comparing mitochondrial dna across species
DESCRIPTION
Comparing Mitochondrial DNA across species. & Mutations in human mitochondrial phylogeny. Alessa Moscoso OEB 275br Module Presentation. Nucleotide Online Databases. A prime tool for analyzing molecular data Accessible from anywhere Incorporate archeological specimens (Neanderthal data). - PowerPoint PPT PresentationTRANSCRIPT
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& M U TAT I O N S I N H U M A N M I T O C H O N D R I A L P H Y L O G E N Y
COMPARING MITOCHONDRIAL DNA ACROSS SPECIES
Alessa MoscosoOEB 275brModule Presentation
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NUCLEOTIDE ONLINE DATABASES
• A prime tool for analyzing molecular data• Accessible from anywhere• Incorporate archeological specimens
(Neanderthal data)
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MODULE OBJECTIVES
• Students will learn how to use online databases for gather molecular data
• Will learn how to analyze molecular data with phylogenetics (creating gene trees and species trees)
• Finally, will use comparative genomics to address human disease. Where do these alleles arise?
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ONLINE DATABASES/PROGRAMS
• Ensembl – gather Human mtDNA, orthologs• BLAST- find Neandertal data• TranslatorX – align sequences• SeaView – compare sequences• Mitomap – disease mutations in mtDNA• PAUP – builds phylogenetic trees, analysis• Fig Tree – builds phylogenetics trees
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NEANDERTHAL DATA
• Data found using BLAST search
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MITOCHONDRIAL GENES
• Looking at ATP6, ATP8, COX1, COX2, COX3, CYB, ND2, ND3
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ORTHOLOGS
• Primates • Chimp• Gorilla• Orangutan• Macaque
http://ec.europa.eu/health/opinions/en/non-human-primates/glossary/pqrs/primates.htm
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TREE CREATED FROM 8 COMBINED GENES
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ATP6 ALIGNED SEQUENCES
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ATP6 PHYLOGENY IN PAUP
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BOOTSTRAPPING
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ATP6 MUTATIONSGene Disease Allele Nucleotide
PositionNucleotide Change
Amino Acid Change Status
MT-ATP6
NARP/Leigh Disease/MILS/other T8993C 8993T-C L-P Cfrm references
MT-ATP6
NARP/Leigh Disease/MILS/other T8993G 8993T-G L-R Cfrm
MT-ATP6
FBSN/Leigh Disease T9176C 9176T-C L-P Cfrm references
MT-ATP6
Leigh Disease/Spastic Paraplegia T9176G 9176T-G L-R Cfrm
MT-ATP6
Leigh Disease/Ataxia syndromes/ NARP-like disease T9185C 9185T-C L-P Cfrm
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DISEASED HUMAN ATP6 GENES
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DISEASE CAUSING ATP6 MUTATION ONLY IN HUMANS
*What does this tell us?
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ATP8 GENE TREE
*no difference between this tree and the ATP6 tree
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ATP8 MUTATIONSGene Disease Allele Nucleotide
PositionNucleotide Change
Amino Acid Change Status
MT-ATP8
MIDD / LVNC cardiomyopathy-assoc. A8381G 8381A-G T-A Reported
MT-ATP8
Reversible Brain Pseudoatrophy C8393T 8393C-T P-S Reported
MT-ATP8
Severe mitochondrial disorder A8411G 8411 A-G M-V Reported
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*ATP8 disease mutations in humans
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ND2 BOOTSTRAPPED TREE
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ND2 MUTATIONSGene Disease Allele Nucleotide
PositionNucleotide Change
Amino Acid Change Status
MT-ND2
LHON/Insulin Resistance/AMD/NRTI-PN A4917G 4917A-G N-D
Reported; haplogroup T marker
MT-ND2
NIDDM helper mutation; AD, PD A4833G 4833A-G T-A
Reported; haplogroup G marker
MT-ND2 LHON C4640A 4640C-A I-M Reported
MT-ND2
Longevity; Extraversion MI/AMS protection; blood iron metabolism C5178A 5178C-A L-M
Reported; haplogroup D marker
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COX1 MUTATIONS
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COX1 MUTATIONSGene Disease Allele Nucleotide
PositionNucleotide Change
Amino Acid Change Status
MT-CO1Prostate Cancer C5911T 5911 C-T A-V Reported
MT-CO1Prostate Cancer G5913A 5913G-A D-N Reported
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* COX1 MutationsIn Humans