UC Davis EVE161 Lecture 11 by @phylogenomics

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UC Davis EVE161 Lecture 11 by @phylogenomics

  1. 1. Lecture 10: EVE 161:
 Microbial Phylogenomics ! Lecture #10: Era III: Genome Sequencing ! UC Davis, Winter 2014 Instructor: Jonathan Eisen Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !1
  2. 2. Where we are going and where we have been • Previous lecture: ! 10: Genome Sequencing • Current Lecture: ! 11: Genome Sequencing II • Next Lecture: ! 12: Genome Sequencing III Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !2
  3. 3. Comparative Genomics Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  4. 4. Structural Diversity Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  5. 5. mosome encodes all the housekeeping functions. Because plasmids typically have only Structural Diversity TABLE 7.1. Examples of bacteria with multiple genetic elements Species Form Size (kb) Shape Streptomyces coelicolor Chromosome Plasmid Plasmid 8667 356 31 Linear Linear Circular Agrobacterium tumefaciens Chromosome Chromosome Plasmid Plasmid 2842 2057 543 214 Circular Linear Circular Circular Borrelia burgdorferi Chromosome Plasmid (n = 11) 911 9–54 Linear Circular/Linear Brucella melitensis Chromosome Chromosome 2117 1178 Circular Circular Clostridium acetobutylicum Chromosome Plasmid 3941 192 Circular Circular Deinococcus radiodurans Chromosome Plasmid Plasmid Plasmid 2649 412 177 46 Circular Circular Circular Circular Ralstonia solanacearum Chromosome Chromosome? 3716 2095 Circular Circular Salmonella typhi Chromosome Plasmid Plasmid 4809 218 107 Circular Circular Circular Sinorhizobium meliloti Chromosome Plasmid Plasmid 3654 1683 1354 Circular Circular Circular Vibrio cholerae Chromosome Chromosome 2941 1072 Circular Circular Yersinia pestis Chromosome Plasmid (n = 3) 4654 10–96 Circular Circular Based on Bentley S.D. and Parkhill J. Annu. Rev. Genet. 38: 771–792, as adapted from Ohmachi M. 2002. Curr. Biol. 12: R427–428. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  6. 6. What is a Plasmid Chapter 7 • B A CT ER IA L A N D A R CH A EA L G E N TABLE 7.2. Plasmid functions Genetic Function of Plasmid Gene Functions Examples Resistance Antibiotic resistance Rbk plasmid of Escherichia coli and other bacteria Fertility Conjugation and DNA transfer F plasmid of E. coli Killer Synthesis of toxins that kill other bacteria Col plasmids of E. coli, for colicin production Degradative Enzymes for metabolism of unusual molecules TOL plasmid of Pseudomonas putida, for toluene metabolism Virulence Pathogenicity Ti plasmid of Agrobacterium tumefaciens, conferring the ability to cause crown gall disease on dicotyledonous plants Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  7. 7. Genome Size Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  8. 8. Eukaryotic genomes are bulky in part because they contain large numbers of repetitive DNA Size Genomeelements (Fig. 7.2). Common eukaryotic repetitive DNA elements include sim- Leishmania Arabidopsis major thaliana Guillardia theta Human Fern Eukaryotes Schizosac- Moss charomyces pombe Cockroach Paramecium tetraurelia Amoeba dubia Escherichia coli P. marius Bacteria Myxobacteria Bradyrhizobium japonicum Nanoarchaeum equitans Archaea Methanosarcina acetivorans 1 105 1 106 1 107 1 108 1 109 1 1010 1 1011 1 1012 1 1013 Number of base pairs FIGURE 7.1. Genome sizes in the three domains of life. A selection of genome sizes and size ranges from specific groups of organisms is indicated. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  9. 9. Gene Density Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  10. 10. Gene Density Chapter 7 • BA CT ERIA L A N D AR C H A EA L G EN E T A Human 0 10 20 30 40 50 kb 20 30 40 50 kb B Escherichia coli 0 10 KEY Gene Human pseudogene Repetitive DNA element FIGURE 7.2. Genome density. Comparison of the genome density and content of humans and Es- cherichia coli. Each segment is 50 kb in length and represents (A) a portion of the human β T-cell receptor locus and (B) a region of the E. coli K12 genome. Note the much greater proportion of genes (red boxes) in E. coli compared to humans. ple sequence repeats (e.g., microsatellites and minisatellites), gene duplications (both tandem arrays and pseudogenes), and transposable by Jonathan Eisen Winter 2014 elements. Although bacterial and arSlides for UC Davis EVE161 Course Taught
