Lecture 21 – Genome Annotation & Sequenced Genomes Based on Chapther 8 Genomics: The Mapping and Sequencing of Genomes Copyright © 2010 Pearson Education Inc.

Arabidopsis Chromosome 5, complete sequence

Genome Assembly and Gene Prediction FEATURES Location/Qualifiers source /organism="Candidatus Solibacter usitatus Ellin6076" /mol_type="genomic DNA" /strain="Ellin6076" /db_xref="taxon:234267" genegene /locus_tag="Acid_0001" genegene /locus_tag="Acid_0002" genegene /locus_tag="Acid_0003" genegene complement( ) /locus_tag="Acid_0004" genegene complement( ) /locus_tag="Acid_0005" genegene / locus_tag="Acid_0006" genegene /locus_tag="Acid_0007" genegene /locus_tag="Acid_0008" genegene /locus_tag="Acid_0009" genegene /locus_tag="Acid_0010" genegene complement( ) /locus_tag="Acid_0011““ genegene complement( ) /locus_tag="Acid_0012" genegene complement( ) /locus_tag="Acid_0013"

The Human GAD1 Gene Sequence

4. Insights from Genome Analysis: Genome Sizes and Gene Densities

5. Genomes of Bacteria Bacterial genomes – a.Carsonella ruddii b.Haemophilus influenzae c.Mycoplasma genitalium d.E. coli e.Bradyrhizobium japonicum f.Sorangium cellosium g.Now have thousands of different species sequenced

6. Genomes of Bacteria: Haemophilus influenzae

7. Genomes of Bacteria: E. coli

8. Genomes of Archaea 1.Archaea are generally extremophiles with regard to conditions such as temperature, pressure, pH, metal ions, or salt. 2.Similarities with Bacteria include: a.Morphology (rods, spheres, spirals). b.Lack of introns in protein-coding genes. c.High gene density. 3.Similarities with Eukarya include: a.Genes for replication, transcription, and translation. b.Introns in tRNA genes. 4.Archaea genomes range widely, from 0.49 Mb (Nanoarchaeum equitans) to 5.75 Mb (Methanosarcina acetivorans). Nanoarchaeum equitans Methanosarcina eaetivorans

9. Genomes of Archaea

10. Genomes of Eukarya: Genome Complexity Sizes

11. Genomes of Eukarya: Gene densities

12. Genomes of Eukarya: Saccharomyces cerevisiae

13. Genomes of Eukarya: Caenorhabditis elegans

14. Genomes of Eukarya: Drosophila melanogaster

15. Genomes of Eukarya: Arabidopsis thaliana

16. Genomes of Eukarya: Rice (Oryza sativa)

17. Genomes of Eukarya: Homo sapiens

18. Genomes of Eukarya: Mouse (Mus musculus)

19. Genomes of Eukarya: Dog (Canis familiaris)

20. Future Directions in Genomics 1. The National Human Genome Research Institute (NHGRI) is supporting sequencing of both eukaryotic and bacterial genomes. a. Sequencing of seven mammalian genomes is fully or nearly complete. More than 40 others are in progress. b. Other organizations are also sequencing additional genomes. 2. Data so far suggest that most mammals have similar genome sizes and gene numbers. 3. Rodents, especially the mouse, are models for human genetics, and about 99% of mouse and rat genes have human counterparts. 4. Other sequences of interest will be: a. Near relatives to humans (e.g., chimps and gorillas). b. Pathogenic versus nonpathogenic strains of E. coli. 5. DNA sequencing technology is developing rapidly, becoming much faster and less expensive. If this trend continues, DNA sequencing may become a part of medical treatment.