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

2. Next Generation technology 3. Puerto Rico 4. El Yunque and Rio Abajo 5. Ricard Valentin an Jafet Vlez 6. Rio Abajo 7. Why sequence the parrot? Rational: Sample is readily available from the breeding programThe genome is relatively small (1.65Gb)Provides a reference for the future comparative genetics of 33 closely related species of the AmazonaIt is very homozygous (bottleneck of 13 individuals in 1972)Emotional Beautiful and endangered birdMascot of the island the peoples parrotThe only extant U.S. parrot species - it is on the U.S. money! 8. 2011: anyone can afford a genome project 9. Where to get $10,000? StrategyDrawbacksAsk the universityUniversity has no money (overhead goes to the government structure) gives seed grants 100 bp)110,3021,005,293,16418,014263,7091129,114Scaffolds (>100 bp)6,5701,125,512,1702,056,51111,107,598896171,310AllpathLG Contigshttp://solexa2.macrogen.com/~macro/HiSeq/201205/Taras_Parrot/Parrot_allpathLG_contigs.tar.gzAllpathLG Scaffoldshttp://solexa2.macrogen.com/~macro/HiSeq/201205/Taras_Parrot/Parrot_allpathLG_scaffolds.tar.gz 12. generatio n of precurso r metabolit es and energy 20%Top 200 expressedBiological processoxidation 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 expressedglucose 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. Parrots of the Caribbean 14. .UPR-RP being investigated for embezzling fundsThe NSF froze federal funds to the UPR 15. facebook.com/amazona.vittata$100/large print (canvas) $25/small print (paper) 16. Amazon species of the world by Audrey Guiblet & Taras K. Oleksyk 17. PUERTO RICO SCIENCE FOUNDATION Est. Oct 4, 2013 18. Why is it important to do fundraising Creates a brand nameIncreases visibility and increases trust of the pubicEngages the public and promotes sense of ownershipConvinces your institution that genomics is important way to build infrastructureAllows to look for the long term donors 19. Top 200 expressedCellular componentmitoc 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% membrainsoluble fraction 1%Not expressedproteina ceous extracell ular matrix 5%proteina ceous extracell ular matrix 4%endoplas mic extracell reticulum ular 7% matrixextracell ular region 84%synapse 1%cation channel complex 100%5% 20. Top 200 expressedmagnesi um ion binding 11%ATPase regulat or activity 35%protein kinase activity 10%channel activity 11%actin binding 65%Not expressedadenyl nucleotid e binding 67%Molecular functionprotein kinase activity 10%motor activity 37% dicarbo xylic acid transme mbrane transpor ter activitcytoske letal protein binding 3% structur al molecul e activity 62%ATPase activity, coupled to transme mbrane movenucleosi 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%