Genome Sequences and Gene Numbers

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Chapter 5

• Genome Sequences and Gene Numbers

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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.
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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.

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Figure 5.02 Sequenced genomes vary from 470 to
30,000 genes.
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5.2 Prokaryotic Gene Numbers Range Over an Order
of Magnitude
Figure 5.03 Bacterial genome size relates to
gene number.
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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

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Figure 5.04 Eukaryotic gene number varies widely.
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Figure 5.05 Yeast genomes are compact.
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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.
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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.

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5.4 How Many Different Types of Genes Are There?
Figure 5.07 The number of gene families plateaus
with genome size.
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Figure 5.08 Family size increases with genome
size.
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Figure 5.09 Most fly genes are specific to the
genus.
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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.

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5.5 The Human Genome Has Fewer Genes Than
Originally Expected
Figure 5.10 1 of the human genome codes for
protein.
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Figure 5.11 Only 5 of the length of the average
human gene codes for protein.
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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.

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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.

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5.6 How Are Genes and Other Sequences Distributed
in the Genome?
Figure 5.12 Most of the human genome is
repetitive DNA.
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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.

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Figure 5.13 The Y chromosome has 70 active
genes.
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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.

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Figure 5.14 Genes for new functions are added
during evolution.
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Figure 5.15 1300 common functions are essential.
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5.8 Morphological Complexity Evolves by Adding
New Gene Functions
Figure 5.16 Complexity requires extracellular
functions.
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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.

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5.9 How Many Genes Are Essential?
Figure 5.17 lt20 of yeast genes are essential.
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Figure 5.18 Most worm genes are not essential.
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Figure 5.19 Most human mutations causing defects
are small.
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Figure 5.20 Nonlethal mutations may be lethal in
combinations.
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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.

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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.

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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.

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5.11 Expressed Gene Number Can Be Measured en
Masse
Figure 5.21 Yeast mRNAs vary widely in abundance.
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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.

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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