introduction to genomics and the tree of life friday, october 22, 2010 (part 1) monday, october 25,...

Introduction to Genomics and the Tree of Life

Friday, October 22, 2010 (part 1)Monday, October 25, 2010 (part 2)

Genomics260.605.01J. Pevsner

[email protected]

Many of the images in this powerpoint presentationare from Bioinformatics and Functional Genomics, 2nd edition by J Pevsner (© 2009 by Wiley-Blackwell).

These images and materials may not be used without permission from the publisher (instructors, email me at [email protected]).

Visit http://www.bioinfbook.org

Copyright notice

We meet 3 times a week, from 10:30 to 11:50 am:

W4013 (lecture/discussion and occasional computer lab)

Announcements: where/when we meet

Textbook: Bioinformatics and Functional Genomics (2nd edition, Wiley-Blackwell, 2009) by J. Pevsner, ISBN 978-0-470-08585-1.

• We’ll cover chapters 13-20 in this course• For those who don’t want to buy a copy, I will share pdfs of

all the chapters with the class• You can buy a copy at the website www.bioinfbook.organd get a nice discount ($80). It’s $80 at Amazon.com.• The JHU bookstore may have copies.• Welch Library may have copies

Book’s website: www.bioinfbook.orgCourse website: http://www.bioinfbook.org/genomics.php or visit www.bioinfbook.org/chapter 13

Announcements: book, website

Outline of this course

Introduction to genomicsVirusesBacteria and archaea (Egbert Hoiczyk)Eukaryotes

The eukaryotic chromosomeFungi; yeast functional genomics (Jef Boeke)Protozoans (David Sullivan)Nematodes (Al Scott)Mosquitoes (George Dimopoulos)Rodents: mouse and ratPrimatesThe human genome (Dave Valle)Human disease

Outline of today’s lecture

Introduction: 5 perspectives, history of life

Genome-sequencing projects: chronology

Genome analysis: criteria, resequencing, metagenomics

DNA sequencing technologies: Sanger, 454, Solexa

Process of genome sequencing: centers, repositories

Genome annotation: features, prokaryotes, eukaryotes

Five approaches to genomics

As we survey the tree of life, consider these perspectives:

Approach I: cataloguing genomic informationGenome size; number of chromosomes; GC

content; isochores; number of genes; repetitive DNA; unique features of each genome

Approach V: Bioinformatics aspectsAlgorithms, databases, websites

Approach IV: Human disease relevance

Approach III: function; biological principles; evolutionHow genome size is regulated; polyploidization; birth and death of genes; neutral theory of

evolution; positive and negative selection; speciation

Approach II: cataloguing comparative genomic informationOrthologs and paralogs; COGs; lateral gene transfer

Page 519

Two projects for this course

Option [1] Select a genome and describe it in detail.

Option [2] Select a gene and describe it in detail.

For each, follow the five approaches just outlined, and apply the principles that we learn in this course.

Reading: Webb Miller et al. (2004) Comparative genomics

IntroductionLessons learned form comparative genomics What have we learned about genes by comparing genomic

sequences? What have we learned about regulation? About 5% of the human genome is under purifying selection Positively regulated regions Mechanisms and history of mammalian evolution Nonuniformity of neutral evolutionary rates within species Nonuniformity of evolution along the branches of phylogenyLearning more form existing data Choice of species Choice of toolsFuture of comparative genomics

Levels of analysis in genomics

level topics databasesDNA genes, chromosomes GenBankRNA ESTs, ncRNA UniGene, GEOprotein ORFs, composition UniProtcomplexes binary, multimeric BINDpathways COGs, KEGGorganellesorgansindividuals variation and disease HapMapspecies speciation TaxBrowser; SGDgenus JAX mouse phylum FishBasekingdom TOL

Definitions of terms

Genomics is the study of genomes (the DNA comprising an organism) using the tools of bioinformatics.

Bioinformatics is the study protein, genes, and genomes using computer algorithms and databases.

Systematics is the scientific study of the kinds and diversity of organisms and of any and all relationships among them.

Classification is the ordering of organisms into groups on the basis of their relationships. The relationships may be evolutionary (phylogenetic) or may refer to similarities of phenotype (phenetic).

Taxonomy is the theory and practice of classifying organisms.


