DNA is added to genomes both by the spontaneous duplication of chromosomal segments that are typically tens of thousands of nucleotide pairs long (as will be discussed shortly) and by insertion of new copies of active transposons. Most transposition events are duplicative, because the original copy of the transposon stays where it was when a copy inserts at the new site; see, for example, Figure 5–63. Comparison of the DNA sequences derived from transposons in the human and the mouse readily reveals some of the sequence additions (Figure 4–69).
It remains a mystery why all mammals have maintained genome sizes of roughly 3 billion nucleotide pairs that contain nearly identical sets of genes, even though only approximately 150 million nucleotide pairs appear to be under sequence-specific functional constraints.
The Size of a vertebrate genome Reflects the Relative Rates of DNA Addition and DNA loss in a lineage
In more distantly related vertebrates, genome size can vary considerably, apparently without a drastic effect on the organism or its number of genes. Thus, the chicken genome, at one billion nucleotide pairs, is only about one-third the size 200,000 bases
Figure 4–67 Synteny between human and mouse chromosomes. In this diagram, the human chromosome set is shown above, with each part of each chromosome colored according to the mouse chromosome with which it is syntenic. The color coding used for each mouse chromosome is shown below. Heterochromatic highly repetitive regions (such as centromeres) that are difficult to sequence cannot be mapped in this way; these are colored black. (Adapted from
E.E. Eichler and D. Sankoff, Science 301:793–797, 2003. with permission  from AAAS.)
Figure 4–68 Comparison of a syntenic portion of mouse and human genomes.
About 90% of the two genomes can be aligned in this way. Note that while there is an identical order of the matched index sequences (red marks), there has been a net loss of DNA in the mouse lineage that is interspersed throughout the entire region. This type of net loss is typical for all such regions, and it accounts for the fact that the mouse genome contains 14% less DNA than does the human genome. (Adapted from mouse genome Sequencing Consortium, Nature 420:520–562, 2002. with permission from macmillan Publishers ltd.) 10,000 nucleotide pairs of the mammalian genome. An extreme example is the puffer fish, Fugu rubripes (Figure 4–70), which has a tiny genome for a vertebrate (0.4 billion nucleotide pairs compared to 1 billion or more for many other fish). The small size of the Fugu genome is largely due to the small size of its introns. Specifically, Fugu introns, as well as other noncoding segments of the Fugu genome, lack the repetitive DNA that makes up a large portion of the genomes of most well-studied vertebrates. Nevertheless, the positions of the Fugu introns between the exons of each gene are almost the same as in mammalian genomes (Figure 4–71).
While initially a mystery, we now have a simple explanation for such large differences in genome size between similar organisms: because all vertebrates experience a continuous process of DNA loss and DNA addition, the size of a genome merely depends on the balance between these opposing processes acting over millions of years. Suppose, for example, that in the lineage leading to Fugu, the rate of DNA addition happened to slow greatly. Over long periods of time, this would result in a major “cleansing” from this fish genome of those DNA sequences whose loss could be tolerated. The result is an unusually compact genome, relatively free of junk and clutter, but retaining through purifying selection the vertebrate DNA sequences that are functionally important. This makes Fugu, with its 400 million nucleotide pairs of DNA, a valuable resource for genome research aimed at understanding humans.
we Can Infer the Sequence of Some Ancient genomes