The chloroplast, where all photosynthesis occurs in plants, is derived from ancient, free-living algae. Over the past 900 million years, however, it has lived inside of plant cells and their green algal ancestors, evolving to be an integral part of these organisms. However, each chloroplast still has it's own separate DNA, encoding many of the key proteins required for all life today. Students taking EBIO 4460/5460 – Genomics study the chloroplast genomes, to understand the important organelle in plant cells, but also to learn how genomes are put together. The highest quality genomes, after careful checking, are published on NCBI (the National Center for Biotechnology Information - Genbank). All of the flowering plant chloroplast genomes to date are published on NCBI's Chloroplast database.
Graduate and advanced undergraduate students contribute substantially to expand the understanding of these sub-cellular engines that ultimately power nearly all carbon-based life. Each student starts the semester with a large file consisting of millions of small DNA sequences (reads); over the course of the semester, students learn to process that information – to identify the informative sequences, assemble the reads into larger sequences (contigs), determine the proper arrangement of the contigs, and ultimately construct the entire chloroplast genome of their organism. The chloroplast genome is typically 140,000-160,000 bases of DNA, in a long circle, placing millions of small pieces of DNA together in the correct order to complete a giant circular sequence is quite a challenge!
However, this is only the beginning, as a long DNA sequence is hard to understand on its own. Students identify the locations of all of the genes that encode many necessary functions: 1) make proteins, tRNAs, and rRNAs; 2) regulate the expression of these products; and 3) replicate the DNA to make new chloroplasts as needed. Once all of this information is known and has been verified, students submit their sequences to NCBI, making the new sequence freely available to scientists around the world. The genome sequences produced in this course will help us better understand this important component of life on earth. So far, students have put together dozens of high quality genomes, a substantial portion of the five hundred that have been assembled for all flowering plants. Browse the gallery below to see visualizations and links to the genbank page for each of these genomes.