Big science: Local funding supports open-access sequencing of the Puerto Rican Parrot genome

Public release date: 28-Sep-2012
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Contact: Hilary Glover
hilary.glover@biomedcentral.com
44-020-319-22370
BioMed Central

The critically endangered Puerto Rican Parrot (Amazona vittata) is the only surviving parrot species native to the United States. A genomic sequencing project, funded by community donations, has published today, in BioMed Central and BGI's open access journal GigaScience, the first sequence of A. vittata, the first of the large Neotropical Amazona birds to be studied at the genomic level.

The Puerto Rican Parrot was once abundant throughout Puerto Rico but destruction of old forest habitats to make way for farming in the 19th Century resulted in a drastic decline in their population. By the mid 1970's only a handful of individuals were thought to remain. Captive breeding programs in Rio Abajo and El Yunque and the release of these birds have had some success, but the number of these birds in the wild is still very low.

In a unique initiative (developing of the Local Community Involvement), funded entirely by contributions from the communities of Puerto Rico alongside staff and students from the Biology Department of the University of Puerto Rico at Mayagez, researchers collaborated internationally to sequence this beautiful parrot.

Dr Taras Oleksyk, who organized the The Puerto Rican Parrot Genome Project, explained their findings, "In this project we managed to cover almost 76% of the A. vittata genome using money raised in art and fashion shows, and going door to door asking for the support of Puerto Rican people and local businesses. When we compared our sequence of our parrot, Iguaca, from Rio Abajo to other species of birds, we found that she had 84.5% similarity to zebra finches and 82.7% to a chicken, but her genome was highly rearranged."

Dr Oleksyk continued, "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. All the data from this project is publically available in GigaDB which we hope will be a starting point for comparative studies across avian genome data, and will be used to develop and promote undergraduate education in genome science in the Caribbean. 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."

###

Media contact

Dr Hilary Glover
Scientific Press Officer, BioMed Central
Tel: +44 (0) 20 3192 2370
Mob: +44 (0) 778 698 1967
Email: hilary.glover@biomedcentral.com

Notes to Editors

1. A Locally Funded Puerto Rican Parrot (Amazona vittata) Genome Sequencing Project Increases Avian Data and Advances Young Researcher Education 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 GigaScience 2012, 1:14

Please name the journal in any story you write. If you are writing for the web, please link to the article. All articles are available free of charge, according to BioMed Central's open access policy.

Please credit pictures to Jose Almodovar

Genomic data of the Puerto Rican Parrot (Amazona vittata) from a locally funded project Oleksyk, TK; Guiblet, W; Pombert, JF; Valentin, R; Martinez-Cruzado, JC GigaScience.

2. GigaScience aims to revolutionize data dissemination, organization, understanding, and use. An online open-access open-data journal, we publish 'big-data' studies from the entire spectrum of life and biomedical sciences. To achieve our goals, the journal has a novel publication format: one that links standard manuscript publication with an extensive database that hosts all associated data and provides data analysis tools and cloud-computing resources. @GigaScience

3. BioMed Central (http://www.biomedcentral.com/) is an STM (Science, Technology and Medicine) publisher which has 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. @BioMedCentral

4. Parrot sequencing data is also fully available as raw reads in the ENA (Accession # PRJEB225) and as scaffolds with assembly parameters in GenBank (Accession # PRJNA171587)

5. The Puerto Rican Parrot Genome project at the University of Puerto Rico-Mayaguez, (http://genomes.uprm.edu/drupal/?q=parrot), can be found at http://www.facebook.com/amazona.vittata

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AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert! system.

Public release date: 28-Sep-2012
[ | E-mail | Share ]

Contact: Hilary Glover
hilary.glover@biomedcentral.com
44-020-319-22370
BioMed Central

The critically endangered Puerto Rican Parrot (Amazona vittata) is the only surviving parrot species native to the United States. A genomic sequencing project, funded by community donations, has published today, in BioMed Central and BGI's open access journal GigaScience, the first sequence of A. vittata, the first of the large Neotropical Amazona birds to be studied at the genomic level.

The Puerto Rican Parrot was once abundant throughout Puerto Rico but destruction of old forest habitats to make way for farming in the 19th Century resulted in a drastic decline in their population. By the mid 1970's only a handful of individuals were thought to remain. Captive breeding programs in Rio Abajo and El Yunque and the release of these birds have had some success, but the number of these birds in the wild is still very low.

In a unique initiative (developing of the Local Community Involvement), funded entirely by contributions from the communities of Puerto Rico alongside staff and students from the Biology Department of the University of Puerto Rico at Mayagez, researchers collaborated internationally to sequence this beautiful parrot.

Dr Taras Oleksyk, who organized the The Puerto Rican Parrot Genome Project, explained their findings, "In this project we managed to cover almost 76% of the A. vittata genome using money raised in art and fashion shows, and going door to door asking for the support of Puerto Rican people and local businesses. When we compared our sequence of our parrot, Iguaca, from Rio Abajo to other species of birds, we found that she had 84.5% similarity to zebra finches and 82.7% to a chicken, but her genome was highly rearranged."

Dr Oleksyk continued, "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. All the data from this project is publically available in GigaDB which we hope will be a starting point for comparative studies across avian genome data, and will be used to develop and promote undergraduate education in genome science in the Caribbean. 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."

###

Media contact

Dr Hilary Glover
Scientific Press Officer, BioMed Central
Tel: +44 (0) 20 3192 2370
Mob: +44 (0) 778 698 1967
Email: hilary.glover@biomedcentral.com

Notes to Editors

1. A Locally Funded Puerto Rican Parrot (Amazona vittata) Genome Sequencing Project Increases Avian Data and Advances Young Researcher Education 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 GigaScience 2012, 1:14

Please name the journal in any story you write. If you are writing for the web, please link to the article. All articles are available free of charge, according to BioMed Central's open access policy.

Please credit pictures to Jose Almodovar

Genomic data of the Puerto Rican Parrot (Amazona vittata) from a locally funded project Oleksyk, TK; Guiblet, W; Pombert, JF; Valentin, R; Martinez-Cruzado, JC GigaScience.

2. GigaScience aims to revolutionize data dissemination, organization, understanding, and use. An online open-access open-data journal, we publish 'big-data' studies from the entire spectrum of life and biomedical sciences. To achieve our goals, the journal has a novel publication format: one that links standard manuscript publication with an extensive database that hosts all associated data and provides data analysis tools and cloud-computing resources. @GigaScience

3. BioMed Central (http://www.biomedcentral.com/) is an STM (Science, Technology and Medicine) publisher which has 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. @BioMedCentral

4. Parrot sequencing data is also fully available as raw reads in the ENA (Accession # PRJEB225) and as scaffolds with assembly parameters in GenBank (Accession # PRJNA171587)

5. The Puerto Rican Parrot Genome project at the University of Puerto Rico-Mayaguez, (http://genomes.uprm.edu/drupal/?q=parrot), can be found at http://www.facebook.com/amazona.vittata

---

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AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert! system.

Source: http://www.eurekalert.org/pub_releases/2012-09/bc-bsl092712.php

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