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

Abstract

BackgroundAmazona 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.FindingsIn 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.ConclusionsThe 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.

A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Macaw (Ara macao)

“…The avian order Psittaciformes is but one example of an underserved biological group, with some genomic resources that have recently become available via completion of the Puerto Rican parrot genome ( Amazona vittata ) [2], and the Budgerigar ( Melopsittacus undulatus budgerigar ) sequencing initiative (http://aviangenomes.org/budgerigar-raw-reads/). Notably, Psittaciformes is comprised of three families: the Psittacidae (true parrots), Cacatuidae (cockatoos), and Strigopidae (New Zealand parrots) [3].…”

Third Report on Chicken Genes and Chromosomes 2015

“…Recently, NGS has been used to sequence the genomes of a further 42 avian species, as part of the G10K initiative (Genome 10K Community of Scientists, 2009). In addition there have also been 15 other genome assemblies recently published, each with a focus on a unique aspect of avian biology, including the Japanese Quail (domestication; Kawahara-Miki et al, 2013), Puerto Rican parrot (speciation; Oleksyk et al, 2012), Scarlet Macaw (speech, intelligence and longevity; Seabury et al, 2013), Medium and Large Ground Finches (speciation; Parker et al, 2012; Rands et al, 2013), Collared and Pied flycatchers (speciation; Ellegren et al, 2012), Peregrine and Saker Falcons (predatory lifestyle; Zhan et al, 2013), rock pigeon (domestication; Shapiro et al, 2013), the Ground tit (adaptation to high altitude; Cai et al, 2013) and the Northern Bobwhite (population history; Halley et al, 2014). Through November 2014 there are currently 57 avian genome sequences completed, either published or in press (Table 1).…”

Comparative Cytogenetics of the Congo African Grey Parrot (Psittacus erithacus)

“…To date, whole genome sequence assemblies are available for only 2 true parrots -the scarlet macaw (Ara macao) [Seabury et al, 2013] and the Puerto Rican parrot (Amazona vittata) [Oleksyk et al, 2012], both representing the New World group. The majority of cytogenetic studies in parrots, including the African grey parrot, were performed in the 1970s and 1980s [De Boer and Belterman, 1980;Van Dongen and De Boer, 1984] and might thus need revisiting with advanced imaging tools for karyotyping.…”