Public Release:  Local funding leads to big things in parrot genomics

A grassroots funding effort in Puerto Rico enables genome sequencing of the critically endangered Puerto Rican parrot

GigaScience

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.be/tXW-pNoM9uU), social-networking sites, and private donations from Puerto Rican citizens wanting to promote research on their local wildlife. This project serves as a signal that work on large-scale whole-genome projects is becoming more democratized, and opens the door for more creative input from outside the large genome centers.

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).

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References:

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.doi.org/10.5524/100039

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Organization Information:

1. GigaScience (http://www.gigasciencejournal.com) is co-published by BGI, the world's largest genomics institute, and BioMed Central, the world's largest open-access publisher. The journal covers research that uses or produces 'big data' from the full spectrum of the life sciences. It also serves as a forum for discussing the difficulties of and unique needs for handling large-scale data from all areas of the life sciences. The journal has a completely novel publication format -- one that integrates manuscript publication with complete data hosting, and analyses tool incorporation. To encourage transparent reporting of scientific research as well as enable future access and analyses, it is a requirement of manuscript submission to GigaScience that all supporting data and source code be made available in the GigaScience database, GigaDB (http://gigadb.org), as well as in their publicly available repositories. GigaScience will provide users access to associated online tools and workflows, and will be integrating a data analysis platform and cloud resources into the database later this year, maximizing the potential utility and re-use of data.

(Follow us on twitter @GigaScience; sina-weibo http://weibo.com/gigasciencejournal, and keep up-to-date on our blogs http://blogs.openaccesscentral.com/blogs/gigablog/feed/entries/rss).

2. BGI (http://www.genomics.cn/en), a China-based scientific institution, was founded in 1999 and has since become the largest genomic organization in the world. With a focus on research and applications in the healthcare, agriculture, conservation, and bio-energy fields, BGI has a proven track record of innovative, high profile research, which has generated over 178 publications in top-tier journals such as Nature and Science. It also contributes to scientific communication by publishing the international research journal GigaScience and hosting its associated database GigaDB. BGI's distinguished achievements have made a great contribution to the development of genomics in both China and the world. Their goal is to make leading-edge genomics highly accessible to the global research community by integrating industry's best technology, economies of scale, and expert bioinformatics resources. BGI and its affiliates, BGI-Americas and BGI-Europe, have established partnerships and collaborations with leading academic and government research institutions, as well as global biotechnology and pharmaceutical companies. (Follow BGI on twitter @BGI_events.)

3. BioMed Central (http://www.biomedcentral.com/) is an STM (Science, Technology and Medicine) publisher, which pioneered the open-access publishing model. All peer-reviewed research articles published by BioMed Central are made immediately and freely accessible online, and are licensed to allow redistribution and reuse. BioMed Central is part of Springer Science+Business Media, a leading global publisher in the STM sector.

4. For more on the Puerto Rican Parrot Genome project at the University of Puerto Rico-Mayaguez, please see their website (http://genomes.uprm.edu/drupal/?q=parrot), and to keep up with the latest news on the project follow them on Facebook http://www.facebook.com/amazona.vittata

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