A Draft Sequence of the Puerto Rican Parrot Genome (Amazona vittata) – a Genome Project funded by a Local Community Effort

Abstract

The genome of the Puerto Rican parrot (Amazona vittata) has been sequenced and assembled in an international collaboration supported by many individual donations from the people of Puerto Rico. This is a critically endangered endemic bird, the only surviving native parrot species in the territory of the United States, and the first parrot belonging to the large genus Amazona to have its genome sequenced and assembled. A genome of one A. vittata female was sequenced resulting in a total of almost 42.5 billion nucleotide bases equivalent to 26.89X average coverage depth. After filtering out the short fragments (<500bp), the assembly resulted in 259,423 short fragment library contigs, half of them (N50) of at least 6,983 bp in length, with a longest contig at 75,003, and 148,255 long fragment library of scaffolds with N50=19,470 with the longest at 206,462 bp length. Further sequencing is needed to generate enough coverage of the genome and close the assembly gaps. To our knowledge, this is the first genome project to be initiated and supported by local community fundraising efforts, and represents a model for the future of de novo genome projects for conservation genetics of nonhuman species.