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Chapter 5
Genome Sequences and Gene
Numbers
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.
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.
Figure 5.02: Sequenced genomes vary from 470 to 30,000 genes.
5.2
Prokaryotic Gene Numbers Range Over
an Order of Magnitude
Figure 5.03: Bacterial genome size relates to gene number.
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
Figure 5.04: Eukaryotic gene number varies widely.
Figure 5.05: Yeast genomes are compact.
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.
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.
5.4
How Many Different Types of Genes Are
There?
Figure 5.07: The number of gene families plateaus with
genome size.
Figure 5.08: Family size increases with genome size.
Figure 5.09: Most fly genes are specific to the genus.
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.
5.5
The Human Genome Has Fewer Genes
Than Originally Expected
Figure 5.10: 1% of the human genome codes for protein.
Figure 5.11: Only 5% of the length of the average human gene codes for
protein.
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.
5.6
How Are Genes and Other Sequences
Distributed in the Genome?
• Repeated sequences (present in more than one
copy) account for >50% of the human genome.
• The great bulk of repeated sequences consist of
copies of nonfunctional transposons.
• There are many duplications of large
chromosome regions.
5.6
How Are Genes and Other Sequences
Distributed in the Genome?
Figure 5.12: Most of the human genome is repetitive DNA.
5.7
The Y Chromosome Has Several MaleSpecific 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.
Figure 5.13: The Y chromosome has ~70 active genes.
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.
Figure 5.14: Genes for new functions are added during evolution.
Figure 5.15: 1300 common functions are essential.
5.8
Morphological Complexity Evolves by
Adding New Gene Functions
Figure 5.16: Complexity requires extracellular functions.
5.9
How Many Genes Are Essential?
• Not all genes are essential. In yeast and flies,
deletions of <50% 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.
5.9
How Many Genes Are
Essential?
Figure 5.17: <20% of yeast genes are
essential.
Figure 5.18: Most worm genes are not essential.
Figure 5.19: Most human mutations causing defects are small.
Figure 5.20: Nonlethal mutations may be lethal in combinations.
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.
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.
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.
5.11 Expressed Gene Number Can Be Measured en Masse
Figure 5.21: Yeast mRNAs vary widely in abundance.
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.
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