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Transcript
Ecological Genomics: Construction of Molecular Pathways Responsible for Gene Regulation and Adaptation to Heavy Metal Stress in Arabidopsis thaliana and Raphanus sativus. By: Lynda Villagomez, Dr. Tatiana Tatarinova and Dr. Gary Kuleck Understanding the many factors involved in gene regulation in plants adapted to environmental stress in harsh, polluted environments remains a major challenge. Utilizing advanced bioinformatics tools and comprehensive Arabidopsis thaliana databases, this challenge can be addressed. First, Ariadne Genomics Pathway Studio was used to explore molecular responses in Arabidopsis to identify genes associated with heavy metal stress responsiveness. This computational tool constructs complex pathways by extracting molecular relationships from scientific journal articles and published microarray datasets. These pathways can be verified in controlled laboratory conditions by analyzing A. thaliana plants grown under heavy metal stress. Secondly, R. sativus ESTs are used to determine the similarities between these two species. The R. sativus genome has not been sequenced, consequently the DNA sequence similarity to A. thaliana’s sequence is unknown. In order to accurately analyze the data, the level of sequence similarity between Arabidopsis and R. sativus was estimated. Using BLASTN, the results of alignment of R. sativus EST sequences to Arabidopsis genes indicated that ~50% of Arabidopsis genes (15,974) match to R. sativus. Using a conservative threshold of 95% sequence similarity, 8,059 pairs of putative orthologs between R. sativus and Arabidopsis were identified. From 50 heavy metal-responsive genes in Arabidopsis identified in the first phase, candidate genes in R. sativus likely to play a role in heavy metal response were selected. Pathway Studio was used to build a prototype heavy metal response network in R. sativus and to select candidates for RT-PCR validation of computational predictions.