The Puerto Rican Parrot Genome Project sequenced the genome of the endangered Puerto Rican parrot using next generation sequencing technologies. The genome was sequenced due to its importance for conservation efforts and comparative genomics with related parrot species. The project was community-funded through various strategies including crowd-funding and donations in order to sequence the relatively small 1.65Gb genome for $10,000. Analysis of the genome assembly identified over 100,000 contigs and 6,500 scaffolds and provides a genomic resource for further research.
14. 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!
16. 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
46. 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%
55. 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
56.
57.
58.
59.
60.
61. 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%
62. 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%
Notes de l'éditeur
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!