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Sunday, 30 September 2012

NGS PubMed Highlights: Puerto Rican Parrot Genome Sequenced

Thanks to a fundraising campaign (small donations from local community), researchers were able to sequence the genome of the critically endangered Puerto Rican Parrot. The study was published Friday in BioMed Central and BGI’s open access journal GigaScience.
Interestingly the Project also has a Facebook page that I guess was instrumental for the fundraising campaign.
I'm wondering how is the sequence of the FOXP2 Parrot gene (just kidding... or maybe not).

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, Daniel Siu, Anyimilehidi Mazo-Vargas, Brian Ramos, Wilfried Guiblet, Yashira Afanador, Christina T Ruiz-Rodriguez, Michael L Nickerson, David M Logue, Michael Dean, Luis Figueroa, Ricardo Valentin and Juan-Carlos Martinez-Cruzado

GigaScience 2012, 1:14 doi:10.1186/2047-217X-1-14
Published: 28 September 2012

Abstract Background
Amazona vittata is a critically endangered Puerto Rican endemic bird, the only surviving native parrot species in the United States territory, and the first parrot in the large Neotropical genus Amazona, to be studied on a genomic scale.
Findings
In a unique community-based funded project, DNA from an A. vittata female was sequenced using a HiSeq Illumina platform, resulting in a total of ~42.5 billion nucleotide bases. This provided approximately 26.89x average coverage depth at the completion of this funding phase. Filtering followed by assembly resulted in 259,423 contigs (N50 = 6,983 bp, longest = 75,003 bp), which was further scaffolded into 148,255 fragments (N50 = 19,470, longest = 206,462 bp). This provided ~76% coverage of the genome based on an estimated size of 1.58 Gb. The assembled scaffolds allowed basic genomic annotation and comparative analyses with other available avian whole-genome sequences.
Conclusions
The current data represents the first genomic information from and work carried out with a unique source of funding. This analysis further provides a means for directed training of young researchers in genetic and bioinformatics analyses and will facilitate progress towards a full assembly and annotation of the Puerto Rican parrot genome. It also adds extensive genomic data to a new branch of the avian tree, making it useful for comparative analyses with other avian species. Ultimately, the knowledge acquired from these data will contribute to an improved understanding of the overall population health of this species and aid in ongoing and future conservation efforts.

1 comment:

Taras Oleksyk said...

Yes, of course we have a facebook webpage :-), and I invite you to join it for the further updates, as we are not about to stop here. Our fundraising effort really relied on reaching as many people as possible, and most of young people prefer Facebook to other media.

We are open to collaboration to analyze the data we produced. You are welcome to look for FOXP2 in the contigs that you can download directly from here http://gigadb.org/puerto-rican-parrot/