Transcript Evolution of eukaryote genomes

•Bacteria have compact genomes rich in genes, having fewer
noncoding regions and no introns. Eukaryotic genomes have much
more DNA content than bacteria.
•While eukaryotes have more genes than bacteria, the
difference in gene content is not as great as the difference in
DNA content: there is much more noncoding DNA in eukaryotes
•In fact, gene-coding regions comprise only about 2% of the
human genome.
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Eukaryotic genes are interrupted by large introns. In
eukaryotes, repeated sequences characterize great
amounts of noncoding DNA.
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The first eukaryotic organism to have its entire genome sequenced was yeast,
Saccharomyces cerevisiae -1996
• Yeast genome contains 5885 protein coding genes:
1. 140 genes specifying ribosomal RNA (rRNA)
2. 40 genes for nuclear RNA molecules
3. over 200 transfer RNA (tRNA) genes
• Deletion in some genes (18.7%) has a lethal effect while on other genes
does not, due to many duplicated genes in the yeast genome
• Genome sequences of other eukaryotic genomes soon followed:
1. Worm, Caenorbabditis elegans -1998
2. Fruit Fly, Drosophila melanogaster and plant model Arabidosis thaliana -
2000
3. Nearly complete Human Genome sequence-2004
• Gene density varies among different eukaryotic species – ranging from
1gene/1900 bp in baker’s yeast to 1gene/127 900 bp in humans
Table: Size and Predicted Gene Content of Selected Eukaryotic Genomes
Species
Protists
Encephalitozoon cuniculi
Plasmodium falciparum
Fungi
Saccharomyces
cerevisae
Nematode
Caemorhabditis elegans
Insects
Drosophila melanogaster
Plant
Arabidopsis thaliana
Vertebrates
Homo sapiens
Common Name
Genome Size in
nucleotide pairs
Predicted Gene
number of Density
genes
(bp/gen
e)
Microsporidian
Malaria protozoan
2,497,519
22,820,308
1,996
5,317
1,300
4,300
baker’s yeast
12,057,909
6,268
1,900
roundworm
100,291,841
20,516
4,900
Fruit fly
131,000,899
13,792
9,500
Mouse ear cress
116,566,763
25,706
4,500
2,851,330’913
22,287
127,900
Human
• Genomes of single-celled eukaryotes eg. yeast have one gene for
every 1000-2000 bp
• Gene density decreases with the increased developmental
complexity eg. gene density is the lowest in mammals i.e 1gene for
every 115,000 to 129,000 bp
• Low gene density in the larger eukaryotic genomes, is also due to
the considerable amounts of repetitive DNA
• Yeast contain very little repetitive DNA, although 30% of its genes
are duplicated. In multicellular eukaryotes there are lots of repetitive
DNA and in most cases, are directly related to genome size
• Only about 10% of C. elegans contains repetitive DNA whereas in
large genomes of mammals there are over 40% of repeat sequences.
Most of these repeats are derived from transposable genetic elements
(transposons)
• Transposons are found in genomes of many organisms (bacteria,
fungi, protozoa, plants and animals) and are structurally diverse.
Transposons are mobile DNA sequences
• Highly repetitive DNA is more abundant in larger genomes but
there is no direct correlation between the amount of highly
repetitive DNA and genome size.
• Much of highly repetitive DNA in most species including humans,
is present in the regions of chromosomes that flank the
centromeres (centromeric heterochromatin) and in the telomeres
• This DNA is difficult to sequence, most of the unsequenced DNA in
human genome (472million bp) consist of highly repetitive sequences
•Introns are more prevalent and longer in the large eukaryotic
genome. Intergenic regions are also longer in the larger eukaryotic
genomes.
•The number of distinct protein domain encoded by genes does
not vary much between genome sizes. Predicted number of
proteins domains encoded by A. thaliana, D. melanogaster and
human genomes are 1012, 1035, and 1262, respectively
Table: Size of Selected Eukaryotic Genomes
Species
Nematode
Caemorhabditis elegans
Insects
Drosophila melanogaster
Plant
Arabidopsis thaliana
Vertebrates
Homo sapiens
Common Name
Genome Size in
nucleotide pairs
Predicted Gene
number of Density
genes
(bp/gen
e)
roundworm
100,291,841
20,516
4,900
Fruit fly
131,000,899
13,792
9,500
Mouse ear cress
116,566,763
25,706
4,500
2,851,330’913
22,287
127,900
Human
•Distantly related species have many genes in common, e.g. 18%
of Arabidosis and 50% of Drosophila have human homologues
• The proportion of homologous genes is even greater in closely
related species. Furthermore, in closely related species, the entire
chromosome often show a similar arrangement of genes
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Discovered in 1970s
Different types of introns
Two hypotheses of origin
‘Introns early’
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Ancient and gradually being lost from eukaryote
genomes
‘Introns late’
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evolved relatively recently and gradually
accumalating in eukaryote genomes
Self
splicing
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‘introns early’
‘exon theory of genes’ – Gilbert 1987
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All genomes originally possessed introns
Bacterial genomes do not have GU-AG
introns
Therefore must have been lost at an early
stage
How? Without disrupting genes?
Not really feasible  introns late hypothesis
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To begin with, genes had no introns
Introns developed in eukaryote genomes and
proliferated
Group II introns and GU-AG introns similar in
terms of splicing
Group II moved from organellar genomes to
nuclear eukaryote genomes?
Or did GU-AG introns evolve from group II
introns? – introns early hypothesis
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Position of introns in homolgous genes from
unrelated organisms should be similar since
all descended from ancestral gene with
introns
Initial evidence showed this was true
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Later evidence (more lineages examined) its
was shown that some introns were lost in
some positions and gained in others
Introns must have moved by recombination
events
Fits both hypotheses
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For introns early, introns should split domains of
different proteins
Again, initial evidence supported this
But more globulin genes showed more than 10
introns- therefore no correlation between introns
and junctions between domains
Domain duplication and shuffling
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Subsequent gain and loss of introns over
time in different lineages
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Belshaw, R. and Bensasson, D. (2006) The
rise and fall of introns. Heredity. 96:204-213.