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 …show more content…
The gene marker is mapped by the line next to the gene name. The Arrows are showing the location it is mapped in other populations. Its locations are inferred based on position of flanking markers. The location of centromeres is indicated by the ovals within the linkage group. The telomeres are indicated by the circles at ends of linkage groups. Breakpoints of chromosomal rearrangements distinguishing the taxa are indicated by the double squiggles. The existence of homologous gene between the populations shows that Poaceace is relatively conservative. However, certain lineages in this family appear to be rapidly evolving. The genome of wheat and rye are different by 13 chromosomal rearrangements after only 6 million years of divergence (Devos). This rate is reshuffling is twice the average rate for nine taxa. Only Brassica-Arabidopsis lineage possesses a faster rate of reshuffling …show more content…
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
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 …show more content…
The gene marker is mapped by the line next to the gene name. The Arrows are showing the location it is mapped in other populations. Its locations are inferred based on position of flanking markers. The location of centromeres is indicated by the ovals within the linkage group. The telomeres are indicated by the circles at ends of linkage groups. Breakpoints of chromosomal rearrangements distinguishing the taxa are indicated by the double squiggles. The existence of homologous gene between the populations shows that Poaceace is relatively conservative. However, certain lineages in this family appear to be rapidly evolving. The genome of wheat and rye are different by 13 chromosomal rearrangements after only 6 million years of divergence (Devos). This rate is reshuffling is twice the average rate for nine taxa. Only Brassica-Arabidopsis lineage possesses a faster rate of reshuffling …show more content…
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