  11. 11. Number of genes Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  12. 12. DNA or selfish DNA. Number of Genes Junk DNA appears to provide little benefit or no function to the organism. (In some cases this designation is a misnomer resulting from a lack of infor30,000 25,000 Bacteria Eukaryotes Viruses Archaea Genes 20,000 15,000 10,000 5,000 0 105 106 107 108 Genome size 109 1010 FIGURE 7.3. Genome size vs. number of protein-coding genes. The number of genes is highly cor- related to genome size for bacteria, archaea, and viruses, but less so for eukaryotes. Many archaeal points (blue triangles) are hidden under bacterial ones (yellow squares). Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  13. 13. Gene Arrangement Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  14. 14. Operons O RI GI N AN D D I V E RSI F ICAT ION O F LIF E lacZ CAP site lacY lacA Operator Promoter -galactosidase Lactose permease transports lactose into the cell transacetylase split lactose to galactose + glucose CH2OH OH H OH H H CH2OH CH2OH H O H + O H H OH H OH Lactose H O OH H H OH OH H OH H H CH2OH O OH H H OH Galactose + H H OH OH H O OH H H OH Glucose FIGURE 7.4. Lac operon from Escherichia coli. This operon consists of three genes whose transcrip- tion is regulated by a single promoter. The genes encode proteins involved in utilizing lactose, including a permease (encoded by lacY), which brings lactose into the cell from the outside, and two enzymes (encoded by lacZ and lacA), which split lactose into glucose + galactose (see pp. 52–53). mation. Some stretches of “junk DNA” have been by Jonathan Eisenbe involved in gene regSlides for UC Davis EVE161 Course Taught determined to Winter 2014
  15. 15. Gene Content Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !15
  16. 16. Shared Genes Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !16
  17. 17. E. coli shared Genes A N D D IV ER SIF ICAT ION OF LIF E MG1655 (K-12) nonpathogenic CFT073 uropathogenic 193 585 1623 2996 514 204 FIGURE 7.7. Number of shared proteins be- 1346 EDL933 (0157:H7) enterohemorrhagic tween strains of Escherichia coli. Note the large number of genes found in one strain but not the others (seen in the outer portions of each circle). substantial variation in gene content among members of the same species have been reported in other lineages of bacteria and archaea. Thus, the diminishing number of core orthologous genes is simply an extension of something happening among close Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 relatives.
  18. 18. Gene Order Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  19. 19. Gene Order Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  20. 20. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  21. 21. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  22. 22. Origin of replication Terminus of replication Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  23. 23. Origin of replication Terminus of replication Artificially Open Circle Origin Terminus Origin Again UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 Slides for
  24. 24. Origin of replication Terminus of replication Artificially Open Circle Genome 2 O T O O Origin Terminus T Genome 1 Origin Again UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 Slides for O
  25. 25. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  26. 26. E. coli 0157:H7 A N D D I V E RSI FICAT ION O F LIF E Repeat Island Inversion E. coli K12 FIGURE 7.10. Conserved gene order in the backbone of Escherichia coli K12 and 0157:H7. The two genomes were aligned with each other and the matching regions were plotted. The conserved order of genes in the backbone of the two E. coli strains is indicated by the diagonal line. Three important genomic regions are circled. An island present in one of the two strains causes a slight shift in the position of the main diagonal. they also occur in virtually the same order in both strains (Fig. 7.10). The genes unique to each strain are clustered into “islands” interspersed among the stretches of common genes. Similar patterns of DNA “islands” within a conserved genome backbone have been found among other related bacteria or archaea. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 How do these islands originate? These are two possibilities: insertion of DNA into
