Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation.

Sofiia Kolchanova,Ricardo Valentin De La Rosa,Juan Rodriguez-Flores,Pavel Dobrinin,Audrey Majeske,Joanne Paul-Murphy,Sergei Kliver,Gaik Tamazian,Michael Court,Taras Oleksyk,Kirill Grigorev,Juan Martínez-Cruzado,Aleksei Komissarov,Jafet Velez-Valentin,Walter Wolfsberger,David Guzman

doi:10.3390/genes10010054

Abstract

Islands have been used as model systems for studies of speciation and extinction since Darwin published his observations about finches found on the Galapagos. Amazon parrots inhabiting the Greater Antillean Islands represent a fascinating model of species diversification. Unfortunately, many of these birds are threatened as a result of human activity and some, like the Puerto Rican parrot, are now critically endangered. In this study we used a combination of de novo and reference-assisted assembly methods, integrating it with information obtained from related genomes to perform genome reconstruction of three amazon species. First, we used whole genome sequencing data to generate a new de novo genome assembly for the Puerto Rican parrot (Amazona vittata). We then improved the obtained assembly using transcriptome data from Amazona ventralis and used the resulting sequences as a reference to assemble the genomes Hispaniolan (A. ventralis) and Cuban (Amazona leucocephala) parrots. Finally, we, annotated genes and repetitive elements, estimated genome sizes and current levels of heterozygosity, built models of demographic history and provided interpretation of our findings in the context of parrot evolution in the Caribbean.

Highlights

The Bird 10,000 Genomes (B10K) Project resulted in a large number of genomic sequences that are being quickly assembled and incorporated into studies on evolution, ecology, population genetics, neurobiology, development and conservation [1,2,3]
Blood samples for DNA sequencing from female Puerto Rican (A. vittata) and Hispaniolan parrots (A. ventralis) were obtained during routine veterinary procedures from birds housed at the US Fish and Wildlife Service “Iguaca” Aviary, a captive-breeding facility for the Puerto Rican parrot near El Yunque
In this study we used a combination of short read paired-end (PE) read sequences, mate pairs (MP)

Summary

Introduction

The Bird 10,000 Genomes (B10K) Project resulted in a large number of genomic sequences that are being quickly assembled and incorporated into studies on evolution, ecology, population genetics, neurobiology, development and conservation [1,2,3]. Genome-wide sequencing and assembly has expanded to the point that it allows for completion of the genome-based phylogeny of all birds. A narrowed focus on speciation and adaptation processes on the species level can allow for decoding of the links between genotypes and phenotypes; determining genetic, evolutionary, biogeographical and biodiversity relationships across species; and evaluation of how various ecological factors affect avian evolution [4]. By focusing on groups that include endangered species, genome studies provide the means to elucidate the conservation issues that would help in our efforts to preserve biodiversity. Neotropical parrots represent a fascinating group that includes many species with endangered conservation status that have not yet been represented in whole-genome phylogenetic analyses [2,3]

Methods

Results

Conclusion