September 28, 2012, Hong Kong, China - The international open-access journal GigaScience (a BGI and BioMed Central journal) announces the publication of a unique study providing the genome sequence of the critically endangered Puerto Rican Parrot (Amazona vittata) by Taras Oleksyk and colleagues at the University of Puerto Rico-Mayaguez. The sequencing and analysis of the genome of the only surviving native parrot in US territory provides numerous benefits for avian genetics, conservation studies, and evolutionary analyses. What is remarkable here, and highlighted in an accompanying commentary by Steven J. O'Brien of St Petersburg State University, is that it shows how accessible genomic technology has become. With the human genome project taking a consortium of the leading international genome centers a decade and $3 Billion USD to carry out, just over a decade later the genome of the Puerto Rico parrot was assembled at a small institution in Puerto Rico, and completely funded by the community. Money was raised in a variety of creative ways, including student organized art and fashion shows (see: http://youtu.
Dr. Oleksyk, the primary organizer of this project, said, "We are very proud of our project and even more proud to be part of a local community dedicated to raising awareness and furthering scientific knowledge of this endangered bird." He further added, "Community involvement may be the key for the future of conservation genetics, and many projects like this are needed reverse the current rate of extinction of birds across the globe."
The Puerto Rican Parrot once flourished throughout Puerto Rico, but its population rapidly declined during the 20th century due to extensive habitat destruction. By 1975, only 16 birds remained. Since then, through extensive conservation efforts including captive breeding programs in Rio Abajo and El Yunque and bird release into the wild, the number of these parrots has grown. The population, however, still remains exceedingly low and on the critically endangered list. Recent conservation efforts for other endangered species are now working to incorporate genome information to better assess the genetic health of endangered species and provide tools for targeted breeding, and the long-term prospects of this enigmatic bird will be given a boost given the new genomic resources provided by Oleksyk and colleagues. The authors estimated the parrot's genome size as ~1.58 Gbp, about half that of the human, and, at this stage of the project, provide 29x sequencing coverage of 76% of the genome. Assembly and annotation of the genome were carried out as part of the undergraduate education program at the university, which is not only a boon for developing technically savvy young scientists in Puerto Rico, but also serves as an example of how students can take part in community curation projects to aid in processing the increasingly unmanageable amounts of data now being generated throughout the world.
In keeping with the scientific community's goals of making all data fully and freely available, all data from this project are available in the GigaScience database, GigaDB, in a citable format, and are available as raw reads in the ENA (Accession # PRJEB225) and as scaffolds with assembly parameters in GenBank (Accession # PRJNA171587).
Steven J. O'Brien. (2012): Genome empowerment for the Puerto Rican parrot - Amazona vittata GigaScience 2012, 1:13
Taras K Oleksyk, Jean-Francois Pombert, Wilfried Guiblet, Brian Ramos, Anyimilehidi Mazo, Christina T Ruiz-Rodriguez, Michael L Nickerson, Yashira Afanador, Daniel Siu, Ricardo Valentin, Luis Figueroa, Michael Dean, David M Logue and Juan-Carlos Martinez-Cruzado (2012) A Locally Funded Puerto Rican Parrot (Amazona vittata) Genome Sequencing Project Increases Avian Data and Advances Young Researcher Education GigaScience 2012, 1:14
Oleksyk, TK; Guiblet, W; Pombert, JF; Valentin, R; Martinez-Cruzado, JC (2012): Genomic data of the Puerto Rican Parrot (Amazona vittata) from a locally funded project. GigaScience. http://dx.
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4. For more on the Puerto Rican Parrot Genome project at the University of Puerto Rico-Mayaguez, please see their website (http://genomes.