  27. 27. Chapter 7 • BACT ERIA L A ND A RCHA EA L G ENET ICS AND H. pylori 26695 chromosome 1,667,867 1,600,000 1,200,000 FIGURE 7.11. The lack of conservation of 800,000 400,000 0 0 400,000 800,000 1,200,000 H. influenzae Rd chromosome 1,830,137 gene order between Haemophilus influenzae and Helicobacter pylori is illustrated. Linearized chromosomes of H. influenzae and H. pylori are plotted on the horizontal and vertical axes, respectively. Each dot represents a single pair of orthologous proteins. Genes in similar operons, which do exist, are too close together to give separated points on the scale used. mon is symmetric inversion around the origin of replication (Fig. 7.14). Such inversions are seen in almost every comparison of moderately closely related strains or species. Although other rearrangements occur, the symmetric inversions serve as a useful tool for understanding some features of general evolution and we focus on them here. Symmetric inversions around the origin are due to a combination of mutation bias and selection bias.Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 To understand how mutation bias could cause this, it is helpful to un-
  28. 28. cently replicated DNA, thereby causing an inversion. As the two replication forks should str S10 spc alpha L11 (rplK) L1 (rplA) L10 (rplJ) L7/L12 (rplL) rpoB rpoC unknown S12 (rpsL) S7 (rpsG) fusA tufA S10 (rpsJ) L3 (rplC) L4 (rplD) L23 (rplW) L2 (rplB) S19 (rpsS) L22 (rplY) S3 (rpsC) L16 (rplP) L29 (rpmC) S17 (rpsQ) L14 (rplN) L24 (rplX) L5 (rplE) S14 (rpsN) S8 (rpsH) L6 (rplF) L18 (rplR) S5 (rpsE) L30 (rpmD) L15 (rplO) secY adk map infA L36 (rpmJ) S13 (rpsM) S11 (rpsK) S4 (rpsD) rpoA L17 (rplQ) rpoBC Sinorhizobium meliloti Bacillus subtilis ? ? ? ? Borrelia burgdorferi Small SUr-protein genes Treponema pallidum Helicobacter pylori Large SUr-protein genes xxx Nonribosomal genes Escherichia coli ? Unknown genes Haemophilus influenzae Breakpoint Rickettsia prowazekii Gene insertion Mycoplasma sp. Aquifex aeolicus Rho-independent terminator S6 Missing gene Thermatoga maritima Deinococcus radiodurans Mycobacterium tuberculosis Chlamydia sp. Synechocystis S4 Archaea SUI1-X1 S-4E L32-L19 X2 cdk-L1--ccm-mms FIGURE 7.12. Conservation of gene order of ribosomal protein operons across bacterial and ar- chaeal species. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  29. 29. Gene Order Again Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  30. 30. V. cholerae vs. E. coli All 5000000 E. coli Coordinates 4000000 3000000 2000000 1000000 0 0 1000000 2000000 V. cholerae Coordinates Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 3000000 Eisen et al., 2000
  31. 31. V. cholerae vs. E. coli Best 5000000 E. coli Coordinates 4000000 3000000 2000000 1000000 0 0 1000000 2000000 V. cholerae Coordinates Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 3000000 Eisen et al., 2000
  32. 32. V. cholerae vs. E. coli, Rotated 5000000 E. coli ORF Coordinates 4000000 3000000 2000000 1000000 0 0 500000 1000000 1500000 2000000 2500000 V. cholerae ORF Coordinates Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 3000000 Eisen et al., 2000
  33. 33. Duplication and Gene Loss Model Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 Eisen et al., 2000
  34. 34. V. cholerae vs. E. coli
 Orthologs on Both Diagonals 5000000 E. coli ORF Coordinates 4000000 3000000 2000000 1000000 0 0 500000 1000000 1500000 2000000 2500000 V. cholerae ORF Coordinates Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 3000000 Eisen et al., 2000
