The BAC sequence and ORFs are searched against the Arabidopsis genome sequence using TBLASTX and TBLASTN with BLOSUM62 substitution matrix. The Arabidopsis sequences with high scoring

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