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Genome Sequences and Gene Numbers

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Title: Genome Sequences and Gene Numbers


1
Chapter 5
  • Genome Sequences and Gene Numbers

2
5.1 Introduction
  • Genome size vary from approximately 470 genes for
    Mycoplasma genitalium to 25,000 for human and
    mouse.

Figure 5.01 Minimum gene numbers range from 500
to 30,000.
3
5.2 Prokaryotic Gene Numbers Range Over an Order
of Magnitude
  • The minimum number of genes for an parasitic
    prokaryote is about 500.
  • For a free-living nonparasitic prokaryote, it is
    about 1500.

4
Figure 5.02 Sequenced genomes vary from 470 to
30,000 genes.
5
5.2 Prokaryotic Gene Numbers Range Over an Order
of Magnitude
Figure 5.03 Bacterial genome size relates to
gene number.
6
5.3 Total Gene Number Is Known for Several
Eukaryotes
  • There are 6000 genes in yeast
  • 18,500 in a worm
  • 13,600 in a fly
  • 25,000 in the small plant Arabidopsis
  • Probably 20,000 to 25,000 in mice and humans

7
Figure 5.04 Eukaryotic gene number varies widely.
8
Figure 5.05 Yeast genomes are compact.
9
Figure 5.06 Functions are known for only half
the fly genes.
Adapted from Drosophila 12 Consortium, Evolution
of genes and genomes on the Drosophila
phylogeny, Nature 450 (2007) 203-218.
10
5.4 How Many Different Types of Genes Are There?
  • The sum of the number of unique genes and the
    number of gene families is an estimate of the
    number of types of genes.
  • The minimum size of the proteome can be estimated
    from the number of types of genes.

11
5.4 How Many Different Types of Genes Are There?
Figure 5.07 The number of gene families plateaus
with genome size.
12
Figure 5.08 Family size increases with genome
size.
13
Figure 5.09 Most fly genes are specific to the
genus.
14
5.5 The Human Genome Has Fewer Genes Than
Originally Expected
  • Only 1 of the human genome consists of exons.
  • The exons comprise 5 of each gene, so genes
    (exons plus introns) comprise 25 of the genome.

15
5.5 The Human Genome Has Fewer Genes Than
Originally Expected
Figure 5.10 1 of the human genome codes for
protein.
16
Figure 5.11 Only 5 of the length of the average
human gene codes for protein.
17
5.5 The Human Genome Has Fewer Genes Than
Originally Expected
  • The human genome has 20,000 to 25,000 genes.
  • 60 of human genes are alternatively spliced.
  • Up to 80 of the alternative splices change
    protein sequence, so the proteome has 50,000 to
    60,000 members.

18
5.6 How Are Genes and Other Sequences Distributed
in the Genome?
  • Repeated sequences (present in more than one
    copy) account for gt50 of the human genome.
  • The great bulk of repeated sequences consist of
    copies of nonfunctional transposons.
  • There are many duplications of large chromosome
    regions.

19
5.6 How Are Genes and Other Sequences Distributed
in the Genome?
Figure 5.12 Most of the human genome is
repetitive DNA.
20
5.7 The Y Chromosome Has Several Male-Specific
Genes
  • The Y chromosome has 60 genes that are expressed
    specifically in the testis.
  • The male-specific genes are present in multiple
    copies in repeated chromosomal segments.
  • Gene conversion between multiple copies allows
    the active genes to be maintained during
    evolution.

21
Figure 5.13 The Y chromosome has 70 active
genes.
22
5.8 Morphological Complexity Evolves by Adding
New Gene Functions
  • Comparisons of different genomes show a positive
    correlation between gene number and morphological
    complexity.
  • Additional genes are needed in eukaryotes,
    multicellular organisms, animals, and
    vertebrates.
  • Most of the genes that are unique to vertebrates
    are concerned with the immune or nervous systems.

23
Figure 5.14 Genes for new functions are added
during evolution.
24
Figure 5.15 1300 common functions are essential.
25
5.8 Morphological Complexity Evolves by Adding
New Gene Functions
Figure 5.16 Complexity requires extracellular
functions.
26
5.9 How Many Genes Are Essential?
  • Not all genes are essential. In yeast and flies,
    deletions of lt50 of the genes have detectable
    effects.
  • When two or more genes are redundant, a mutation
    in any one of them may not have detectable
    effects.
  • We do not fully understand the persistence of
    genes that are apparently dispensable in the
    genome.

27
5.9 How Many Genes Are Essential?
Figure 5.17 lt20 of yeast genes are essential.
28
Figure 5.18 Most worm genes are not essential.
29
Figure 5.19 Most human mutations causing defects
are small.
30
Figure 5.20 Nonlethal mutations may be lethal in
combinations.
31
5.10 About 10,000 Genes Are Expressed at Widely
Differing Levels in a Eukaryotic Cell
  • In any given cell, most genes are expressed at a
    low level.
  • Only a small number of genes, whose products are
    specialized for the cell type, are highly
    expressed.

32
5.10 About 10,000 Genes Are Expressed at Widely
Differing Levels in a Eukaryotic Cell
  • mRNAs expressed at low levels overlap extensively
    when different cell types are compared.
  • The abundantly expressed mRNAs are usually
    specific for the cell type.
  • 10,000 expressed genes may be common to most
    cell types of a higher eukaryote.

33
5.11 Expressed Gene Number Can Be Measured en
Masse
  • DNA microarray technology allows a snapshot to be
    taken of the expression of the entire genome in a
    yeast cell.
  • 75 (4500 genes) of the yeast genome is
    expressed under normal growth conditions.

34
5.11 Expressed Gene Number Can Be Measured en
Masse
Figure 5.21 Yeast mRNAs vary widely in abundance.
35
5.11 Expressed Gene Number Can Be Measured en
Masse
  • DNA microarray technology allows detailed
    comparisons of related animal cells to determine
    (for example) the differences in expression
    between a normal cell and a cancer cell.

36
5.11 Expressed Gene Number Can Be Measured en
Masse
Figure 5.22_1 Individual mRNAs can be measured.
Photos courtesy of Rick A. Young, Whitehead
Institute, Massachusetts Institute of Technology
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