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Evolution of Mitochondrial Genome Architecture in Nematodes. Sita Ping Department of Zoology Mentor: Dr. Dee Denver HHMI Summer 2010. Background: Mitochondria. organelle in eukaryotic cells that is responsible for energy production. - PowerPoint PPT Presentation
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Evolution of Mitochondrial Genome Architecture in Nematodes
Sita PingDepartment of ZoologyMentor: Dr. Dee Denver
HHMI Summer 2010
Background: Mitochondriaorganelle in eukaryotic cells that is
responsible for energy productionElectron transport chain,
located in the inner membrane of Mitochondria produces usable energy and in doing so gives off reactive oxygen species (ROS) ROS is a chemical body that
has an unpaired electronspeculated to be a part of the
aging process, and causes genetic mutations
Background: MtDNAHas genome separate from the nucleus
Small, circular chromosomeMany chromosomes per organelle
Mitochondrial (mt) DNA may be related to longevity, cognition, and neurodegenerative and cancer diseases2
Mitochondrial gene order used in analyzing deep evolutionary relationshipsThought to be very slow evolving
Used in evaluating arthropod evolution
Human vs. Nematode mitochondria
(Ss) Strongyloides stercoralis human parasite 600 million infections
estimated worldwide1(Rs) Rhabditophanes sp KR3021
Close relative to Strongyloides spp.Non-parasiticFound in Oregon
(Pr) Panagrolaimus rigidusAble to grow in labFound in Antarctica(Ce) Caenorhabditis elegans
first animal to have its genome sequenced
important model organism
Comparison of gene order in S. stercoralis [Ss], Rhabditophanes sp KR3021 [Rs], Panagrolaimus rigidus [Pr], and Caenorhabditis elegans [Ce], created by Dr. Dee Denver and Dana Howe of the Denver lab
Hypothesis of mt gene order rearrangement: Denver Lab Recombination base fission and fusion
model
Courtesy of Dee Denver and Dana Howe
Ce
Pr
Alloionema appendiculatum
Rs
Parastrongyloides trichosuri
Ss
Conventional mt gene order; single chromosome
Conventional mt gene order; single chromosome
Highly scrambled mt gene order; single chromosome
Semi-conserved gene order; two chromosome mtDNA
Analyze mtDNA of evolutionary intermediates to evaluate both hypotheses
Ss = Strongyloides stercoralisPr = Panagrolaimus rigidus
Rb = Rhabditophanes sp KR3021Ce = Caenorhabditis elegans
Parastrongyloides tricorhosuri Australian possum parasite Has both free-living and parasitic lifecyclespossible model mammalian parasite?
Ce
Pr
Rs
Ss
Aa
Pt
Alloionema appendiculatumSlug parasitePossible bio-control agent?
If hypothesis A is true: presence of a large super chromosome mtDNA
molecule as an evolutionary intermediate is expected
If hypothesis B is true: presence of multi-chromosome mtDNA as the
evolutionary transition is expected
Method Worm lysis
A. appendiculatum received from Irma DeLey at UC Riverside; P. trichosuri from Dr. Sparky Lok at University of Pennsylvania
Long PCR amplification in overlapping amplicons Initial primers created by Dana Howe of the Denver Lab
Run a gel-electrophoresis to estimate amplicon size purify PCR product with invitrogen beading Sequence reaction
PCR product directly sequenced using the primer walk strategy
Ethanol precipitation Sent to CGRB for sequence results
Amplicon 1 Amplicon 2
~2800bp~3100bp
~2500bp
~11000bp~10000bp ~5000bp
~2200bp
~500bp
12
3
4
1 2
3
4
1: C. elegans = ~13,800 bp2: P. trichosuri = ~13,100 bp 3: A. appendiculum = ~4,700 bp4: Rhabditophanes spp. = ~5,500 bp
Gene order results
A. appendiculatum - Amplicon 1, Reverse
rrnScox3
rrnS728
EWND4L-proteinND6-protein1092
VPLKATPase6~2305
P. trichosuri - Amplicon 1, Reverse
C. elegans MtDNA
~1000
Project Reflection
Ce
Pr
Rs
Ss
Pt
Aa
Conventional mt gene order; single chromosome
Conventional mt gene order; single chromosome
Highly scrambled mt gene order; single chromosome
Semi-conserved gene order; two chromosome mtDNA
unknown gene order; single chromosome
Semi-conserved gene order; two chromosome mtDNA
Future DirectionsIllumina sequence
Sequence the other A. appendiculatum chromosome(s)
Evaluate mtDNA of more Strongyloides species
Acknowledgements
Howard Hughes Medical Institute (HHMI) OSU Computational Genome Bio Initiative
Dr. Dee Denver and Denver LabDana HoweLarry WilhelmKatie ClarkMichael RaboinDanika KusumaKristin Gafner
Dr. Kevin AhernDr. Sparky Lok
Irma DeLeyOSU CGRB
References1. Dorris, M., Viney, M.E., Blaxter, M.L.,
2002. Molecular phylogenetic analysis of the genus Strongyloides and related nematodes.
2. Montiel, R., Lucena, M.A., Medeiros, J., Simoes, N., 2005. The Complete Mitochondrial Genome of the Entomopathogenic Nematode Steinernema carposcapsae: Insights into Nematode Mitochondrial DNA Evolution and Phylogeny.