Open Access Highly Accessed Data Note

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

Taras K Oleksyk1*, Jean-Francois Pombert2, Daniel Siu3, Anyimilehidi Mazo-Vargas1, Brian Ramos1, Wilfried Guiblet1, Yashira Afanador1, Christina T Ruiz-Rodriguez14, Michael L Nickerson4, David M Logue1, Michael Dean4, Luis Figueroa5, Ricardo Valentin6 and Juan-Carlos Martinez-Cruzado1

Author Affiliations

1 University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico

2 University of British Columbia, Vancouver, BC, Canada

3 Axeq Technologies, Seoul, South Korea

4 Cancer and Inflammation Program, National Cancer Institute, NIH, Frederick, MD, USA

5 Compañía de Parques Nacionales de Puerto Rico, San Juan, Puerto Rico

6 Department of Natural and Environmental Resources, San Juan, Puerto Rico

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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.

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