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10.2 Genome Architecture and Evolution 347

that are not translated, such as rRNAs and tRNAs that
essential concepts participate in translation, and the snRNAs that function in
• Long open reading frames (ORFs) in genomic DNA spliceosomes. These numbers are much lower than ex-
usually identify protein-coding exons. pected. Estimates made before the initiation of the Hu-
• DNA sequences conserved between the genomes of man Genome Project had suggested that 100,000 or more
widely divergent species often correspond to the exons genes might exist. Many of these estimates anticipated
of genes. that because humans have much greater biological com-
• Reverse transcriptase produces complementary DNA plexity than simpler model organisms such as bacteria,
(cDNA) from mRNA transcripts; cDNA clones thus yeasts, nematodes, and fruit flies, our genomes must have
represent only the exons of genes. many more genes. Although the human genome indeed
• cDNA sequences reveal how a primary transcript is has more genes than these organisms, the difference in
spliced in a given cell type, and thus predict the amino gene number is not nearly as great as had been thought
acid sequence(s) of a gene’s protein product(s) in that (review Table 9.2). Mechanisms other than changes in
cell type. gene number must therefore underly metazoan (multi-
cellular animal) complexity.
The total length of genomes varies much more markedly
over the course of evolution than the number of genes (com-
10.2 Genome Architecture pare especially the genomes of mammals such as mice and

and Evolution humans with model eukaryotes like worms and flies; Table 9.2).
This generalization holds because the exome, the part of the
genome corresponding to the exons of all known genes, con-
stitutes only a small proportion of genomes, roughly 1.5–2.0%
learning objectives of the total in humans. The vast majority of DNA sequences

1. Discuss the arrangement of genes in genomes, instead are found in introns, in the spaces between genes
including the number of genes, transcription direction, (intergenic regions), in transposable elements that can move
and gene density. from one chromosomal position to another, and in structural
2. Explain how gene duplication and divergence lead to features like centromeres and telomeres.
the formation of gene families and pseudogenes. The tremendous variation seen in the size of genomes
3. List three ways in which genomes can change over of different species is thus mostly due to expansions and
evolutionary time. contractions of noncoding DNA outside of the exome,
4. Describe how mechanisms at the DNA, RNA, and rather than changes in gene number or gene sizes. For ex-
protein levels can produce complexity from a small ample, half or more of the human genome appears to be
number of genes. composed of transposable elements, often regarded as self-
ish or parasitic DNA that uses our genomes as a host for
their own propagation. In a second example, the human
genome also contains many simple repeating sequences
The complete sequences of the human and other genomes (such as CGCGCGCG, etc.).
have provided striking new insights into the organization In this section, we focus on the small proportion of the
and evolution of genomes. Our detailed knowledge of ge- genome corresponding to the genes, with an emphasis on
nomic sequences has changed profoundly the practice of those that encode proteins. Later chapters will describe in
biology. We now briefly describe some of the main lessons greater detail the nature of DNA sequences that constitute
and surprises from these genome projects, focusing on the other chromosomal elements about which some informa-
following three questions: How are the genes arranged in tion is available (centromeres, telomeres, and transposable
genomes? How do genes and genomes change during evo- elements). However, you should know that a large percent-
lution? Lastly, how can genomes with a relatively small age of the human genome is “dark matter” whose presence
number of genes produce the vast complexity of pheno- we do not yet understand. Some of this DNA may have
types that results in living organisms, including humans? functions that are currently obscure, but much of it may in
fact not have any function at all and may instead be the
The Arrangement of Genes vestiges of chance events that occurred during evolution.
in the Genome Is Not Uniform
A major shock to emerge from the completion of the hu- Random orientation of transcription of most genes
man genome sequence was the discovery of only about Students sometimes assume that all the genes on a chromo-
27,000 genes. Of these genes, roughly 19,000 encode some are transcribed in the same direction, always using
proteins, while the remainder are transcribed into RNAs the same strand of double-stranded genomic DNA as the