1. Environmental Genome Shotgun Sequencing of the Sargasso Sea
J. Craig Venter et al.
Presented by: Hormuzdiyar Dasenbrock and Ryan Wong

2. Environmental Genome Shotgun Sequencing of the Sargasso Sea
J. Craig Venter et al.
What is bacteriorhodopsin (aka proteorhodopsin)!?!?
Presented by: Hormuzdiyar Dasenbrock and Ryan Wong

3. J. Craig Venter 1992 TIGR 1995 H. Influenza 1998 Celera
Human Genome

4. Continuing the Quest…

5. Working Hard!

6. Sargasso Sea Sites
Fig. 1. MODIS-Aqua satellite image of ocean chlorophyll in the Sargasso Sea grid about the BATS site from 22 February The station locations are overlain with their respective identifications.
Venter et al. Science Apr 2;304(5667): Epub 2004 Mar 04

7. Sampling, Sequencing, and Assembly
Focus on microbial organisms
Shotgun Sequencing
Assembly through computation

8. Whole Genome Shotgun Sequencing

9. Whole Genome Shotgun Sequencing
Figure 3. Anatomy of whole-genome assembly. Overlapping shredded bactig fragments (red lines) and internally derived reads from five different individuals (black lines) are combined to produce a contig and a consensus sequence (green line). Contigs are connected into scaffolds (red) by using mate pair information. Scaffolds are then mapped to the genome (gray line) with STS (blue star) physical map information.
Venter et al. Science Feb 16;291(5507):

10. Sargasso Sea Data
Table S2. Summary statistics on the sequence and assembly data.
Samples Samples 5-7
Sequence reads 1,662, ,608
sequence (Mbp) 1,
Contigs ,477 N/A
sequence (Mbp) N/A
Scaffolds 64,398 N/A
span (Mbp) N/A
Mini-scaffolds , ,458
span (Mbp)
sequence (Mbp)
Singletons , ,692
sequence (Mbp)
Total nonredundant
sequence (Mbp)
Scaffolds>3x N/A
Span>3x (Mbp) N/A
Annotated genes 1,001, ,220
16S rRNA genes 1,
rhodopsin homologs
Venter et al. Science Apr 2;304(5667): Epub 2004 Mar 04

11. Interpretation of DNA sequences
Compare to published sequences
Identify possible genes

12. Shewanella
Figure S3. Gene conservation among closely related Shewanella species. The outermost concentric circle of the above diagram depicts the competed genomic sequence of Shewanella oneidensis MR1 []. Fragments from environmental sequencing were compared to this completed Shewanella genome and are shown in the inner concentric circles and were given boxed outlines. Genes for the outermost circle have been assigned pseudo-spectrum colors based on the position of those genes along the chromosome, where genes nearer to the start of the genome are colored in red, genes neared to the end of the genome are colored in blue. Fragments from environmental sequencing were subjected to an analysis that identifies conserved gene order between those fragments and the completed Shewanella genome. Genes on the environmental genome segments that exhibited conserved gene order are colored with the same color assignments as the Shewanella MR1 chromosome. Colored regions on the environmental segments xhibiting color differences from the adjacent outermost concentric ircle are the result of conserved gene order with other MR1 regions and probably represent chromosomal rearrangments. Genes that did not exhibit conserved gene order are colored in black.
Venter et al. Science Apr 2;304(5667): Epub 2004 Mar 04

13. Prochlorococcus
Fig. 2. Gene conservation among closely related Prochlorococcus. The outermost concentric circle of the diagram depicts the competed genomic sequence of Prochlorococcus marinus MED4 (11). Fragments from environmental sequencing were compared to this completed Prochlorococcus genome and are shown in the inner concentric circles and were given boxed outlines. Genes for the outermost circle have been assigned psuedospectrum colors based on the position of those genes along the chromosome, where genes nearer to the start of the genome are colored in red, and genes nearer to the end of the genome are colored in blue. Fragments from environmental sequencing were subjected to an analysis that identifies conserved gene order between those fragments and the completed Prochlorococcus MED4 genome. Genes on the environmental genome segments that exhibited conserved gene order are colored with the same color assignments as the Prochlorococcus MED4 chromosome. Colored regions on the environmental segments exhibiting color differences from the adjacent outermost concentric circle are the result of conserved gene order with other MED4 regions and probably represent chromosomal rearrangements. Genes that did not exhibit conserved gene order are colored in black.
Venter et al. Science Apr 2;304(5667): Epub 2004 Mar 04

