title: A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education.
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.
  
  
  RESULTS
  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.
authors.affiliation: University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico. taras.oleksyk@upr.edu.
authors.forename: Taras K
authors.initials: TK
authors.lastname: Oleksyk
authors.forename: Jean-Francois
authors.initials: JF
authors.lastname: Pombert
authors.forename: Daniel
authors.initials: D
authors.lastname: Siu
authors.forename: Anyimilehidi
authors.initials: A
authors.lastname: Mazo-Vargas
authors.forename: Brian
authors.initials: B
authors.lastname: Ramos
authors.forename: Wilfried
authors.initials: W
authors.lastname: Guiblet
authors.forename: Yashira
authors.initials: Y
authors.lastname: Afanador
authors.forename: Christina T
authors.initials: CT
authors.lastname: Ruiz-Rodriguez
authors.forename: Michael L
authors.initials: ML
authors.lastname: Nickerson
authors.forename: David M
authors.initials: DM
authors.lastname: Logue
authors.forename: Michael
authors.initials: M
authors.lastname: Dean
authors.forename: Luis
authors.initials: L
authors.lastname: Figueroa
authors.forename: Ricardo
authors.initials: R
authors.lastname: Valentin
authors.forename: Juan-Carlos
authors.initials: JC
authors.lastname: Martinez-Cruzado