Nuclear Genome Evolution

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Nuclear Genome Evolution

• Number of chromosomes polyploidy
• Genome size length in bp
• Number of genes
• Gene expression
• Gene sequence

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Genome size and complexity

• Over a broad scale, genome size (c-value) is
  loosely correlated to complexity (mammals have
  larger genome sizes than viruses)?
• However, the relationship between genome size and
  complexity is weak within any of the major
  lineages is weak at best
• This lack of correlation is referred to as the
  c-value paradox

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Plant and Metazoan Genomes
Plants Asterids 0.3 24.8 pg
Rosids 0.1 -- 16.5 pg Ranunculales
0.5 25.1 pg Monocots 0.3 127.4 pg
Animals Fruit fly 0.18 pg Sea
urchin 0.87 Chicken 1.13
Zebrafish 1.64 Mouse 3.01
Human 3.19 Octopus 4.56
Grasshopper 13.4 Salamander 38.3
Lungfish 140
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Plant genome sizes

• Asterids 0.3 24.8 pg
• Rosids 0.1 -- 16.5 pg
• Ranunculales 0.5 25.1 pg
• Monocots 0.3 127.4 pg

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Plant Nuclear Genome Size Variation

• 4000 species surveyed and databased
• 2300X difference

54 mbp Cardamine amara Brassicaceae
124,852 mbp Fritillaria assyriaca Liliaceae
http//www.rbgkew.org.uk/cval/database1.html
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Chromosome Number Variation
Chromosome numbers vary n 2 to n
680 Euploid variation polyploidy 35 of
vascular plants are neopolyploids Most are
likely paleopolyploids Aneuploid variation
gain or less of one or more chromosomes
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Post polyploid genome size change is
variable -Additive sum of parents -Increase
-Decrease
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Correlation of Chromosome Number and Genome Size
Angiosperm r -0.023 Gymnosperm r
0.106 Pteridophytes r 0.913
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Predicted number of nuclear genes

• Small difference in gene number, although rice
  genome is 3x the size

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Plant Nuclear Gene Overlap
90 of genes have homologs in other
genomes Does not appear to be large differences
most genomes around 40,000 Not a substantial
contributor to variation in genome size
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Ribsomal DNA
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Centromeric DNA
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• The telomeres of most organisms' chromosomes
  consist of short sequence-asymmetric repeated
  sequences. Lengths are typically greater than 50
  repeats in holotrichous ciliates, less than 350
  repeats in Arabidopsis and 300 to 500 bp in
  Saccharomyces.
• Drosophila, an exception, has transposable
  elements at the end of of its chromosomes.
• Examples
• Tetrahymena, Paramecium CCCCAA
• Oxytrichia, Euplotes CCCCAAAA
• Trypanosoma, Leishmania CCCTA
• Physarum CCCTA
• Saccharomyces C1-3A
• Arabidopsis CCCTAAA
  
• Homo
  CCCTAAA
• Caenorhabditis CCCTAAA
  Telomeres
  Centromeres
• Drosophila
  transposable element

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Junk DNA
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Transposable Elements (TEs)?
50-80 of plant genomes are TEs Discovered by
Barbara McClintock by studying unstable corn
kernel phenotypes Fragments of DNA that can
insert into new chromosomal locations Often
duplicate themselves during the process of moving
around
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Class 1 TEs use RNA intermediates to move around
and undergo duplicative transposition Class 2
TEs are excised during transposition and may
undergo cut and paste transposition with no
duplication or gap repair where the gap is
filled with a copy of the transposon Autonomous
elements contain necessary genes for
transposition Non-autonomous elements rely on
products of other elements for transposition
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MITES Miniature Inverted Repeat Transposable
Elements
Class 2 elements found in or near genes A few
dozen to few hundred base pairs in length Two
inverted repeats Non-autonomous activated by
other autonomous TEs 6 of Arabidopsis and 12
of rice genomes are composed of MITES
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LTRs Long Terminal Repeat Retrotransposons
Class 1 elements found between genes Autonomous
self activating Duplicative transposition Sing
le largest component of plant genomes 50-80 of
maize genome is LTR
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Class 1 TEs use RNA intermediates to move around
and undergo duplicative transposition Class 2
TEs are excised during transposition and may
undergo cut and paste transposition with no
duplication or gap repair where the gap is
filled with a copy of the transposon Autonomous
elements contain necessary genes for
transposition Non-autonomous elements rely on
products of other elements for transposition
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Transposons
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Non-LTR Phylogeny
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Plant TEs are Generally Younger than 15 MYA
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Hybridization Induced Expansion in Helianthus
H. annuus
H. petiolaris
H. paradoxus
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Rate of Transposable Element Insertion and
Fitness Effects
Average reductions in fitness per insertion 0.5
-1.5
Are genome size and TE growth unchecked?
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TEs are most active during meiosis Tag1
transposon example
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Ages of LTRs in Rice
Bursts of LTR expansion Hopi is currently active
and accounts for 30 of rice genome Half life of
3 MYR By examining the number of truncated
LTRs, it appears that 61-78 of the DNA has been
removed since insertion in the last 5 MYR
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Ages of LTRs in Rice
Bursts of LTR expansion Hopi is currently active
and accounts for 30 of rice genome Half life of
3 MYR By examining the number of truncated
LTRs, it appears that 61-78 of the DNA has been
removed since insertion in the last 5 MYR
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LTRs Reduced Through Solo-LTR Formation
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Do Transposable Element Copy Numbers Stabilize?
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Strong Selection Against Transposable Elements
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Boom Bust Cycle Fueled by Hybridization Stress
Data do not suggest stabilization -no old
TEs -TEs demonstrate boom/bust patterns TEs
proliferate in naïve hosts (hybridization)? Stress
overwhelms host ability to limit TEs
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