Stephan Schuster, Penn State University - “Genomics of Extinct and Endangered Species”
Last year, introduced nanosequencing of complete extinct species. What are the implication of extinct genomes on endangered species.
Mammoth: went extinct 3 times... 45,000ya, 10,000 ya, and 3,500ya. Wooly rhino: 10,000 years ago, Moa 500 years ago (were eaten), Thylacine 73 years ago.. And Tasmanian devils, which are expected only to last another 10 years.
Makes you wonder about dinosaurs.. maybe dinosaurs just tasted like chicken.
Looking at population structure and biological diversity from a genomic perspective. (Review of Genotyping Biodiversity.) Mitochondrial genome is generally higher copy, and thus was traditionally the one used, but now with better sequencing, we can target nuclear DNA.
Mammoth Mitochondrial genome has been done. ~16,500bp. Includes ribosomal, coding and noncoding regions. In 2008, can get 1000x coverage on the mitochrondrial. You need extra coverage to correct for damaged DNA.
This has now allowed 18 mammoth mitochondrial genome sequences. 20-30 SNPs between members of same groups, and 200-300 between groups. WAY more sequencing than is available for african elephants!
Have now switched to using hair instead of bone, and can use hair shaft. (not just follicle)
Ancient DNA = highly fragmented. 300,000 sequences, 45% was nuclear DNA.
Now: Sequenced bases: 4.17Gb. Genome size is 4.7Gb. 77 Runs, got 32.6 million bases.
Can visit mammoth.psu.edu for more info.
Sequenced mammoth orthologs of human genes. Compared to watson/venter... rate of predicted genes of chromosomes (“No inferrences here”), Complete representation of genome available. SAP =Single Amino acid Polymorphism.
(Discussion Divergence for mammoth) coalescence time for human and neandethal, 600,000. Same thing happens for mammoth, but not really well accepted because the biological evidence doesn't show it.
Did the same thing for the Tasmanian Tiger. Two complete genomes – only 5 differences between them.
Hair for one sample was taken from what fell off when preserved in a jar of ethanol!
Moa: did it from egg shell!
Wooly rhino: did the wooly rhino from hair – did other rhinos. (wooly is the only extinct one.) Rhinos radiated only a million years ago, so couldn't resolve phylogenic tree. Tried: hair, horn, hoof, and bone.. bone was by far the worst.
Now, to jump to the living: the tasmanian devil. Highly endangered. 1996 infectious cancer discovered (not figured out till 2004). Devils protected since 1941. Isolations with fences, islands, mainland, insurance population. Culling and vaccination are also possible.
Genome markers will be very useful. Problem is probably because there is nearly no diversity in population. Sequenced museum sample devils, and show mitochondrial DNA had more diversity in non-living population.
Project for full genome is now underway – two animals. (More information on plans on what to do with this data and how to save them.) SNP info for genotyping to direct captive breeding program.
(“Project Arc”) Trying to breed resistant animals.
Mammoth: went extinct 3 times... 45,000ya, 10,000 ya, and 3,500ya. Wooly rhino: 10,000 years ago, Moa 500 years ago (were eaten), Thylacine 73 years ago.. And Tasmanian devils, which are expected only to last another 10 years.
Makes you wonder about dinosaurs.. maybe dinosaurs just tasted like chicken.
Looking at population structure and biological diversity from a genomic perspective. (Review of Genotyping Biodiversity.) Mitochondrial genome is generally higher copy, and thus was traditionally the one used, but now with better sequencing, we can target nuclear DNA.
Mammoth Mitochondrial genome has been done. ~16,500bp. Includes ribosomal, coding and noncoding regions. In 2008, can get 1000x coverage on the mitochrondrial. You need extra coverage to correct for damaged DNA.
This has now allowed 18 mammoth mitochondrial genome sequences. 20-30 SNPs between members of same groups, and 200-300 between groups. WAY more sequencing than is available for african elephants!
Have now switched to using hair instead of bone, and can use hair shaft. (not just follicle)
Ancient DNA = highly fragmented. 300,000 sequences, 45% was nuclear DNA.
Now: Sequenced bases: 4.17Gb. Genome size is 4.7Gb. 77 Runs, got 32.6 million bases.
Can visit mammoth.psu.edu for more info.
Sequenced mammoth orthologs of human genes. Compared to watson/venter... rate of predicted genes of chromosomes (“No inferrences here”), Complete representation of genome available. SAP =Single Amino acid Polymorphism.
(Discussion Divergence for mammoth) coalescence time for human and neandethal, 600,000. Same thing happens for mammoth, but not really well accepted because the biological evidence doesn't show it.
Did the same thing for the Tasmanian Tiger. Two complete genomes – only 5 differences between them.
Hair for one sample was taken from what fell off when preserved in a jar of ethanol!
Moa: did it from egg shell!
Wooly rhino: did the wooly rhino from hair – did other rhinos. (wooly is the only extinct one.) Rhinos radiated only a million years ago, so couldn't resolve phylogenic tree. Tried: hair, horn, hoof, and bone.. bone was by far the worst.
Now, to jump to the living: the tasmanian devil. Highly endangered. 1996 infectious cancer discovered (not figured out till 2004). Devils protected since 1941. Isolations with fences, islands, mainland, insurance population. Culling and vaccination are also possible.
Genome markers will be very useful. Problem is probably because there is nearly no diversity in population. Sequenced museum sample devils, and show mitochondrial DNA had more diversity in non-living population.
Project for full genome is now underway – two animals. (More information on plans on what to do with this data and how to save them.) SNP info for genotyping to direct captive breeding program.
(“Project Arc”) Trying to breed resistant animals.
Labels: AGBT 2009
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