HAPLOID GENOME SIZES

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HAPLOID GENOME SIZES (DNA PER HAPLOID
CELL) Size range Example species Ex. Size
BACTERIA 1-10 Mb E. coli 4.639 Mb FUNGI 10-40
Mb S. cerevisiae 13 Mb INSECTS 100-5000 Mb D.
melanogaster 165 Mb BIRDS 1000-1500
Mb Chicken 1300 Mb FLOWERING 100 to
Arabidopsis 120 Mb PLANTS 100,000 Mb
Corn 2500 Mb MAMMALS 3000-4000 Mb Human 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.)
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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
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• 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.

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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
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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.
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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
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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.)
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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.
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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.
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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.
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XII. The utimate physical map is the complete
sequence of the genome. (pp. 152-156) GENOME SIZE
(Mb) PHYSICAL MAP COMPLETE SEQUENCE ?
phage DNA 0.05 ca. 1970 1982 EBV
0.2 ca. 1980 1984 H. influenzae
1.8 1995 July, 1995 E. coli 4.7 1987
Feb. 1997 S. cerevisiae 13 ca.
1990 total 4/24/96 C. elegans 80 near,
1993 Dec. 1998 D. melanogaster 140
est. 1999 2/2000 Arabidopsis
120 1992-3 est. 2000 12/2000 Human
3000 1st gen., Dec. 1993 est.
2003-5 draft Feb. 2001 finished, est.
2003
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