Puerto Rican Parrot Genome Project:
from the community sponsored genome
to a new evolutionary model
Taras K. Oleksyk
Next Generation technology
Puerto Rico
El Yunque and Rio Abajo
Ricard Valentin an Jafet Vélez
Rio Abajo
Why sequence the parrot?


Rational:




Sample is readily available from the breeding program



The genome is relati...
2011:
anyone can afford a genome project
Where to get $10,000?
Strategy

Drawbacks

Ask the university





University has no money (overhead
goes to the governm...
ALEXANDRA WISCOVITCH
Second Assembly Results

Assembly

#Contigs

Contigs_sum

N50

Longest

Shortest

Average

Contigs
(>100 bp)

110,302

1,0...
generatio
n of
precurso
r
metabolit
es and
energy
20%

Top 200 expressed

Biological process

oxidation
reduction
process
...
Parrots of the Caribbean
.

UPR-RP being investigated
for embezzling funds

The NSF froze federal funds
to the UPR
facebook.com/amazona.vittata

$100/large print (canvas)
$25/small print (paper)
Amazon species of the world
by Audrey Guiblet & Taras K. Oleksyk
PUERTO RICO SCIENCE FOUNDATION
Est. Oct 4, 2013
Why is it important to do fundraising


Creates a brand name



Increases visibility and increases trust
of the pubic

...
Top 200 expressed

Cellular component

mitoc
hondri
al
inner
memb
rane
34%

envel
ope
66%

ne
85%

membra
ne
fraction
1%

...
Top 200 expressed

magnesi
um ion
binding
11%

ATPase
regulat
or
activity
35%

protein
kinase
activity
10%

channel
activi...
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model
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Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model

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Taras Oleksyk talk at #ICG8: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model, Shenzhen, 30th October 2013

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  • I want to start with a metaphor, and it is a beautiful oneAnd beautiful metaphors as you know are the best way to convince someone to give you their money
  • I compare our times to the Great Age of DiscoveryWhen it started, our conception of the world was that it was very small and our explanation of what was outside was naïve,
  • Then the new technology was discovered – the caravelIt was not user friendly it would break down all the tieBut there were those who dared to cross oceans And at that time it did not matter in what direction you would goIf you would not give upYou would eventually discover a continentThe lesson they taught us isNo matter how small your boat or how large it isWhether you are on a small caravel or a luxury titanicIt is not the SIZE, but the TIMING that determines the success in reaching your destination
  • When Columbus went on his second voyage, he discovered and island of Puerto RicoOn this island there lived about 100K of TainoindiansAndPerhaps more importantly to this talk, there were about a million parrotsAfter about 500 years after the initial discovery, the tainos cultural legacy lives in three words: huracan, hamaca and barbeque.Its genetic language is mixed into the genomes of the modentpuertoricans,As you will soon read in the excellent paper by the Taino Group of the 1000 Genomes project, among which are C.B, and myself, are submitting to PLoS Genetics this month.
  • The parrots suffered even more dramatic fateIn 1972, from millions, the population was reduced to a dozennly 13 of them have survivedAfter a hurricane threatened a total devastation, the population has been removed from its natural habitatAnd the captive breeding program has begunAmazona vittata is the only native parrot species surviving in the United States territory. This bird was once seen throughout Puerto Rico, but with time, population declined because of habitat destruction, especially in the last one hundred years, when most of the old rainforest was cut down.
  • I was fortunate to meet one of the heroes of this effortRicardo ValentinThe parrot whisperer
  • The effort is a success, and more than 200 parrots are in captivity, while about 50 of them have survived after being released in the wild
  • By 2011 I started watching the progress of G10K, and I saw this graphI might have been a little optimistic, but I stareted to believeThat the caravel has been inventedAnd anyone can afford a sequencing projectEven an independent in a small regional university like mine
  • We are organizing more activities, and trying to bring together artists, designers, conservation activists and university students and faculty to help. To follow these efforts you can join our Facebook page www.facebook.com/amazona.vittata
  • These included selling art, going door to door of the local businesses in the Western Puerto Rico, and even running a fashion showhttp://youtu.be/tXW-pNoM9uU
  • In conclusion, on behalf of all the people involved in the project, I ask you:We need your support!
  • Taras Oleksyk: Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model