Introduction: 5 perspectives, history of life: trees






Fig. 13.1Page 521

Pace (2001) described a tree of life based on small subunit rRNA sequences.

This tree shows the mainthree branches describedby Woese and colleagues.

Ernst Haeckel (1834-1919), a supporter of Darwin,published a tree of life (1879) including Monera(formless clumps, later named bacteria).

Introduction: Systematics

Page 520

plants

animals

monera

fungi

protistsprotozoa

invertebrates

vertebrates

mammalsFive kingdom

system(Haeckel, 1879)

Page 516

Chatton (1937) distinguished prokaryotes (bacteriathat lack nuclei) from eukaryotes (having nuclei).

Whittaker (1969) and others described the five-kingdomsystem: animals, plants, protists, fungi, and monera.

In the 1970s and 1980s, Carl Woese and colleaguesdescribed the archaea, thus forming a tree of lifewith three main branches: archaea, bacteria, eukaryotes.

Introduction: Systematics

Page 520

Whittaker RH (1969) New concepts of kingdoms or organisms. Evolutionary relations are better represented by new classifications than by the traditional two kingdoms. Science. 163(863):150-60.

Whittaker (1969): The two-kingdom system as it might have appeared in the early 1900s

Plantae Animalia


The Copeland four-kingdom system of the 1930s-1950s

Monera

Metaphyta

Metazoa

Protoctista

Pro

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Un

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Whittaker (1969): The five-kingdom system

Plantae Fungi Animalia

Monera

Protista

Levels:prokaryotic (Monera)eukaryotic unicellulareukaryotic multicellular

Historically, trees were generated primarily usingcharacters provided by morphological data. Molecularsequence data are now commonly used, includingsequences (such as small-subunit RNAs) that arehighly conserved.

Visit the European Small Subunit Ribosomal RNAdatabase for 20,000 SSU rRNA sequences.

Molecular sequences as basis of trees

Page 523

Pace (2001) described a tree of life based on small subunit rRNA sequences.

This tree shows the mainthree branches describedby Woese and colleagues. It is the best currently accepted model of the tree of life.

Fig. 13.1Page 521

http://www.zo.utexas.edu/faculty/antisense/Download.html

Tree of life from David Hillis’ lab (based on ~3000 rRNAs)

animalsplants

fungi

protists

bacteriaarchaea

you are here

10-10

http://www.zo.utexas.edu/faculty/antisense/Download.html

you are here

Tree of life from David Hillis’ lab (based on ~3000 rRNAs)

10-10

Ribosomal RNA Database

Ribosomal Database Projecthttp://rdp.cme.msu.edu/index.jsp

Santos, S. R. and Ochman H. Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environmental Microbiology. 2004. Jul(6)7:754-9.

►Download fusA (translation elongation factor 2 [EF-2])►Obtain DNA in the fasta format►Align by ClustalW in MEGA►Create a neighbor-joining tree

Page 524

10-10

European Small Subunit Ribosomal RNA database(http://www.psb.ugent.be/rRNA/ssu/) 10-10

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Lactococ lactis Il1403 fusA

Strep agalactiae NEM316 fusA

Strep agalactiae 2603VR fusA

Strep pneumoniae R6 fusA

Strep pneumoniae TIGR4 fusA

Strep pyogenes M1 GAS fusA

Strep pyogenes MGAS8232 fusA

Strep pyogenes MGAS315 fusAStrep pyogenes SSI1 fusAOnion yel phytoplasm OYM fusAMycoplas mobile 163K fusAMycoplas pulmonis UAB CTIP fusAMycoplas mycoides PG1 fusA

Mycoplas penetrans HF2 fusA

Ureaplasma parvum 700970 fusA

Mycoplas galli R fusA

Mycoplas genita G37 fusA

Mycoplas pneumon M129 fusA

Thermoanaero tengcongensis fusA

Fuso nucleatum ATCC25586 fusA

Clost perfringens 13 fusA

Clost acetobutylicum 824 fusA

Clost tetani E88 fusA

Parachlamydia UWE25 fusA

Chlamy muridarum fusA

Chlamy tracho DUW3CX fusA

Chlamydo caviae GPIC fusA

Chlamydo pneumon J138 fusA

Chlamydo pneumon CWL029 fusA

Chlamydo pneumon AR39 fusA

Chlamydo pneum

on TW183 fusA

Prochloro marinus CCM

P1375 fusA

Prochloro marinus CCM

P1986 fusA

Nostoc PCC7120 fusA

Synechocystis PCC6803 fusA

Gloeo violaceus PC

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Thermosynecho elongatus BP1 fusA

