8_22genomesho

7/31/2019 8_22genomesHO

http://slidepdf.com/reader/full/822genomesho 1/10

1

The The Structure and Organization of Genomes Structure and Organization of Genomes

Genome = The totality of DNA in a cell.

—ome = the full set of <something > in

the cell or genome of an organism

… and new ‘omes are still being defined

The The Structure and Organization of Genomes Structure and Organization of Genomes

Genome: The totality of DNA in a cell.

Chromosome: Continuous threads of DNA in a cell or nucleus

Karyotype: Chromosome complement an of individual (often photographed at

metaphase showing the chromosomes arranged by size).

7/31/2019 8_22genomesHO


2

The Structure and Organization of Genomes The Structure and Organization of Genomes





1. DNA of eukaryotes is contained in a membrane-

bound nucleus

2. Eukaryotes contain other membrane-bound

organelles (mitochondria, chloroplast, Golgi)

3. Prokaryotes have a rigid plasma membrane

whereas eukaryotes have a semi-permeable

membrane with an internal cytoskeleton.

Prokaryotic vs . Eukaryotic Genomes

Domains of Life (groups above Kingdoms): Archaea, Bacteria, Eukaryotes

The Structure and Organization of Genomes The Structure and Organization of Genomes





Prokaryotic vs . Eukaryotic Genomes

Domains of Life (groups above Kingdoms): Archaea, Bacteria, Eukaryotes

Archaea

Bacteria

Eukaryotes

7/31/2019 8_22genomesHO


3

Features of some sequenced genomes Features of some sequenced genomes

Species Genome size (mb) # of Genes

Eukaryotes (41, up from 37 last year )

Arabidopsis thaliana 125 25,500

Caenorhabditis elegans 97 19,000

Drosophila melanogaster 108 13,600

Homo sapiens 3200 32,000

Saccharomyces cerevisiae 12 5,800

Bacteria (341, up from 233 last ye ar )

Escherichia coli 4.64 4,400

Mycobacterium tuberculosis 4.41 4,000

Mycoplasma genitalium 0.58 500

Pseudomonas aeruginosa 6.26 5,700

Streptococcus pneumoniae 2.16 2,300

Vibrio cholerae 4.03 4,000

Yersinia pestis 4.65 4,100

Archaea (27, up from 23 last year ) Archaeglobus fulgidus 2.18 2,500

Methanococcus jannaschii 1.66 1750

Nanoarchaeum equitans 0.49 550

Plus there are 976 “ongoing” bacterial genome sequencing projects,629 eukaryotic & 57 archaeal (and 50+ “metagenomic” datasets)

Sizes (C-values) of assorted genomes

Species Genome size (kb)

Navicola pelliculosa (diatom) 35,000

Drosophila melanogaster (fruitfly) 180,000

Parameciumaurelia (ciliate) 190,000

Gallus domesticus (chicken) 1,200,000

Cyprinus carpio (carp) 1,700,000

Boa constrictor (snake) 2,100,000

Rattus norvegicus (rat) 3,100,000

Xenopus laevis (toad) 3,100,000

Homo sapiens (bubba) 3,200,000

Nicotiana tabaccum (tobacco) 3,800,000

Paramecium caudatum (cilate) 8,600,000

Allium cepa (onion) 18,000,000

Lilium formosanum (lily) 36,000,000

Amphiuma means (newt) 68,000,000

Pinus resinosa (pine) 84,000,000

Protopterus aethiopicus (lungfish) 140,000,000

Ophioglossum petiolatum (fern) 160,000,000

Amoeba dubia 670,000,000

What is the source of the variation in genome sizes?

7/31/2019 8_22genomesHO


4

Foldback DNA

Highly Repetitive DNA

Middle Repetitive

Single copy DNA

C o t curves can show the nature of sequences in a genome

DNA is purified, sheared and melted into single strands, and then allowed to

renature by gradual cooling. % of reassociated dsDNA (y-axis) is shown as afunction of the product of DNA concentration and time (x-axis)

Determining the relative amounts of repetitive & scDNA via C ot curves

Species C value (gb) %scDNA

Tetrahymena pyriformis 0.2 90

Aplysia californica 1.8 55

Drosophila melanogaster 0.2 60

Limulus polyphemus 2.7 70Gallus domesticus (chicken) 1.2 80

Ciona intestinalis 0.2 70

Bufo bufo 6.9 20

Xenopus laevis 3.1 75

Mus musculus 3.4 70

Homo sapiens (bubba) 3.4 64

7/31/2019 8_22genomesHO


5

Classes of Repetitive Elements in Eukaryotes

Highly repetitive: long rows of short repeats (100s bp, 10000s of copies)

Middle repetitive : longer repeats, tandem/dispersed, some transpose (1000s bp)

Mini- or Microsatellites : few tandem copies of simple sequence repeats (10s bp)

Gene & segmental duplications : multiple copies of genes/regions that have acommon ancestry (related function, multigene family) (up to 100000s bp)

Types of Repetitive Elements Prevalent in Mammalian Genomes

Classes & Ages of Repetitive Elements in Mickey & Bubba

How might it be possible to determine the age of repetitive elements in a genome?