    1. 1. Puerto Rican Parrot Genome Project: from the community sponsored genome to a new evolutionary model Taras K. Oleksyk
    2. 2. Next Generation technology
    3. 3. Puerto Rico
    4. 4. El Yunque and Rio Abajo
    5. 5. Ricard Valentin an Jafet Vélez
    6. 6. Rio Abajo
    7. 7. Why sequence the parrot?  Rational:   Sample is readily available from the breeding program  The genome is relatively small (1.65Gb)   Provides a reference for the future comparative genetics of 33 closely related species of the Amazona It is very homozygous (bottleneck of 13 individuals in 1972) Emotional  Beautiful and endangered bird  Mascot of the island – the people’s parrot  The only extant U.S. parrot species - it is on the U.S. money!
    8. 8. 2011: anyone can afford a genome project
    9. 9. Where to get $10,000? Strategy Drawbacks Ask the university   University has no money (overhead goes to the government structure) gives seed grants <$3,000 (but not regularly)   It takes over a year to get the money, and who hard to justify for a place with no sequencing  Interested in phylogenetically distributed sample, and another parrot (parakeet) is the best sequenced nonhuman genome Write a research grant  Ask an consortium: G10K
    10. 10. ALEXANDRA WISCOVITCH
    11. 11. Second Assembly Results Assembly #Contigs Contigs_sum N50 Longest Shortest Average Contigs (>100 bp) 110,302 1,005,293,164 18,014 263,709 112 9,114 Scaffolds (>100 bp) 6,570 1,125,512,170 2,056,511 11,107,598 896 171,310 AllpathLG Contigs http://solexa2.macrogen.com/~macro/HiSeq/201205/Taras_Parrot/Parrot_allpathLG_contigs.tar.gz AllpathLG Scaffolds http://solexa2.macrogen.com/~macro/HiSeq/201205/Taras_Parrot/Parrot_allpathLG_scaffolds.tar.gz
    12. 12. generatio n of precurso r metabolit es and energy 20% Top 200 expressed Biological process oxidation reduction process 61% neuron differenti ation 36% heart develop ment 13% behavior 14% biological adhesion 50% biologica l adhesion 5% eye develop ment 15% Not expressed glucose metaboli sm 4% protein phospho rylation 41% phospho rus metaboli sm 39% protein dephosp horylatio n 8% phosphor us metaboli sm 33% translatio nal elongatio n 16% actomyo sin structure organizat ion 83% nitric oxide biosynth esis 58% biologica l adhesion 27% ion transport 73%
    13. 13. Parrots of the Caribbean
    14. 14. . UPR-RP being investigated for embezzling funds The NSF froze federal funds to the UPR
    15. 15. facebook.com/amazona.vittata $100/large print (canvas) $25/small print (paper)
    16. 16. Amazon species of the world by Audrey Guiblet & Taras K. Oleksyk
    17. 17. PUERTO RICO SCIENCE FOUNDATION Est. Oct 4, 2013
    18. 18. Why is it important to do fundraising  Creates a brand name  Increases visibility and increases trust of the pubic  Engages the public and promotes sense of ownership  Convinces your institution that genomics is important way to build infrastructure  Allows to look for the long term donors
    19. 19. Top 200 expressed Cellular component mitoc hondri al inner memb rane 34% envel ope 66% ne 85% membra ne fraction 1% collagen 1% cytosolic ribosome 96% cell projecti on 26% extracell ular matrix 7% integral to plasma membra ne 62% cell cell microtub projectio surface ule n 1% cytoskel 9% eton 4% neuron projectio n plasma 1% membra insoluble fraction 1% Not expressed proteina ceous extracell ular matrix 5% proteina ceous extracell ular matrix 4% endoplas mic extracell reticulum ular 7% matrix extracell ular region 84% synapse 1% cation channel complex 100% 5%
    20. 20. Top 200 expressed magnesi um ion binding 11% ATPase regulat or activity 35% protein kinase activity 10% channel activity 11% actin binding 65% Not expressed adenyl nucleotid e binding 67% Molecular function protein kinase activity 10% motor activity 37% dicarbo xylic acid transme mbrane transpor ter activit… cytoske letal protein binding 3% structur al molecul e activity 62% ATPase activity, coupled to transme mbrane move… nucleosi detriphosph atase regulator activity 2% calcium ion binding 49% structur al constitu ent of ribosom e 35% magnesi um ion binding 11% channel activity 11% magnesi um ion binding 78% protein kinase activity 10% adenyl nucleotid e binding 67%

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