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

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dc.contributor.authorOleksyk, Taras K.
dc.contributor.authorPombert, Jean-Francois
dc.contributor.authorSiu, Daniel
dc.contributor.authorMazo-Vargas, Anyimilehidi
dc.contributor.authorRamos, Brian
dc.contributor.authorGuiblet, Wilfried
dc.contributor.authorAfanador, Yashira
dc.contributor.authorRuiz-Rodriguez, Christina T.
dc.contributor.authorNickerson, Michael L.
dc.contributor.authorLogue, David M.
dc.contributor.authorDean, Michael
dc.contributor.authorFigueroa, Luis
dc.contributor.authorValentin, Ricardo
dc.contributor.authorMartinez-Cruzado, Juan-Carlos
dc.date.accessioned2020-04-16T22:42:19Z
dc.date.available2020-04-16T22:42:19Z
dc.date.issued2012
dc.descriptionSherpa Romeo green journal. Open access article. Creative Commons Attribution 2.0 (CC BY 2.0) appliesen_US
dc.description.abstractBackground: 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.en_US
dc.description.peer-reviewYesen_US
dc.identifier.citationOleksyk, T. K., Pombert, J., Siu, D., Mazo-Vargas, A., Ramos, B., Guiblet, W., .... Martinez-Cruzado, J. (2012). A locally funded Peurto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young research education. GigaScience, 1(1), 1-14. doi:10.1186/2047-217X-1-14en_US
dc.identifier.urihttps://hdl.handle.net/10133/5707
dc.language.isoen_USen_US
dc.publisherOxford University Pressen_US
dc.publisher.departmentDepartment of Psychologyen_US
dc.publisher.facultyArts and Scienceen_US
dc.publisher.institutionUniversity of Puerto Rico at Mayagüez,en_US
dc.publisher.institutionUniversity of British Columbiaen_US
dc.publisher.institutionAxeq Technologiesen_US
dc.publisher.institutionNational Cancer Institute (U.S.)en_US
dc.publisher.institutionCompañía de Parques Nacionales de Puerto Rico,en_US
dc.publisher.institutionDepartment of Natural and Environmental Resources (Peurto Rico)en_US
dc.publisher.institutionUniversity of Lethbridgeen_US
dc.publisher.urlhttps://doi.org/10.1186/2047-217X-1-14en_US
dc.subjectAmazona vittataen_US
dc.subjectGenome sequenceen_US
dc.subjectAnnotationen_US
dc.subjectAssemblyen_US
dc.subjectLocal fundingen_US
dc.subjectYoung researcher educationen_US
dc.subject.lcshPeurto Rican parrot
dc.subject.lcshGenomics
dc.titleA locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher educationen_US
dc.typeArticleen_US
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