14. Crenarchaeal 4B7
Fig. 3. Comparison of Sargasso Sea scaffolds to Crenarchaeal clone 4B7. Predicted proteins from 4B7 and the scaffolds showing significant homology to 4B7 by tBLASTx are arrayed in positional order along the x and y axes. Colored boxes represent BLASTp matches scoring at least 25% similarity and with an e value of better than 1e-5. Black vertical and horizontal lines delineate scaffold borders.
Venter et al. Science Apr 2;304(5667): Epub 2004 Mar 04

15. Genes Found TIGR role category Total genes
Amino acid biosynthesis   37,118  
Biosynthesis of cofactors, prosthetic groups, and carriers   25,905  
Cell envelope ,883  
Cellular processes   17,260  
Central intermediary metabolism   13,639  
DNA metabolism 25,346  
Energy metabolism   69,718  
Fatty acid and phospholipid metabolism 18,558  
Mobile and extrachromosomal element functions 1,061  
Protein fate  8,768  
Protein synthesis ,012  
Purines, pyrimidines, nucleosides, and nucleotides 19,912  
Regulatory functions  8,392  
Signal transduction 4,817  
Transcription  12,756  
Transport and binding proteins 49,185  
Unknown function   ,067  
Miscellaneous  1,864  
Conserved hypothetical  794,061
Total number of roles assigned  1,242,230  
Total number of genes   1,214,207  
Table 1. Gene count breakdown by TIGR role category. Gene set includes those found on assemblies from samples 1 to 4 and fragment reads from samples 5 to 7. A more detailed table, separating Weatherbird II samples from the Sorcerer II samples is presented in the SOM (table S4). Note that there are 28,023 genes which were classified in more than one role category.
Venter et al. Science Apr 2;304(5667): Epub 2004 Mar 04

16. Applications: Community Ecology
Species Diversity and Richness
PCR Approaches or Genomic Sequencing?
1412 rRNA Genes and 148 New Phylotypes

17. Phylogenetic Comparisons
Rec A
Venter et al. Science Apr 2;304(5667): Epub 2004 Mar 04

18. Major Phylogenetic Groups and Abundance
Venter et al. Science Apr 2;304(5667): Epub 2004 Mar 04

19. Variability in Species Abundance
Stoichiometry
Shewanella and Burkholderia
Archaea clone 4B7

20. Plasmids 10 Plasmids with Transfer Genes Metal Resistance
UmuCD DNA Pol
Venter et al. Science Apr 2;304(5667): Epub 2004 Mar 04

21. Other Filtered Organisms
Eukaryotic
69 18S rRNA Genes
Low Coverage
Phages
71 Scaffolds with Phage Genes

22. Photobiology of the Sargasso Sea
Photosynthesis: Rubis CO genes
Light-Driven Proton Pump Proteorhodopsin
Beja O. et al. Science Sep 15;289(5486):

23. Distribution of Rhodopsins
13 Subfamilies
CFB Scaffold
Energy
Venter et al. Science Apr 2;304(5667): Epub 2004 Mar 04

24. Conclusions
New way to characterize ecosystems and evaluate species diversity
Identification of novel genes
Phylogenetic Trees

25. Future Directions Sorcerer II Expedition Return to Sargasso Sea
Eukaryotic and Viral Analysis
Evolutionary Analysis
Energy Sources?
Synthetic Genomes

26. Criticisms Limitations of Shotgun Sequencing realized?
Only 2 Genomes Sequenced
Complimentary Studies
Cost and Availability