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E coli CFT073 fusA

E coli K12 fusA

Shigella flexneri 2457T fusA

Shigella flexneri 301 fusA

Lepto inter lai 56601 fusA

Lepto inter Copen Fio L1130 fusA

Pirellula 1 fusA

Aquifex aeolicus fusA

Thermotoga maritima MSB8 fusA

Bacteroides thetaio VPI5482 fusA

Porphyro gingiv W83 fusA

Geo sulfur PCA fusAChloro tepidum TLS fusA

Bordet bronchi RB50 fusABordet pertussis TohamaI fusABordet parapert 12822 fusARalstonia solan GMI1000 fusA

Chromo violaceum 12472 fusA

Xanthomonas axonopodis 306 fusA

Xanthomonas campestris 33913 fusA

Pseudo aeruginosa PA01 fusA

Pseudo putida KT2440 fusA

Pseudo syringae DC3000 fusA

Desulfo vulgaris Hilden fusA

Agro tumefaciens C58 fusA

Sinorhiz meliloti 1021 fusA

Mesorhiz loti MAFF303099 fusA

Bruc suis 1330 fusA

Caulo crescentus CB15 fusA

Bradyrhiz japonicum USDA110 fusA

Rhodopseudo palustris CGA009 fusA

Deino radiodurans R1 fusA

Thermus therm

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Coryne efficiens YS314 fusA

Coryne gluta 13032 fusA

Coryne diphtheriae N

CTC

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Bifido longum

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Mycobac avium

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Mycobac bovis A

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Neighbor-joining tree of ~150 fusA (GTPase) DNA sequences

Fig. 15.1Page 603

Eukaryotes(Baldauf et al. 2000)

Fig. 18.1Page 730


Introduction: 5 perspectives, history of life: time lines






History of life on earth

4.55 BYA formation of earth (violent 100 MY period)4.4-3.8 BYA last ocean-evaporating impacts3.9 BYA oldest dated rocks3.8 BYA sun brightened to 70% of today’s luminosity

Ammonia, methane, or carbon dioxide atmosphere.Earliest life: RNA, protein

Source: Schopf J.W. (ed.), Life’s Origins (U. Calif. Press, 2002) Page 521

History of life on earth: two major eons

Source: Schopf J.W. (ed.), Life’s Origins (U. Calif. Press, 2002)

Precambrian eon Phanerozoic eon

Extends from the formation of the planetto the appearance of fossils of hard-shelled animals 550 MYA

From Cambrian explosion to the present

1 BYA234

4 3 2 1 0

Billions of years ago (BYA)

Origin oflife

Origin ofeukaryotes insects

Fungi/animalPlant/animal

Hadean eon

Archean eon Proterozoic eon Phanerozoic eon

Earliestfossils

Page 522

1000 100 0500

InsectsCambrianexplosion

Age of Reptiles ends

Land plants

Proterozoic eon Phanerozoic eon

deuterostome/protostome

echinoderm/chordate

Millions of years ago (MYA)

Page 522


Dinosaurs extinct;Mammalian radiation

Human/chimpdivergence

100 10 050

Mass extinction

Page 522


Homo sapiens/Chimp divergence

Emergence ofHomo erectus

Earlieststone tools

10 1 05

AustralepithecusLucy

Page 522

Homo erectusemerges in Africa

MitochondrialEve

1,000,000 100,000 0500,000

Years ago

Page 523

Years ago

Neanderthal and Homo erectus disappear

Emergence ofanatomically

modern H. sapiens

100,000 10,000 050,000

Page 523

Years ago

“Ice Man”from Alps Aristotle

10,000 1,000 05,000

Earliestpyramids

Page 523

Years ago

algebra calculusDarwin,MendelGutenberg

1,000 100 0500

Page 523

Today’s continents derive from earlier land masses (Laurasia, Gondwana), affecting evolution of species

We will next summarize the major achievements ingenome sequencing projects from a chronologicalperspective.

