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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 1..9965640
/organism="Candidatus Solibacter usitatus Ellin6076" /mol_type="genomic DNA"
/strain="Ellin6076"
/db_xref="taxon:234267"
gene
89..1402
/locus_tag="Acid_0001"
gene
1637..2755
/locus_tag="Acid_0002"
gene
2781..5228
/locus_tag="Acid_0003"
gene
complement(5232..6827)
/locus_tag="Acid_0004"
gene
complement(6844..8496)
/locus_tag="Acid_0005"
gene
8627..9400 /
locus_tag="Acid_0006"
gene
9397..10986
/locus_tag="Acid_0007"
gene
10983..11723
/locus_tag="Acid_0008"
gene
12211..12804
/locus_tag="Acid_0009"
gene
12823..12996
/locus_tag="Acid_0010"
gene
complement(13323..13550)
/locus_tag="Acid_0011“
gene
complement(13560..17015)
/locus_tag="Acid_0012"
gene
complement(17148..19577)
/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.
b.
c.
Morphology (rods, spheres, spirals).
Lack of introns in protein-coding genes.
High gene density.
3. Similarities with Eukarya include:
a.
b.
Genes for replication, transcription, and
translation.
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.