Genome Organization and Evolution
I.
There are three major topics involved in genome organization and evolution.
1. Genome size
2. Genetic information included within genomes.
3. Nucleotide composition of the genome.
II. Genome Size
1. a.k.a. C-Value: the amount of DNA in the haploid genomic set
i. “C” stands for “constant” or “characteristic”, which denotes that the size
of the haploid genome is fairly constant within any one species. (Li, 204)
ii. C values vary greatly in prokaryotes and eukaryotes.
iii. Genome sizes in eukaryotes are usually measured in_______ (1pg =
10⁻¹²g), while smaller prokaryotic genomes are usually measured in
______ (unit of relative atomic or molecular mass). In even smaller
genomes, (some organelles and viruses) size is expressed in _____ (bp) or
________(kbp).
2. Evolution of genome size in bacteria:
i. Variation in C-Values is roughly a 20-fold range (from about 6x10⁵bp to
10⁷bp)
ii. The distribution of genome sizes in bacteria can be explained through a
combination of different processes:
1. Genome duplication during the independent evolution of a
respiratory metabolism in several lines
2. Subsequent genome duplications occurring independently in
many lineages
3. Small-scale deletions and insertions
4. Duplicative transposition
5. Horizontal transfer of genes (derived mainly from plasmids)
6. Loss of massive chunks of DNA in many parasitic lines.
3. Genome size of Eukaryotes and the C-Value paradox.
i. Usually, C-values in eukaryotes are larger than in prokaryotes (although
there are some exceptions).
ii. Variation in C-Values in Eukaryotes is much larger than in bacteria
(approx. 80,000-fold range).
1. The three amniote classes (mammals, birds, and reptiles) have
very small variation in genome size (up to four-fold). This does
not seem to have a correlation with complexity or number of
genes encoded by the organism (C-Value paradox).
iii. C-value Paradox: _________.
1. A substantial portion of the eukaryotic genome consists of DNA
that does not contain genetic information.
4. The repetitive structure of the eukaryotic genome:
i. Characterized by two major features:
1. Repetition of sequences: ______________ consists of nucleotide
sequences of various lengths and compositions that occur several
times in the genome either in tandem or in a dispersed fashion.
2. Compositional compartmentalization into distinct fragments
characterized by specific nucleotide compositions: __________ or
_________ are segments of DNA that do not repeat themselves.
ii. Genome of higher eukaryotes can be divided (roughly) into four fractions:
1. Foldback DNA
2. Highly repetitive DNA
3. Middle-repetitive DNA
4. Single-copy DNA
III. Mechanisms for Increasing Genome Size
i. Global increases: entire genome or a major part of it (such as a
chromosome) is duplicated.
ii. Regional increase: a particular sequence is multiplied to generate
repetitive DNA.
a. Genome Duplication
i. a.k.a Genome Doubling: new genes arise as copies
of pre-existing genes.
ii. Gene duplication (polyploidy) : common
occurrence in nature, but over evolutionary
history, polyploids often did not survive because
polyploidy is harmful and will be strongly selected
against.
1. Harmful effects of polyploidism:
b. Chromosomal duplication
i. Duplication of single chromosome (aneuploidy)
ii. Can be lethal or lead to infertility in mammals. In
humans, examples include Down’s syndrome and
trisomy 18.
iii. B-chromosomes: Products of partial chromosome
duplication.
c. Regional increases of genome size
i. Brought about by transposition, unequal crossing over:
dispersed repetitive sequences. Also can come from
the acquisition of foreign DNA (although the total DNA
size is not greatly affected): Tandemly repeated
sequences.
IV. Maintenance of nongenic DNA
1. Hypotheses which try to explain long-term maintenance of vast quantities of
nongenic, extra DNA.
i. The nongenic DNA performs essential functions, such as global regulation of
gene expression. The excess of DNA is only apparent, and the DNA is
completely functional. Will have a negative effect on fitness.
ii. The nongenic DNA is useless junk DNA, carried passively by the chromosome
merely because of its physical linkage to functional genes. Excess DNA does not
affect fitness, will be carried from generation to generation.
iii. The nongenic DNA is a functionless “parasite” that accumulates and is actively
maintained by intragenomic selection.
iv. DNA has a structural function (unrelated to the task of carrying genetic
information)
2. GC content
i. Amount of guanine and cytosine in genomic sequences.
ii. Bacterial GC content may be related to phylogeny.
iii. 2 types of hypotheses to explain variation in GC content:
1. Selectionist: GC content is a form of adaptation to environmental
conditions.
2. Mutationist: the GC content is determined by the balance between the
a) the rate of substitution from G or C to T or A and b) the rate of
substitution from A or T to G or C.
iv. Compositional organization of the vertebrate genome
1. GC content shows a smaller variation in eukaryotes than in prokaryotes;
vertebrates range 40%-45%. This may be because vertebrates have not
diverged long enough from one another to allow for considerable
differences in GC content.
2. There are obvious differences in compositional organization between
the genomes of warm- and cold-blooded vertebrates.
3. Composition of DNA fragments is independent of the size of the
fragments, and results in compositional homogeneity over long DNA
stretches (isochors).
v. Location of genes within isochors
1. Many genes have been localized on the isochors by hybridization.
vi. Origins of isochors
1. We don’t really know; may be that, in warm-blooded organisms, an
increase in GC content can protect DNA, RNA, and proteins from
degradation by heat (selectionist hypothesis).
2. The mutationist hypothesis explains the difference in GC content
between the α- and β-globin clusters in the mammalian genome by
assuming that they are located in an early- and a late-replicating region.
References
1.
Li, W.H., D. Graur 1991. Fundamentals of Molecular Evolution. Sinauer Associates, Inc.,
Sunderland, Mass.
2.
Cabalier-Smith, T. 1985. The evolution of Genome Size. Wiley, New York