Chronology of genome sequencing projects

Page 525

1976: first viral genomeFiers et al. sequence bacteriophage MS2 (3,569 base pairs,Accession NC_001417).

1977:Sanger et al. sequence bacteriophage X174.This virus is 5,386 base pairs (encoding 11 genes).See accession J02482; NC_001422.


Page 527

Fig. 13.5Page 528

Entrez nucleotide record for bacteriophage X174 (graphics display)

1981Human mitochondrial genome16,500 base pairs (encodes 13 proteins, 2 rRNA, 22 tRNA)Today (10/10), over 2200 mitochondrial genomes sequenced

1986Chloroplast genome 156,000 base pairs (most are 120 kb to 200 kb)


Page 527

mitochondrion

chloroplast

Lackmitochondria (?)

http://www.ncbi.nlm.nih.gov/genomes/ORGANELLES/organelles.html

Entrez Genomes organelle resource at NCBI

10-10

There are ~2500 eukaryotic organelles (10/10)

http://www-lecb.ncifcrf.gov/mitoDat/

MitoDat: resource for organelle genomes

“This database is dedicated to the nuclear genes specifying the enzymes, structural proteins, and other proteins, many still not identified, involved in mitochondrial biogenesis and function. MitoDat highlights predominantly human nuclear-encoded mitochondrial proteins.”

Not updated recently.

10-10

http://www.mitomap.org/

MitoMap: resource for organelle genomes

10-10

It is possible to map mutations in human mitochondrial DNA that are responsible for disease

1995: first genome of a free-living organism, the bacterium Haemophilus influenzae


Page 530

1995: genome of the bacterium Haemophilus influenzae is sequenced

Fig. 13.7Page 531

How to find information about a genome: NCBI All databases Genome follow link to Bacteria

Overview of bacterialcomplete genomes(2000) n=30

Overview of bacterialcomplete genomes(2010) n=3,330

Fig. 12.9Page 411

You can find functionalannotation through theCOGs database

(Clusters ofOrthologousGenes)

Click the circle to access the genomesequence

You can find functionalannotation through theCOGs database (Clusters ofOrthologous Genes)

Entrez Genome view of H. influenzae (October 2009)

Click the circle to access the genomesequence

Genes are color-codedaccording to theCOGs scheme

1996: first eukaryotic genome

The complete genome sequence of the budding yeastSaccharomyces cerevisiae was reported. We willdescribe this genome soon.

Also in 1996, TIGR reported the sequence of the firstarchaeal genome, Methanococcus jannaschii.


Page 532

1996: a yeast genome is sequenced

To learn about a genome of interest, visit NCBI TaxBrowser Genome Projects

To learn about a genome of interest, follow theTaxBrowser Genome Projects links

Size (in megabases), number of chromosomes are given here

To place the sequencingof the yeast genomein context, these are theeukaryotes…

Tree of eukaryotes(Baldauf et al. 2000)

Fungi

1997:More bacteria and archaeaEscherichia coli4.6 megabases, 4200 proteins (38% of unknown function)

1998: first multicellular organismNematode Caenorhabditis elegans 97 Mb; 19,000 genes.

1999: first human chromosomeChromosome 22 (49 Mb, 673 genes)


Page 532

See the article by Webb Miller et al. (2004), “Comparative genomics” for a discussion of annotation and analysis progress made since 1998

1999: Human chromosome 22 sequenced

1999: Human chromosome 22 sequenced

49 MB701 genes

2000:Fruitfly Drosophila melanogaster (13,000 genes)

Plant Arabidopsis thaliana

Human chromosome 21

2001: draft sequence of the human genome(public consortium and Celera Genomics)


Page 534

To explore human chromosome 21 at NCBIFind MapViewerChoose humanClick chromosome 21

2001 draft human genome sequence2002 S. pombe (just 4,800 genes)2004 “finished” human genome2007 first individual human genome2009 1000 Genomes Project

Outline of Monday’s lecture (Chapter 13)







introduction to genomics and the tree of life friday, october 22, 2010 (part 1) monday, october 25,...

Documents

form comparative genomics

sequencing projects

genomic sequences

copiesbooks website

history of lifegenome

purifying selection

j pevsner

eukaryotesfive approaches