Transcript Kudoa ciliatae

Panagrolaimus Mitochondrial
Genome Evolution:
Impact of Reproductive Mode
Samantha C. Lewis ♦ Dr. Dee Denver
Zoology Dept. ♦ Center for Genome Research
and Biocomputing
Background
• Recombination: a force at the
population, organismal and molecular
levels
• Gonochorists and parthenogens
(Sexual species and asexual species)
MUTATION
MUTATION
∞
Background
• Theory: asexual organisms do not
persist as long as sexual ones
• “Mutational Meltdown”
• Can reduced selection efficiency be
observed at the molecular level?
Hypothesis
• Inefficient selection may be observed as
non-synonymous protein-coding gene
changes that lead to deleterious mutation
• These changes may
be observed in the
mitochondrial genome
www.nsf.gov/news/biology/assets/interact08.jpg
Methods
•
Sequence the mitochondrial genomes of
one sexual and one asexual organism;
compare
Extract DNA from
nematodes
Genome content comparisons
Amplify mtDNA
Analysis in MEGA
and DNAsp
Sequence amplified
products
Perform DNA
sequence alignments
Work to Date
Gene
rRNA
No sequence
PS 1579
AF 36
C. elegans
AF36
PS1579
sexual
asexual
nad2
nad2
nad2
tRNA I
tRNA I
tRNA I
…………..
tRNA R
tRNA R
tRNA G
tRNA G
tRNA G
tRNA
tRNA F
tRNA F
tRNA F
cob
cob
cob
Genome Comparisons
• Insertions; Deletions; Gene order
• Ka/Ks ratio
 An index of selection efficiency
 The lower the ratio, the stronger selection is
• Nucleotide diversity
 A measure of genetic diversity
 Highest in sexual species
• Homopolymer repeats
Theory
• Insertions; Deletions;
Gene order
Similar to C. elegans
• Ka/Ks ratio
Higher in asexual
Lower in sexual
• Nucleotide diversity
Higher in sexual
Lower in asexual
• Homopolymer repeats
Higher in asexual
Lower in sexual
Results
AF36 - sexual
• Homopolymers
cause slipped
strand mispairing
during DNA
replication
Number of Repeats
25
PS1579 - asexual
20
15
10
5
0
6T
6
77T
88T
9
9T
10T
10
11T
11
Length of Repeats (bp)
• Considerably more mononucleotide runs were
observed in the asexual strain
Results
0.4
[Nucleotide diversity]
[Ka/Ks]
0.35
0.3
0.25
0.2
• Sexual Panagrolaimus
did show higher
nucleotide diversity
values
0.15
• Asexual Panagrolaimus
did not show higher
Ka/Ks values
0.1
0.05
0
Label
Reproductive Mode
PI-P
PI-G
PII-P*
Panagrolaimus Parthenogens
Panagrolaimus Gonochorists
Other Nematode Parthenogens
Theory Support
Theory Support
• Insertions; Deletions;
Gene order
Similar to C. elegans
Theory Support
• Insertions; Deletions;
Gene order
Similar to C. elegans
• Nucleotide diversity
Higher in sexual
Lower in asexual
Theory Support
• Insertions; Deletions;
Gene order
Similar to C. elegans
• Nucleotide diversity
Higher in sexual
Lower in asexual
• Homopolymer repeats
Higher in asexual
Lower in sexual
Theory Support
• Insertions; Deletions;
Gene order
Similar to C. elegans
• Ka/Ks ratio
Higher in asexual
Lower in sexual
• Nucleotide diversity
Higher in sexual
Lower in asexual
• Homopolymer repeats
Higher in asexual
Lower in sexual
Conclusions
• Panagrolaimus is a superb model to study
the evolutionary causes and consequences
of transitions to asexuality in animals
• While some analyses were consistent with a
reduced efficiency of natural selection in
asexual species, others were not
• Further studies with expanded data sets are
needed
Future Work
•
Confirm presence/absence of Arg tRNA in
mt genome
•
Sequence more genes from
Panagrolaimus and other nematodes – add
to Ka/Ks analysis
•
Apply genome scale technologies to the
Panagrolaimus system – high-throughput
sequencing
Acknowledgments
• The Denver lab: Dee, Dana, Bobby, Leslie,
Steph, Caroline, Peter, Larry, Ashley
• Dr. Kevin Ahern
• Howard Hughes Medical Institute
We thank many individuals for providing Panagrolaimus strains:
James Baldwin (UC-Riverside, USA) ♦ Ann Burnell (National
University of Ireland Maynooth) ♦ Marie-Anne Felix (Institut Jacques
Monod, France) Einhard Schierenberg (Universität Köln, Germany)
Paul Sternberg (Caltech, USA) ♦ the Caenorhabditis Genetics Center
(University of Minnesota, USA)