7/31/2019 8_22genomesHO


6

Have any functions been ascribed to this large non-coding fraction?

1. Correlation between C-value and (i ) duration of meiosis and mitosis, (ii )

metabolic rate, (iii ) generation time, (iv ) development time in lizards, seed sizeand CO2 response in plants, morphological complexity in amphibian brains

2.Genome architecture, e.g ., for the spacing and regulation of genes

3. “Junk” DNA with no function (Ohno 1972)

4. “Selfish” DNA, which is actively maintained by intragenomic selection

How do the copy numbers of repeats increase?

1. “Passive” processes: unequal crossing over; replication slippage

2. “Active” processes by transposable elements: replicative transposition(via a DNA intermediate); retrotransposition (via an RNA intermediate)

Types of genome-wide repeats in the human genome (adapted from Brown, Table 1.2 )

Type of Repeat Subtype Number of Copies

SINES Alu 1,190,000

100 – 300 bp MIR 393,000

GC-rich, No RT MIR3 75,000

LINES LINE-1 516,000

3 – 5 kb LINE-2 315,000

AT-rich LINE-3 37,000

LTR elements ERV class 1 112,000

Retrotransposons EVR(K) 8,000

Encode RT EVR(L) 83,000

MaLR 240,000

DNA transposons hAT 195,000

Tc-1 75,000

PiggyBac 2000

_____________________________________________________________

7/31/2019 8_22genomesHO


7

Contents of a eukaryotic genome (adapted from Page & Holmes, Molecular Evolution , 1998)

Coding DNA

Single copy genes

Regulatory sequences

Multigene families

Transposons (& retroelements)

Spacer DNA (& non-coding within genes)

Non-coding DNA

Tandem repeats

Multicopy RNA genes Tandem

Dispersed

Satellite

Microsatellites

Minisatellites

Large scale expansions in eukaryotic genomes: multigene families & segmental duplications

Are eukaryotic genomes ever-expanding?

Are there any limits to genome size?

What are the determinants of overall genome size?

7/31/2019 8_22genomesHO


8

Bacteria differ from eukaryotes in genome organization and in having very little repetitive DNA

Figure 2.2 from Brown, page 34

Human

Fruit fly

Maize

E. coli

Yeast

Structure and Organization of Genomes: Chromosomes

Chromosome features:

• Number (variation among species)• Size (variation within genome)• Centromere Position (p,q arms)• Variable (orange) regions (within species)• Banding patterns (G,R,Q,C)

7/31/2019 8_22genomesHO


9

Structure and Organization of Genomes: Isochores

Structure and Organization of Genomes: Isochores

________________________________________________

Fraction % GC % Genomea

% Genes Gene densityb

________________________________________________

L1 38% 30% —} 34% 1 per 100 kb

L2 41% 32% —

H1 44% 21% —} 38% 1 per 50 kb

H2 49% 10% —

H3 53% 3% 39% 1 per 6.4 kb ________________________________________________

aRemaining portion of the genome corresponds to satellite and

ribosomal sequences.b Calculations were based on a 3 gigabase genome containing50,000 (!?!) genes.

7/31/2019 8_22genomesHO


10

Organellar Genomes

Species Size (kb) # Genes

Mitochondria

Plasmodium falciparum (protozoan) 6 5

Chlamydomonas reinhardtii (alga) 16 12

Mus musculus (mouse) 16

Homo sapiens (human) 17 37

Drosophila melanogaster (fruitfly) 19

Aspergillus nidulans (fungus) 33

Reclinomonas americiana (protozoan) 69 92

Saccharomyces cerevisiae (yeast) 75 35

Brassica oleracea (cabbage) 160

Arabidopsis thaliana (vetch) 367 52

Zea mays (corn) 570

Cucumis melo (melon) 2500

Chloroplast

Pisum sativum (pea) 120

Pryza sativa (rice) 136

Nico tabacum (tobacco) 156

Chlamydomonas reinhardtii (alga) 195

8_22genomesho

Documents