  35. 35. C. trachomatis vs C. pneumoniae C. pneumoniae AR39 Origin Terminus C. trachomatis MoPn Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  36. 36. Symmetric Inversion Model A3 A2 32 1 2 30 31 3 29 4 28 5 27 6 26 7 25 8 24 9 23 10 22 11 21 12 20 13 19 14 18 17 16 15 A1 32 1 2 30 31 3 29 4 28 5 27 6 26 7 25 8 24 9 23 10 22 11 21 12 20 13 19 14 18 17 16 15 Common Ancestor of A and B B1 32 1 2 30 31 3 29 4 28 5 27 6 26 7 25 8 24 9 23 10 22 11 21 12 20 13 14 19 15 16 17 18 A1 A2 Inversion Around Terminus (*) * * 4 5 * 27 A2 26 25 24 23 22 21 20 Inversion Around Origin (*) A1 B1 B2 * A3 14 15 16 17 18 A3 A2 Inversion Around Terminus (*) 29 28 6 7 8 9 10 11 12 13 19 B3 B2 31 32 1 2 30 3 29 4 28 5 27 6 26 7 25 8 24 9 23 10 22 11 21 12 20 13 19 14 18 17 16 15 1 32 31 3 2 30 * 31 32 1 2 30 3 29 4 28 5 27 6 26 7 8 25 9 24 10 23 11 22 12 21 13 20 14 19 15 16 17 18 * B2 Inversion Around Origin (*) 3 29 28 27 26 8 9 10 11 12 13 14 * 2 1 32 31 30 * 4 B3 15 16 17 18 19 5 6 7 25 24 23 22 21 20 B3 B2 B1 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 Eisen et al., 2000
  37. 37. The X-Files Streps Pseudomonas B. subt vs. Staph 13623200 3000 9952000 2500 13622725 9950425 2000 Series1 9948850 Series1 13622250 1500 1000 9947275 13621775 500 9945700 0 0 2125 4250 6375 8500 M. tb vs. M. leprae 13621300 2632200 0 625 1250 1875 Pyrococcus 2632700 2633200 Mycobacterium tuberculosis 3000000 2000000 1000000 0 1000000 2000000 2634200 2634700 2635200 2635700 2636200 Thermoplasmas 4000000 0 2633700 2500 3000000 Mycobacterium leprae Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 2636700
  38. 38. Chapter 7 • BACT E RI AL AND ARCH AEAL G EN ET ICS AND G E NO MI CS 181 A A2 31 32 1 2 3 30 4 29 5 28 6 27 7 26 8 25 9 24 10 23 11 22 12 21 13 20 14 19 18 17 16 15 A1 31 32 1 2 3 30 4 29 5 28 6 27 7 26 8 25 9 24 10 23 11 22 12 21 13 20 14 19 18 17 16 15 Common ancestor of A and B A3 A1 Inversion around terminus (*) B1 31 32 1 2 3 30 4 29 5 28 6 27 7 26 8 25 9 24 10 23 11 22 12 21 13 20 19 14 15 16 17 18 A2 A2 Inversion around origin (*) B2 A1 3 4 27 26 25 24 23 22 21 20 20 14 B1 Inversion around terminus (*) A3 15 16 17 18 29 28 6 7 8 9 10 11 12 13 19 B3 A2 31 32 1 2 3 30 4 29 5 28 6 27 7 26 8 25 9 24 10 23 11 22 12 21 13 20 14 19 18 17 16 15 2 1 32 31 30 A3 31 32 1 2 3 30 4 29 5 28 6 27 7 26 8 25 9 24 10 23 11 22 12 21 13 20 14 19 18 17 16 15 B2 B2 Inversion around origin (*) 3 29 28 27 26 8 9 10 11 12 13 14 2 1 32 31 30 4 B3 15 16 17 18 19 5 6 7 25 24 23 22 21 20 B3 B1 B2 C Escherichia coli V. parahaemolyticus chromosome I B V. cholerae chromosome I V. cholerae chromosome I FIGURE 7.14. X-alignments. (A) Schematic model of symmetric genome inversions. The model shows an initial speciation event, followed by a series of inversions in the different lineages (A and B). Inversions occur between the asterisks (*). Numbers on the chromosome refer to hypothetical genes 1–32. At time point 1, the genomes of the two species are still colinear (as indicated in the scatterplot of A1 vs. B1). Between time point 1 and time point 2, each species (A and B) undergoes a large inversion about the terminus (as indicated in the scatterplots of A1 vs. A2 and B1 vs. B2). This results in the between-species scatterplot looking as if there have been two nested inversions (A2 vs. B2). Between time point 2 and time point 3, each species undergoes an additional inversion (as indicated in the scatterplots of B2 vs. B3 and A2 vs. A3). This results in the between-species scatterplots beginning to resemble an X-alignment. (B) X-like alignment in dotplot of the main chromosomes of Vibrio cholerae (x-axis) and Vibrio parahaemolyticus (y-axis). (C) A weak X-like pattern exists even when comparing more distantly related species, in this case V. cholerae and E. coli. An X-like pattern indicates that the distance of a gene from the origin is conserved, but the side of the origin on which it is located is not conserved. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  39. 39. Gene Loss bolA tig clpP clpX a hupB ybaU ybaX ybaW ybaV ybaE BA CT E R I A L A N D A R C H A EA L G EN E T I CS A ND G E ybaO cof • mdlA mdlB amtB tesB ginK RNA-ffs ybaZ ybaY acrB acrR acrA aefA recR ybaB dnaX apt ybaN priC ybaM htpG adk Chapter 7 Ancestor Buchnera 10 kb FIGURE 7.5. Genome reduction in Buchnera endosymbionts of aphids. A fragment of two genomes is shown. (Top row) The putative ancestor of all aphid endosymbionts in the Buchnera genus. (Bottom row) The genome of the symbionts today. The massive amounts of gene loss are indicated by the genes colored white in the ancestral genome that are missing from the modern genome below. Orthologous genes between the two genomes are shown in the same color. Note the conservation of gene order between the two genomes despite the gene loss. The direction of gene transcription is indicated by the gene box being shifted above or below the black line. ple, B. aphidicola APS has undergone a massive reduction in its genome since it shared a common ancestor with E. coli (Fig. 7.5). This symbiont lives inside aphid cells where many genes required for the free-living lifestyle of E. coli are not needed. