Genome Galleries and Bioinformatics
The Garden of Prokaryotic Genomes
The Garden of Prokaryotic Genomes is a somewhat mazelike garden, located to the north of the terrace, that displays objects representing the genomes of several prokaryotes. For many years, the variety and complexity of prokaryotic genomes was inadequately appreciated because of the relatively small size and structural simplicity of bacterial and archaeal cells. However, as more and more prokaryotic genomes are sequenced, it is apparent that although prokaryotic genomes may be small and compact, they are incredibly diverse, even within species assigned to the same genus.
A small sampling of prokaryotic genomes is offered here to illustrate their diversity. Although the selection is biased by a focus on the bacterial agents of human infectious diseases, it ranges from tiny intracellular symbionts to large photosynthetic bacteria. Each genome is represented by its map on a ring-shaped object. Within the garden, the size of each ring is proportional to the size of its genome. In a few cases related species are displayed to illustrate genomic changes related to pathogenicity.
Each genome is an active object and clicking on it will deliver a notecard with information about the species and its special genetic features. In most cases, a photomicrograph of the species is also displayed. Most of the photomicrographs are from Wikimedia Commons. The genome maps are from the University of Alberta BacMap Genome Atlas . The notecards were written by Elizabeth Gloucester. The genomes included in the Prokaryote Garden are the following:
- Anabaena variabilis
- Escherichia coli K12
- Bacillus subtilis
- Salmonella typhimurium
- Staphylococcus aureus
- E. coli O157H7
- Yersinia pestis
- Vibrio cholerae
- Helicobacter pylori
- Mycobacterium tuberculosis
- Mycobacterium leprae
- Listeria monocytogenes
- Environmental Chlamydia
- Chlamydia pneumoniae
- Chlamydia trachomatis
- Rickettsia prowazekii
- Buchnera aphidicola
- Carsonella rudii
Because of the importance of lateral gene transfer to prokaryotic diversity, a “Plasmid Patio” is also included. Although within the patio the size of the plasmid genomes is also proportional to the size of the circles that display them, they are set to a different reference scale than the genomes of the organisms they inhabit. The plasmids represented include the following:
- Anabaena variabilis plasmid A
- Shigella dysenteriae plasmid Sd1_197
- E. coli 0157H7 plasmid 0157
- Rhizobium leguminosarum plasmid RL10
- E. coli pBR322
- Bacillus anthracis plasmid pX01
- Staphylococcus aureus plasmid VRSAp
The Eukaryotic Boardwalk
The Eukaryotic Boardwalk is companion to the Garden of Prokaryotic Genomes, and allows visitors to compare genome size and other features of these two major groups of organisms. It can be reached by a path from the Cell Terrace. The genomes represented on the Eukaryote Boardwalk include the following:
- Saccharomyces cerevisiae (yeast)
- Dictyostelium discoideum (slime mold)
- Caenorhabditis elegans (roundworm)
- Drosophila melanogaster (fruit fly)
- Strongylocentrotus purpuratus (sea urchin)
- Ciona intestinalis (sea squirt)
- Branchiostoma floridae (Amphioxus)
- Tetraodon nigroviridans (puffer fish)
- Gallus gallus (chicken)
- Monodelphis domestica (opossum)
- Canis familiaris (dog)
- Bos taurus (cow)
- Equus caballus (horse)
- Chlamydomonas reinhardtii (green alga)
- Arabidopsis thaliana (cress)
- Oryza sativa (rice)
- Zea mays (maize)
- Populus trichocarpa (poplar)
Each genome includes a picture of the organism and basic information about the karyotype, genome size and number of genes for each of the species represented. In addition to the genomes on the boardwalk, the genomes of humans, chimpanzees, macaques, mice and rats are described in the Tower.
A new section on mitochondrial and chloroplast genomes is under development in this section.
The Bioinformatics Platform:
The Bioinformatics Platform can be reached in several ways. One is by a teleport terminal located along the central walkway in the Prokaryote Garden. There is another teleport from the Tower. Teleports on the Kitchen platform brings you back to the ground, to the Tower, or to the Eukaryotic Boardwalk. You can also walk to the platform along a walkway that begins from the base of the Tower.
In this section, various genetics databases are used to compare gene and protein sequences of different individuals or species.
The following activities are located on the Bioinformatics Platform:
Link to The Genographic Project: The Genographic Project, sponsored by the National Geographic Society, is a bioinformatics project for tracing human migration patterns. Individuals can send samples of cells scraped from their cheek lining. Mitochondrial or Y chromosome DNA extracted from the sample can be analyzed to reveal its ancient geographic origin.
Mitochondrial Genes from Extinct Species: In this activity, a mitochondrial gene sequence from one of five different extinct species is given. Visitors can guess what living species might be most closely related to the extinct species selected. Comparison of the sequence with those of living species available in public genetics databases then shows the closest match. A link to the database is provided, along with instructins for using it.
Beta Globin Alignments and Phylogenetic Trees: Genes and proteins can be compared to discover relationships between species and to construct phylogenetic trees based on similarities within a group of organisms. Two sample trees based on horse beta globin are displayed. Students are asked to select two pairs of species -- one pair that they think will be different and one pair they think will be similar. They can then test their predictions by comparing the sequences in the database. A link to the database and instructions for using it are provided.
Gene Duplication and Color Vision: Humans and some other primates have color vision, while most other mammals do not. Where did our ability to "see red" come from? Comparison of the genes for the red and green cone opsins suggests an answer to this question. A link to the database and instructions for using it are provided. A related activity explains the inheritance of red/green color blindness in humans. A brief slideshow describes the sex-linked inheritance of color vision in humans, and includes a mystery pedigree to analyze.
Historical Mysteries and DNA: Questions about historical figures can sometimes be addressed by analyzing the DNA of their descendants. In this activity, we consider the following historical mysteries:
Was the woman who called herself Anna Anderson really the lost Grand Duchess Anastasia?
Did Thomas Jefferson really father one or more of the children of his slave Sally Hemings?
Were the bones recently found in a Polish cathedral really those of Nicolas Copernicus?
Cat Show: Do the genes of different species reflect physical requirements or ancestral history? Comparison of three cat species and three primate species helps to answer this question. The reference sequences are the beta globins of housecats and humans. Students can compare these to the sequences of 3 large cats (leopard, lion and jaguar) and three small primates (spider monkey, gibbon, and colobus monkey) to the human and housecat sequences.
Water Sample with Mystery Genes: The analysis of DNA collected from water or other environmental samples can reveal the presence of organisms that might otherwise be hidden. In this activity, the visitor is given a DNA sample whose origin can be identified by comparison with sequences in public databases. A link to the database and an instructional slideshow are provided by the computers.
Link to Origin Unknown: If evidence of life is discovered during space exploration, how can we be sure that we didn't accidentally introduce it? Origin Unknown is a series of online Bioinformatics exercises developed by the Southwest Biotechnology and Informatics Center at New Mexico State University.
Bioinformatics Database Gateway: A panel with multiple links offers quick access to ten different public databases. Each button gives a brief description of the type of data found in each database.