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A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education

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Author(s): Oleksyk Taras K | Pombert Jean-Francois | Siu Daniel | Mazo-Vargas Anyimilehidi | Ramos Brian | Guiblet Wilfried | Afanador Yashira | Ruiz-Rodriguez Christina T | Nickerson Michael L | Logue David M | Dean Michael | Figueroa Luis | Valentin Ricardo | Martinez-Cruzado Juan-Carlos

Journal: GigaScience
ISSN 2047-217X

Volume: 1;
Issue: 1;
Start page: 14;
Date: 2012;
Original page

Keywords: Amazona vittata | Puerto rican parrot | Genome sequence | Annotation | Assembly | Local funding | Education

ABSTRACT
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.

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