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.

Figure 5.03: Bacterial genome size relates to gene number.

5.2 Prokaryotic Gene Numbers Range Over an Order of Magnitude

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 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.

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.

• 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.

5.10 About 10,000 Genes Are Expressed at Widely Differing Levels in a Eukaryotic Cell

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.

Figure 5.21: Yeast mRNAs vary widely in abundance.

5.11 Expressed Gene Number Can Be Measured en Masse

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.

Figure 5.22_1: Individual mRNAs can be measured.

Photos courtesy of Rick A. Young, Whitehead Institute, Massachusetts Institute of Technology

5.11 Expressed Gene Number Can Be Measured en Masse