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  40. 40. Gene Duplication Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  41. 41. Why Duplications Are Useful to Identify • Allows division into orthologs and paralogs ! • Improves functional predictions ! • Helps identify mechanisms of duplication ! • Can be used to study mutation processes in different parts of a genome ! • Lineage specific duplications may be indicative of species’ specific adaptations Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  42. 42. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  43. 43. C. pneumoniae - All Paralogs 1250000 Subject Orf Position 1000000 750000 500000 250000 0 0 250000 500000 750000 Query Orf Position 1000000 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 1250000
  44. 44. C. pneumoniae Lineage-Specific Paralogs 1250000 Subject Orf Position 1000000 750000 500000 250000 0 0 250000 500000 750000 Query Orf Position 1000000 Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 1250000
  45. 45. Expansion of MCP Family in V. cholerae NJ ** ** V.cholerae VC0512 V.cholerae VCA1034 V.cholerae VCA0974 V.cholerae VCA0068 ** V.cholerae VC0825 * V.cholerae VC0282 V.cholerae VCA0906 V.cholerae VCA0979 V.cholerae VCA1056 V.cholerae VC1643 V.cholerae VC2161 V.cholerae VCA0923 ** V.cholerae VC0514 ** V.cholerae VC1868 V.cholerae VCA0773 V.cholerae VC1313 V.cholerae VC1859 V.cholerae VC1413 V.cholerae VCA0268 V.cholerae VCA0658 ** V.cholerae VC1405 V.cholerae VC1298 * V.cholerae VC1248 V.cholerae VCA0864 V.cholerae VCA0176 V.cholerae VCA0220 ** V.cholerae VC1289 V.cholerae VCA1069 ** V.cholerae VC2439 V.cholerae VC1967 V.cholerae VCA0031 V.cholerae VC1898 V.cholerae VCA0663 V.cholerae VCA0988 V.cholerae VC0216 V.cholerae VC0449 * V.cholerae VCA0008 V.cholerae VC1406 V.cholerae VC1535 V.cholerae VC0840 B.subtilis gi2633766 Synechocystis sp. gi1001299 Synechocystis sp. gi1001300 * Synechocystis sp. gi1652276 * Synechocystis sp. gi1652103 * H.pylori gi2313716 ** H.pylori99 gi4155097 C.jejuni Cj1190c ** C.jejuni Cj1110c A.fulgidus gi2649560 A.fulgidus gi2649548 ** B.subtilis gi2634254 B.subtilis gi2632630 B.subtilis gi2635607 B.subtilis gi2635608 ** B.subtilis gi2635609 ** ** B.subtilis gi2635610 B.subtilis gi2635882 E.coli gi1788195 E.coli gi2367378 ** E.coli gi1788194 * E.coli gi1787690 V.cholerae VCA1092 V.cholerae VC0098 E.coli gi1789453 H.pylori gi2313186 H.pylori99 gi4154603 ** C.jejuni Cj0144 C.jejuni Cj1564 ** C.jejuni Cj0262c ** C.jejuni Cj1506c H.pylori gi2313163 * H.pylori99 gi4154575 ** H.pylori gi2313179 ** ** H.pylori99 gi4154599 C.jejuni Cj0019c C.jejuni Cj0951c C.jejuni Cj0246c B.subtilis gi2633374 T.maritima TM0014 V.cholerae VC1403 V.cholerae VCA1088 T.pallidum gi3322777 T.pallidum gi3322939 ** T.pallidum gi3322938 ** B.burgdorferi gi2688522 T.pallidum gi3322296 B.burgdorferi gi2688521 * T.maritima TM0429 ** T.maritima TM0918 ** T.maritima TM0023 * T.maritima TM1428 T.maritima TM1143 T.maritima TM1146 P.abyssi PAB1308 P.horikoshii gi3256846 ** P.abyssi PAB1336 ** P.horikoshii gi3256896 ** P.abyssi PAB2066 ** P.horikoshii gi3258290 ** * P.abyssi PAB1026 P.horikoshii gi3256884 ** D.radiodurans DRA00354 D.radiodurans DRA0353 ** D.radiodurans DRA0352 ** V.cholerae VC1394 P.abyssi PAB1189 P.horikoshii gi3258414 ** B.burgdorferi gi2688621 M.tuberculosis gi1666149 V.cholerae VC0622 Heidelberg et al. (2000) Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
  46. 46. After the Genomes • Better analysis and annotation • Comparative genomics • Functional genomics (Experimental analysis of gene function on a genome scale) • Genome-wide gene expression studies • Proteomics • Genome wide genetic experiments Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014

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