HAPLOID GENOME SIZES
(DNA PER HAPLOID CELL)
Size range Example species
BACTERIA 1-10 Mb
E. coli:
FUNGI
10-40 Mb
S. cerevisiae
INSECTS 100-5000 Mb D. melanogaster
BIRDS 1000-1500 Mb Chicken
FLOWERING 100 to
Arabidopsis
PLANTS 100,000 Mb
Corn
MAMMALS 3000-4000 Mb Human
Ex. Size
4.639 Mb
13 Mb
165 Mb
1300 Mb
120 Mb
2500 Mb
3000 Mb
1 Mb = 1 million base pairs. (Probably the number of
essential genes does not differ greatly among various
multicellular organisms. Most estimates are that
humans have about 40,000 genes.)
KEY DIFFERENCES IN
PROKARYOTIC VS. EUKARYOTIC
GENOMES:
SIZE: Haploid human genome ~700 X E.
coli genome
GENE NO.: Human genome has ~10 X the
genes of E. coli
MULTIPLE LINEAR CHROMOSOMES
DIPLOID (2n) FOR MOST OF LIFE
CYCLE
DIFFERENT SEXUAL CYCLE = MEIOSIS
2n chromosomes segregate during meiosis (each
pair segregates independently of the other pairs)to
generate haploid (n) germ cells. Germ cells unite to
form 2n zygote/organism. In addition to the genetic
reassortment of different chromosome pairs,
additional reassortment arises from recombination
between the two chromosomes of each pair
DIFFERENT PHENOTYPES OF MOST INTEREST
(e.g., complex developmental, behavioral, etc., traits
for which there often is no obvious biochemical
explanation via a known enzyme or gene.
EUKARYOTIC GENOMES CONSIST OF
VARIABLE AMOUNTS OF 3 CLASSES OF DNA
A. Single copy or unique DNA sequences:
present once per haploid genome.
B. Moderately repetitive DNA: present in 10-1000
copies per haploid genome
C. Highly repetitive DNA: present in thousands of
copies per haploid genome;
GENOME MAPS: Genome maps allow us to understand the
specific arrangment of genes and other sequences on each
chromosome of a given species. This is important when we wish
to relate one gene or landmark to another in the genome.
Genome maps are of 4 major types.
A. GENETIC: measures distances between genes by the
RECOMBINATION FREQUENCY between Mendelian genetic
markers
B. CYTOLOGICAL (or cytogenetic): measures distances
between VISIBLE BANDS OR STAINED REGIONS found in
chromosome KARYOTYPES
C. RADIATION HYBRID: measures distances between markers
according to the likelihood of a radiation-induced chromosome
break between them
D. PHYSICAL: measures distances between genetic elements
in terms of the LENGTH OF DNA between them.
GENETIC LINKAGE MAPPING
A. POLYMORPHISM: In order to map genes, one
must have at least two different alleles for any given
gene and the two alleles must give rise to an observable
phenotype. This difference is called
POLYMORPHISM. Three of these polymorphic
assays will be discussed further:
B. RFLP, Restriction Fragment Length
Polymorphism
C. STSs (SEQUENCE TAGGED SITE) A short
region of DNA whose sequence is known, so that it can
be amplified by PCR; may contain sequence
polymorphisms.
One particularly useful type of STS is the
microsatellite marker. A microsatellite is an STS
which contains a tandem repeat of a very simple DNA
sequence, e.g., (CA)n. Because errors are made in
replicating such sequences the “n” often varies from one
individual to another (i.e., it is polymorphic.)
D. SNPs (Single Nucleotide Polymorphisms). A
single nucleotide difference between the sequences of
two homologous chromosomes (for example, the
homologous chromosome 1 copies that you received, one
from your mother and one from your father). Most
human haploid genomes differ by about 1-3 million
SNPs from each other. There are a variety of
mechanisms used to identify SNPs. The disadvantage
of SNPs is that they are not as polymorphic as
microsatellite sequences.
PHYSICAL MAPPING OF EUKARYOTIC
CHROMOSOMES REQUIRES THAT WE BE
ABLE TO HANDLE VERY LARGE DNAs (~1 Mb).
A. Sizing and Separating Large DNA Fragments:
Large DNA fragments (up to 10 Mb) can be separated
on special gels in which the direction of the electric
field is altered in pulses (PULSED FIELD GEL
ELECTROPHORESIS).
B. Large Scale Restriction Maps:
C. Cloning Large DNA: Large DNA fragments can
be cloned in special vectors, such as YEAST
ARTIFICIAL CHROMOSOME (YAC) AND
BACTERIAL ART. CHROMOSOME (BAC)
VECTORS.
How to correlate genetic, cytological and
physical maps? A Cloned Gene or STS is the key.
(Remember, any time you have an STS, you can
always use PCR to make lots of that DNA.)
A. Physical maps are often restriction maps
produced by overlapping cloned DNA fragments.
B. Genetic maps are produced using RFLPs deduced
from Southern blots using cloned DNA as the probe or
STSs using DNA sequence information derived by
sequencing a cloned DNA fragment.
C. Cytological maps are derived using in situ
hybridization, again using a cloned DNA as the
hybridization probe.
XII. The utimate physical map is the complete sequence of
the genome. (pp. 152-156)
GENOME
SIZE (Mb)
PHYSICAL MAP
 phage DNA
EBV
H. influenzae
E. coli
S. cerevisiae
C. elegans
D. melanogaster
0.05
0.2
1.8
4.7
13
80
140
ca. 1970
ca. 1980
1995
1987
ca. 1990
near, 1993
Arabidopsis
120
1992-3
Human
3000
1st gen., Dec. 1993
COMPLETE
SEQUENCE
1982
1984
July, 1995
Feb. 1997
total 4/24/96
Dec. 1998
est. 1999
2/2000
est. 2000
12/2000
est. 2003-5
draft: Feb. 2001
finished, est. 2003